##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data curatedOvarianData
###
##############################################################################
##############################################################################
* checking for file ‘curatedOvarianData/DESCRIPTION’ ... OK
* preparing ‘curatedOvarianData’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
Hmm ... looks like a package
Converting Rd files to LaTeX ...
Creating pdf output from LaTeX ...
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 2
L3 programming layer <2020-02-14>
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 378.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 378.
) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
No file Rd2.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}] [2]
Overfull \hbox (42.89548pt too wide) in paragraph at lines 99--102
[]\T1/ptm/m/n/10 For "pri-mary_therapy_outcome_success": com-pletere-sponse|par
tialresponse|progressivedisease|stabledisease:
Overfull \hbox (14.36601pt too wide) in paragraph at lines 120--122
[]\T1/ptm/m/n/10 For "site_of_tumor_first_recurrence": (metas-ta-sis / lo-core-
gional / none / lo-core-gional_plus_metastatic).
[3]
Overfull \hbox (1107.93701pt too wide) in paragraph at lines 192--192
[] \T1/zi4/m/n/10 Experimenter name: Bentink S, Haibe-Kains B, Risch T, Fan J
-B, Hirsch MS, Holton K, Rubio R, April C, Chen J, Wickham-Garcia E, Liu J, Cul
hane A, Drapkin R, Quackenbush J, Matulonis UA: Angiogenic mRNA and microRNA ge
ne expression signature predicts a novel subtype of serous ovarian cancer. PLoS
ONE 2012, 7:e30269.[]
Overfull \hbox (146.38962pt too wide) in paragraph at lines 195--195
[] \T1/zi4/m/n/10 Title: Angiogenic mRNA and microRNA gene expression signatu
re predicts a novel subtype of serous ovarian cancer.[]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [4] [5]
[6]
Overfull \hbox (591.34872pt too wide) in paragraph at lines 314--314
[] \T1/zi4/m/n/10 Experimenter name: Partheen K, Levan K, Osterberg L, Horvat
h G.Expression analysis of stage III serous ovarian adenocarcinoma distinguishe
s a sub-group of survivors. Eur J Cancer. 2006 Nov; 42(16):2846-54.[]
Overfull \hbox (134.72977pt too wide) in paragraph at lines 317--317
[] \T1/zi4/m/n/10 Title: Expression analysis of stage III serous ovarian aden
ocarcinoma distinguishes a sub-group of survivors.[]
[7]
Overfull \hbox (34.73999pt too wide) in paragraph at lines 353--353
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[8]
Overfull \hbox (1299.59686pt too wide) in paragraph at lines 431--431
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Komata D, Yamamot
o T, Kodama S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H,
Kudo Y, Inoue I, Tanaka K.Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis. Cancer Sci. 2009 Aug; 100(8):1421-8.[]
[9]
Overfull \hbox (379.70932pt too wide) in paragraph at lines 434--434
[] \T1/zi4/m/n/10 Title: Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis.[]
[10] [11]
Overfull \hbox (861.2976pt too wide) in paragraph at lines 523--523
[] \T1/zi4/m/n/10 Experimenter name: Crijns AP, Fehrmann RS, de Jong S, Gerbe
ns F, Meersma GJ, Klip HG, Hollema H, Hofstra RM, te Meerman GJ, de Vries EG, v
an der Zee AG.Survival-related profile, pathways, and transcription factors in
ovarian cancer. PLoS Med. 2009 Feb 3; 6(2):e24.[]
Overfull \hbox (31.41006pt too wide) in paragraph at lines 526--526
[] \T1/zi4/m/n/10 Title: Survival-related profile, pathways, and transcriptio
n factors in ovarian cancer.[]
[12] [13] [14]
Overfull \hbox (636.3385pt too wide) in paragraph at lines 641--641
[] \T1/zi4/m/n/10 Experimenter name: Denkert C, Budczies J, Darb-Esfahani S,
Gy??rffy B et al. A prognostic gene expression index in ovarian cancer - valida
tion across different independent data sets. J Pathol 2009 Jun;218(2):273-80.[]
Overfull \hbox (146.38962pt too wide) in paragraph at lines 644--644
[] \T1/zi4/m/n/10 Title: A prognostic gene expression index in ovarian cancer
- validation across different independent data sets.[]
[15]
Underfull \vbox (badness 10000) has occurred while \output is active [16]
Overfull \hbox (3.12666pt too wide) in paragraph at lines 754--755
[]\T1/ptm/m/n/10 Advanced-stage ovar-ian can-cer pa-tients are gen-er-ally trea
ted with platinum/taxane-based chemother-
Overfull \hbox (1289.58664pt too wide) in paragraph at lines 767--767
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Yahata T, Kodama
S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H, Kudo Y, Kot
era K, Masuzaki H, Tashiro H, Katabuchi H, Inoue I, Tanaka K.Gene expression pr
ofile for predicting survival in advanced-stage serous ovarian cancer across tw
o independent datasets. PLoS One. 2010 Mar 12; 5(3):e9615.[]
[17]
Overfull \hbox (221.38962pt too wide) in paragraph at lines 770--770
[] \T1/zi4/m/n/10 Title: Gene expression profile for predicting survival in a
dvanced-stage serous ovarian cancer across two independent datasets.[]
[18]
Underfull \vbox (badness 10000) has occurred while \output is active [19]
Overfull \hbox (1551.22604pt too wide) in paragraph at lines 905--905
[] \T1/zi4/m/n/10 Experimenter name: Mok SC, Bonome T, Vathipadiekal V, Bell
A, Johnson ME, Wong KK, Park DC, Hao K, Yip DK, Donninger H, Ozbun L, Samimi G,
Brady J, Randonovich M, Pise-Masison CA, Barrett JC, Wong WH, Welch WR, Berkow
itz RS, Birrer MJ.A gene signature predictive for outcome in advanced ovarian c
ancer identifies a survival factor: microfibril-associated glycoprotein 2. Canc
er Cell. 2009 Dec 8; 16(6):521-32.[]
Overfull \hbox (293.04947pt too wide) in paragraph at lines 908--908
[] \T1/zi4/m/n/10 Title: A gene signature predictive for outcome in advanced
ovarian cancer identifies a survival factor: microfibril-associated glycoprotei
n 2.[]
[20] [21]
Underfull \vbox (badness 10000) has occurred while \output is active [22]
Overfull \hbox (904.64798pt too wide) in paragraph at lines 1040--1040
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (353.03925pt too wide) in paragraph at lines 1043--1043
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[23] [24] [25]
Overfull \hbox (904.64798pt too wide) in paragraph at lines 1138--1138
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (353.03925pt too wide) in paragraph at lines 1141--1141
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
Underfull \vbox (badness 1881) has occurred while \output is active [26]
[27]
Overfull \hbox (1481.23627pt too wide) in paragraph at lines 1236--1236
[] \T1/zi4/m/n/10 Experimenter name: Meyniel JP, Cottu PH, Decraene C, Stern
MH, Couturier J, Lebigot I, Nicolas A, Weber N, Fourchotte V, Alran S, Rapinat
A, Gentien D, Roman-Roman S, Mignot L, Sastre-Garau X.A genomic and transcripto
mic approach for a differential diagnosis between primary and secondary ovarian
carcinomas in patients with a previous history of breast cancer. BMC Cancer. 2
010 May 21; 10:222.[]
Overfull \hbox (451.35895pt too wide) in paragraph at lines 1239--1239
[] \T1/zi4/m/n/10 Title: A genomic and transcriptomic approach for a differen
tial diagnosis between primary and secondary ovarian carcinomas in patients wit
h a previous history of breast cancer.[]
[28] [29]
Overfull \hbox (101.41006pt too wide) in paragraph at lines 1344--1344
[] \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[30] [31] [32]
Overfull \hbox (126.38962pt too wide) in paragraph at lines 1456--1456
[] \T1/zi4/m/n/10 Experimenter name: Mateescu B, Batista L, Mariani O, Meynie
l J, Cottu PH, Sastre-Garau X, Mechta-Grigoriou F[]
Overfull \hbox (81.39984pt too wide) in paragraph at lines 1459--1459
[] \T1/zi4/m/n/10 Title: miR-141 and miR-200a act on ovarian tumorigenesis by
controlling oxidative stress response.[]
[33]
Underfull \vbox (badness 10000) has occurred while \output is active [34]
Overfull \hbox (917.96768pt too wide) in paragraph at lines 1582--1582
[] \T1/zi4/m/n/10 Experimenter name: Bonome T, Levine DA, Shih J, Randonovich
M, Pise-Masison CA, Bogomolniy F, Ozbun L, Brady J, Barrett JC, Boyd J, Birrer
MJ: A Gene Signature Predicting for Survival in Suboptimally Debulked Patients
with Ovarian Cancer. Cancer Research 2008, 68:5478 -5486.[]
[35]
Overfull \hbox (99.72977pt too wide) in paragraph at lines 1585--1585
[] \T1/zi4/m/n/10 Title: A gene signature predicting for survival in suboptim
ally debulked patients with ovarian cancer.[]
[36]
Underfull \vbox (badness 10000) has occurred while \output is active [37]
[38]
Overfull \hbox (724.66843pt too wide) in paragraph at lines 1725--1725
[] \T1/zi4/m/n/10 Experimenter name: Gillet JP, Calcagno AM, Varma S, Davidso
n B et al. Multidrug resistance-linked gene signature predicts overall survival
of patients with primary ovarian serous carcinoma. Clin Cancer Res 2012 Jun 1;
18(11):3197-206.[]
Overfull \hbox (218.0597pt too wide) in paragraph at lines 1728--1728
[] \T1/zi4/m/n/10 Title: Multidrug resistance-linked gene signature predicts
overall survival of patients with primary ovarian serous carcinoma.[]
[39]
Underfull \vbox (badness 10000) has occurred while \output is active [40]
Overfull \hbox (84.71954pt too wide) in paragraph at lines 1847--1847
[] \T1/zi4/m/n/10 Experimenter name: Ferriss JS, Kim Y, Duska L, Birrer M, Le
vine DA, Moskaluk C,Theodorescu D, Lee JK[]
Overfull \hbox (299.71954pt too wide) in paragraph at lines 1850--1850
[] \T1/zi4/m/n/10 Title: Multi-gene expression predictors of single drug resp
onses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resist
ance.[]
[41] [42]
Underfull \vbox (badness 10000) has occurred while \output is active [43]
[44]
Overfull \hbox (834.6582pt too wide) in paragraph at lines 1993--1993
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (318.04947pt too wide) in paragraph at lines 1996--1996
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[45]
Underfull \vbox (badness 10000) has occurred while \output is active [46]
[47]
Overfull \hbox (834.6582pt too wide) in paragraph at lines 2120--2120
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (318.04947pt too wide) in paragraph at lines 2123--2123
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[48]
Underfull \vbox (badness 10000) has occurred while \output is active [49]
[50]
Overfull \hbox (66.39984pt too wide) in paragraph at lines 2250--2250
[] \T1/zi4/m/n/10 Title: COL11A1 promotes tumor progression and predicts poor
clinical outcome in ovarian cancer.[]
Overfull \hbox (34.73999pt too wide) in paragraph at lines 2286--2286
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[51] [52]
Overfull \hbox (456.32828pt too wide) in paragraph at lines 2356--2356
[] \T1/zi4/m/n/10 Experimenter name: Pils D1, Hager G, Tong D, Aust S, Heinze
G, Kohl M, Schuster E, Wolf A, Sehouli J, Braicu I, Vergote I, Cadron I, Mahne
r S, Hofstetter G, Speiser P, Zeillinger R[]
Overfull \hbox (156.3794pt too wide) in paragraph at lines 2359--2359
[] \T1/zi4/m/n/10 Title: Validating the impact of a molecular subtype in ovar
ian cancer on outcomes: a study of the OVCAD Consortium.[]
[53] [54] [55]
Overfull \hbox (139.70932pt too wide) in paragraph at lines 2483--2483
[] \T1/zi4/m/n/10 Experimenter name: Karlan BY, Dering J, Walsh C, Orsulic S,
Lester J, Anderson LA, Ginther CL, Fejzo M, Slamon D[]
Overfull \hbox (133.06992pt too wide) in paragraph at lines 2486--2486
[] \T1/zi4/m/n/10 Title: POSTN/TGFBI-associated stromal signature predicts po
or prognosis in serous epithelial ovarian cancer.[]
[56] [57]
Underfull \hbox (badness 1337) in paragraph at lines 2604--2604
[] \T1/ptm/m/it/10 Lysophos-pha-tidic acid-induced tran-scrip-tional pro-file r
ep-re-sents
[58]
Overfull \hbox (1007.96768pt too wide) in paragraph at lines 2622--2622
[] \T1/zi4/m/n/10 Experimenter name: Murph MM, Liu W, Yu S, Lu Y, Hall H, Hen
nessy BT, Lahad J, Schaner M, Helland A, Kristensen G, Brresen-Dale AL, Mills G
B. Lysophosphatidic acid-induced transcriptional profile represents serous epit
helial ovarian carcinoma and worsened prognosis. PLoS One. 2009; 4(5):e5583.[]
Overfull \hbox (246.39984pt too wide) in paragraph at lines 2625--2625
[] \T1/zi4/m/n/10 Title: Lysophosphatidic acid-induced transcriptional profil
e represents serous epithelial ovarian carcinoma and worsened prognosis.[]
[59] [60]
Overfull \hbox (972.96768pt too wide) in paragraph at lines 2730--2730
[] \T1/zi4/m/n/10 Experimenter name: Ouellet V, Provencher DM, Maugard CM, Le
Page C, Ren F, Lussier C, Novak J, Ge B, Hudson TJ, Tonin PN, Mes-Masson A-M:
Discrimination between serous low malignant potential and invasive epithelial o
varian tumors using molecular profiling. Oncogene 2005, 24:4672-4687.[]
[61] [62]
Overfull \hbox (929.62753pt too wide) in paragraph at lines 2826--2826
[] \T1/zi4/m/n/10 Experimenter name: Marchini S, Mariani P, Chiorino G, Marra
zzo E, Bonomi R, Fruscio R, Clivio L, Garbi A, Torri V, Cinquini M, Dell\TS1/zi
4/m/n/10 '\T1/zi4/m/n/10 Anna T, Apolone G, Broggini M, D\TS1/zi4/m/n/10 '\T1/z
i4/m/n/10 Incalci M.Analysis of gene expression in early-stage ovarian cancer.
Clin Cancer Res. 2008 Dec 1; 14(23):7850-60.[]
[63] [64]
Underfull \vbox (badness 10000) has occurred while \output is active [65]
Overfull \hbox (1302.91656pt too wide) in paragraph at lines 2952--2952
[] \T1/zi4/m/n/10 Experimenter name: Tothill RW, Tinker AV, George J, Brown R
, Fox SB, Lade S, Johnson DS, Trivett MK, Etemadmoghadam D, Locandro B, Trafica
nte N, Fereday S, Hung JA, Chiew YE, Haviv I, Gertig D, DeFazio A, Bowtell DD.N
ovel molecular subtypes of serous and endometrioid ovarian cancer linked to cli
nical outcome. Clin Cancer Res. 2008 Aug 15; 14(16):5198-208.[]
Overfull \hbox (94.72977pt too wide) in paragraph at lines 2955--2955
[] \T1/zi4/m/n/10 Title: Novel molecular subtypes of serous and endometrioid
ovarian cancer linked to clinical outcome.[]
[66] [67]
Underfull \vbox (badness 10000) has occurred while \output is active [68]
[69]
Overfull \hbox (1011.28738pt too wide) in paragraph at lines 3107--3107
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Lancaster JM, Pi
ttman J, Luo J, Lee P, Murphy S, Dressman HK, Febbo PG, West M, Nevins JR, Mark
s JR.Patterns of gene expression that characterize long-term survival in advanc
ed stage serous ovarian cancers. Clin Cancer Res. 2005 May 15; 11(10):3686-96.[
]
Overfull \hbox (153.0597pt too wide) in paragraph at lines 3110--3110
[] \T1/zi4/m/n/10 Title: Patterns of gene expression that characterize long-t
erm survival in advanced stage serous ovarian cancers.[]
[70]
Overfull \hbox (34.73999pt too wide) in paragraph at lines 3148--3148
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[71] [72]
Overfull \hbox (1221.25671pt too wide) in paragraph at lines 3230--3230
[] \T1/zi4/m/n/10 Experimenter name: Dressman HK, Berchuck A, Chan G, Zhai J,
Bild A, Sayer R, Cragun J, Clarke J, Whitaker RS, Li L, Gray J, Marks J, Ginsb
urg GS, Potti A, West M, Nevins JR, Lancaster JM.An integrated genomic-based ap
proach to individualized treatment of patients with advanced-stage ovarian canc
er. J Clin Oncol. 2007 Feb 10; 25(5):517-25.[]
Overfull \hbox (184.72977pt too wide) in paragraph at lines 3233--3233
[] \T1/zi4/m/n/10 Title: An integrated genomic-based approach to individualiz
ed treatment of patients with advanced-stage ovarian cancer.[]
[73]
Underfull \vbox (badness 10000) has occurred while \output is active [74]
Overfull \hbox (1237.92679pt too wide) in paragraph at lines 3358--3358
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Luo J, Clarke JP
, Horne H, Levine DA, Boyd J, Alonso MA, Secord AA, Bernardini MQ, Barnett JC,
Boren T, Murphy SK, Dressman HK, Marks JR, Lancaster JM.Microarray analysis of
early stage serous ovarian cancers shows profiles predictive of favorable outco
me. Clin Cancer Res. 2009 Apr 1; 15(7):2448-55.[]
Overfull \hbox (148.0597pt too wide) in paragraph at lines 3361--3361
[] \T1/zi4/m/n/10 Title: Microarray analysis of early stage serous ovarian ca
ncers shows profiles predictive of favorable outcome.[]
[75] [76]
Underfull \vbox (badness 10000) has occurred while \output is active [77]
Overfull \hbox (64.73999pt too wide) in paragraph at lines 3490--3490
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[78] [79]
Underfull \vbox (badness 10000) has occurred while \output is active [80]
Underfull \vbox (badness 10000) has occurred while \output is active [81]
Overfull \hbox (64.73999pt too wide) in paragraph at lines 3666--3666
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[82] [83]
Underfull \vbox (badness 10000) has occurred while \output is active [84]
[85]
Overfull \hbox (64.73999pt too wide) in paragraph at lines 3839--3839
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[86] [87]
Underfull \vbox (badness 10000) has occurred while \output is active [88]
No file Rd2.ind.
[89]
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.aux
)
Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
)
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (89 pages, 220437 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 2
L3 programming layer <2020-02-14>
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 378.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 378.
) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.aux
) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.out
)
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.out
) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.toc
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Underfull \vbox (badness 10000) has occurred while \output is active [2]
Overfull \hbox (42.89548pt too wide) in paragraph at lines 99--102
[]\T1/ptm/m/n/10 For "pri-mary_therapy_outcome_success": com-pletere-sponse|par
tialresponse|progressivedisease|stabledisease:
Overfull \hbox (14.36601pt too wide) in paragraph at lines 120--122
[]\T1/ptm/m/n/10 For "site_of_tumor_first_recurrence": (metas-ta-sis / lo-core-
gional / none / lo-core-gional_plus_metastatic).
[3] [4]
Overfull \hbox (1107.93701pt too wide) in paragraph at lines 192--192
[] \T1/zi4/m/n/10 Experimenter name: Bentink S, Haibe-Kains B, Risch T, Fan J
-B, Hirsch MS, Holton K, Rubio R, April C, Chen J, Wickham-Garcia E, Liu J, Cul
hane A, Drapkin R, Quackenbush J, Matulonis UA: Angiogenic mRNA and microRNA ge
ne expression signature predicts a novel subtype of serous ovarian cancer. PLoS
ONE 2012, 7:e30269.[]
Overfull \hbox (146.38962pt too wide) in paragraph at lines 195--195
[] \T1/zi4/m/n/10 Title: Angiogenic mRNA and microRNA gene expression signatu
re predicts a novel subtype of serous ovarian cancer.[]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [5]
Underfull \vbox (badness 10000) has occurred while \output is active [6]
Overfull \hbox (591.34872pt too wide) in paragraph at lines 314--314
[] \T1/zi4/m/n/10 Experimenter name: Partheen K, Levan K, Osterberg L, Horvat
h G.Expression analysis of stage III serous ovarian adenocarcinoma distinguishe
s a sub-group of survivors. Eur J Cancer. 2006 Nov; 42(16):2846-54.[]
Overfull \hbox (134.72977pt too wide) in paragraph at lines 317--317
[] \T1/zi4/m/n/10 Title: Expression analysis of stage III serous ovarian aden
ocarcinoma distinguishes a sub-group of survivors.[]
[7]
Overfull \hbox (34.73999pt too wide) in paragraph at lines 353--353
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[8] [9]
Overfull \hbox (1299.59686pt too wide) in paragraph at lines 431--431
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Komata D, Yamamot
o T, Kodama S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H,
Kudo Y, Inoue I, Tanaka K.Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis. Cancer Sci. 2009 Aug; 100(8):1421-8.[]
Overfull \hbox (379.70932pt too wide) in paragraph at lines 434--434
[] \T1/zi4/m/n/10 Title: Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis.[]
[10] [11]
Overfull \hbox (861.2976pt too wide) in paragraph at lines 523--523
[] \T1/zi4/m/n/10 Experimenter name: Crijns AP, Fehrmann RS, de Jong S, Gerbe
ns F, Meersma GJ, Klip HG, Hollema H, Hofstra RM, te Meerman GJ, de Vries EG, v
an der Zee AG.Survival-related profile, pathways, and transcription factors in
ovarian cancer. PLoS Med. 2009 Feb 3; 6(2):e24.[]
Overfull \hbox (31.41006pt too wide) in paragraph at lines 526--526
[] \T1/zi4/m/n/10 Title: Survival-related profile, pathways, and transcriptio
n factors in ovarian cancer.[]
[12] [13] [14]
Overfull \hbox (636.3385pt too wide) in paragraph at lines 641--641
[] \T1/zi4/m/n/10 Experimenter name: Denkert C, Budczies J, Darb-Esfahani S,
Gy??rffy B et al. A prognostic gene expression index in ovarian cancer - valida
tion across different independent data sets. J Pathol 2009 Jun;218(2):273-80.[]
Overfull \hbox (146.38962pt too wide) in paragraph at lines 644--644
[] \T1/zi4/m/n/10 Title: A prognostic gene expression index in ovarian cancer
- validation across different independent data sets.[]
[15] [16]
Overfull \hbox (3.12666pt too wide) in paragraph at lines 754--755
[]\T1/ptm/m/n/10 Advanced-stage ovar-ian can-cer pa-tients are gen-er-ally trea
ted with platinum/taxane-based chemother-
[17]
Overfull \hbox (1289.58664pt too wide) in paragraph at lines 767--767
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Yahata T, Kodama
S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H, Kudo Y, Kot
era K, Masuzaki H, Tashiro H, Katabuchi H, Inoue I, Tanaka K.Gene expression pr
ofile for predicting survival in advanced-stage serous ovarian cancer across tw
o independent datasets. PLoS One. 2010 Mar 12; 5(3):e9615.[]
Overfull \hbox (221.38962pt too wide) in paragraph at lines 770--770
[] \T1/zi4/m/n/10 Title: Gene expression profile for predicting survival in a
dvanced-stage serous ovarian cancer across two independent datasets.[]
[18] [19] [20]
Overfull \hbox (1551.22604pt too wide) in paragraph at lines 905--905
[] \T1/zi4/m/n/10 Experimenter name: Mok SC, Bonome T, Vathipadiekal V, Bell
A, Johnson ME, Wong KK, Park DC, Hao K, Yip DK, Donninger H, Ozbun L, Samimi G,
Brady J, Randonovich M, Pise-Masison CA, Barrett JC, Wong WH, Welch WR, Berkow
itz RS, Birrer MJ.A gene signature predictive for outcome in advanced ovarian c
ancer identifies a survival factor: microfibril-associated glycoprotein 2. Canc
er Cell. 2009 Dec 8; 16(6):521-32.[]
Overfull \hbox (293.04947pt too wide) in paragraph at lines 908--908
[] \T1/zi4/m/n/10 Title: A gene signature predictive for outcome in advanced
ovarian cancer identifies a survival factor: microfibril-associated glycoprotei
n 2.[]
[21] [22] [23]
Overfull \hbox (904.64798pt too wide) in paragraph at lines 1040--1040
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (353.03925pt too wide) in paragraph at lines 1043--1043
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[24] [25]
Overfull \hbox (904.64798pt too wide) in paragraph at lines 1138--1138
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (353.03925pt too wide) in paragraph at lines 1141--1141
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[26] [27] [28]
Overfull \hbox (1481.23627pt too wide) in paragraph at lines 1236--1236
[] \T1/zi4/m/n/10 Experimenter name: Meyniel JP, Cottu PH, Decraene C, Stern
MH, Couturier J, Lebigot I, Nicolas A, Weber N, Fourchotte V, Alran S, Rapinat
A, Gentien D, Roman-Roman S, Mignot L, Sastre-Garau X.A genomic and transcripto
mic approach for a differential diagnosis between primary and secondary ovarian
carcinomas in patients with a previous history of breast cancer. BMC Cancer. 2
010 May 21; 10:222.[]
Overfull \hbox (451.35895pt too wide) in paragraph at lines 1239--1239
[] \T1/zi4/m/n/10 Title: A genomic and transcriptomic approach for a differen
tial diagnosis between primary and secondary ovarian carcinomas in patients wit
h a previous history of breast cancer.[]
[29] [30]
Overfull \hbox (101.41006pt too wide) in paragraph at lines 1344--1344
[] \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[31] [32]
Overfull \hbox (126.38962pt too wide) in paragraph at lines 1456--1456
[] \T1/zi4/m/n/10 Experimenter name: Mateescu B, Batista L, Mariani O, Meynie
l J, Cottu PH, Sastre-Garau X, Mechta-Grigoriou F[]
Overfull \hbox (81.39984pt too wide) in paragraph at lines 1459--1459
[] \T1/zi4/m/n/10 Title: miR-141 and miR-200a act on ovarian tumorigenesis by
controlling oxidative stress response.[]
[33] [34] [35]
Overfull \hbox (917.96768pt too wide) in paragraph at lines 1582--1582
[] \T1/zi4/m/n/10 Experimenter name: Bonome T, Levine DA, Shih J, Randonovich
M, Pise-Masison CA, Bogomolniy F, Ozbun L, Brady J, Barrett JC, Boyd J, Birrer
MJ: A Gene Signature Predicting for Survival in Suboptimally Debulked Patients
with Ovarian Cancer. Cancer Research 2008, 68:5478 -5486.[]
Overfull \hbox (99.72977pt too wide) in paragraph at lines 1585--1585
[] \T1/zi4/m/n/10 Title: A gene signature predicting for survival in suboptim
ally debulked patients with ovarian cancer.[]
[36] [37] [38]
Overfull \hbox (724.66843pt too wide) in paragraph at lines 1725--1725
[] \T1/zi4/m/n/10 Experimenter name: Gillet JP, Calcagno AM, Varma S, Davidso
n B et al. Multidrug resistance-linked gene signature predicts overall survival
of patients with primary ovarian serous carcinoma. Clin Cancer Res 2012 Jun 1;
18(11):3197-206.[]
Overfull \hbox (218.0597pt too wide) in paragraph at lines 1728--1728
[] \T1/zi4/m/n/10 Title: Multidrug resistance-linked gene signature predicts
overall survival of patients with primary ovarian serous carcinoma.[]
[39] [40] [41]
Overfull \hbox (84.71954pt too wide) in paragraph at lines 1847--1847
[] \T1/zi4/m/n/10 Experimenter name: Ferriss JS, Kim Y, Duska L, Birrer M, Le
vine DA, Moskaluk C,Theodorescu D, Lee JK[]
Overfull \hbox (299.71954pt too wide) in paragraph at lines 1850--1850
[] \T1/zi4/m/n/10 Title: Multi-gene expression predictors of single drug resp
onses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resist
ance.[]
[42] [43] [44]
Overfull \hbox (834.6582pt too wide) in paragraph at lines 1993--1993
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (318.04947pt too wide) in paragraph at lines 1996--1996
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[45] [46] [47]
Overfull \hbox (834.6582pt too wide) in paragraph at lines 2120--2120
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (318.04947pt too wide) in paragraph at lines 2123--2123
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[48] [49] [50]
Overfull \hbox (66.39984pt too wide) in paragraph at lines 2250--2250
[] \T1/zi4/m/n/10 Title: COL11A1 promotes tumor progression and predicts poor
clinical outcome in ovarian cancer.[]
[51]
Overfull \hbox (34.73999pt too wide) in paragraph at lines 2286--2286
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[52]
Overfull \hbox (456.32828pt too wide) in paragraph at lines 2356--2356
[] \T1/zi4/m/n/10 Experimenter name: Pils D1, Hager G, Tong D, Aust S, Heinze
G, Kohl M, Schuster E, Wolf A, Sehouli J, Braicu I, Vergote I, Cadron I, Mahne
r S, Hofstetter G, Speiser P, Zeillinger R[]
Overfull \hbox (156.3794pt too wide) in paragraph at lines 2359--2359
[] \T1/zi4/m/n/10 Title: Validating the impact of a molecular subtype in ovar
ian cancer on outcomes: a study of the OVCAD Consortium.[]
[53] [54]
Underfull \vbox (badness 10000) has occurred while \output is active [55]
Overfull \hbox (139.70932pt too wide) in paragraph at lines 2483--2483
[] \T1/zi4/m/n/10 Experimenter name: Karlan BY, Dering J, Walsh C, Orsulic S,
Lester J, Anderson LA, Ginther CL, Fejzo M, Slamon D[]
Overfull \hbox (133.06992pt too wide) in paragraph at lines 2486--2486
[] \T1/zi4/m/n/10 Title: POSTN/TGFBI-associated stromal signature predicts po
or prognosis in serous epithelial ovarian cancer.[]
[56] [57]
Underfull \vbox (badness 10000) has occurred while \output is active [58]
Underfull \hbox (badness 1337) in paragraph at lines 2604--2604
[] \T1/ptm/m/it/10 Lysophos-pha-tidic acid-induced tran-scrip-tional pro-file r
ep-re-sents
Overfull \hbox (1007.96768pt too wide) in paragraph at lines 2622--2622
[] \T1/zi4/m/n/10 Experimenter name: Murph MM, Liu W, Yu S, Lu Y, Hall H, Hen
nessy BT, Lahad J, Schaner M, Helland A, Kristensen G, Brresen-Dale AL, Mills G
B. Lysophosphatidic acid-induced transcriptional profile represents serous epit
helial ovarian carcinoma and worsened prognosis. PLoS One. 2009; 4(5):e5583.[]
[59]
Overfull \hbox (246.39984pt too wide) in paragraph at lines 2625--2625
[] \T1/zi4/m/n/10 Title: Lysophosphatidic acid-induced transcriptional profil
e represents serous epithelial ovarian carcinoma and worsened prognosis.[]
[60] [61]
Overfull \hbox (972.96768pt too wide) in paragraph at lines 2730--2730
[] \T1/zi4/m/n/10 Experimenter name: Ouellet V, Provencher DM, Maugard CM, Le
Page C, Ren F, Lussier C, Novak J, Ge B, Hudson TJ, Tonin PN, Mes-Masson A-M:
Discrimination between serous low malignant potential and invasive epithelial o
varian tumors using molecular profiling. Oncogene 2005, 24:4672-4687.[]
[62] [63]
Overfull \hbox (929.62753pt too wide) in paragraph at lines 2826--2826
[] \T1/zi4/m/n/10 Experimenter name: Marchini S, Mariani P, Chiorino G, Marra
zzo E, Bonomi R, Fruscio R, Clivio L, Garbi A, Torri V, Cinquini M, Dell\TS1/zi
4/m/n/10 '\T1/zi4/m/n/10 Anna T, Apolone G, Broggini M, D\TS1/zi4/m/n/10 '\T1/z
i4/m/n/10 Incalci M.Analysis of gene expression in early-stage ovarian cancer.
Clin Cancer Res. 2008 Dec 1; 14(23):7850-60.[]
[64] [65] [66]
Overfull \hbox (1302.91656pt too wide) in paragraph at lines 2952--2952
[] \T1/zi4/m/n/10 Experimenter name: Tothill RW, Tinker AV, George J, Brown R
, Fox SB, Lade S, Johnson DS, Trivett MK, Etemadmoghadam D, Locandro B, Trafica
nte N, Fereday S, Hung JA, Chiew YE, Haviv I, Gertig D, DeFazio A, Bowtell DD.N
ovel molecular subtypes of serous and endometrioid ovarian cancer linked to cli
nical outcome. Clin Cancer Res. 2008 Aug 15; 14(16):5198-208.[]
Overfull \hbox (94.72977pt too wide) in paragraph at lines 2955--2955
[] \T1/zi4/m/n/10 Title: Novel molecular subtypes of serous and endometrioid
ovarian cancer linked to clinical outcome.[]
[67]
Underfull \vbox (badness 10000) has occurred while \output is active [68]
[69]
Overfull \hbox (1011.28738pt too wide) in paragraph at lines 3107--3107
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Lancaster JM, Pi
ttman J, Luo J, Lee P, Murphy S, Dressman HK, Febbo PG, West M, Nevins JR, Mark
s JR.Patterns of gene expression that characterize long-term survival in advanc
ed stage serous ovarian cancers. Clin Cancer Res. 2005 May 15; 11(10):3686-96.[
]
Overfull \hbox (153.0597pt too wide) in paragraph at lines 3110--3110
[] \T1/zi4/m/n/10 Title: Patterns of gene expression that characterize long-t
erm survival in advanced stage serous ovarian cancers.[]
[70]
Overfull \hbox (34.73999pt too wide) in paragraph at lines 3148--3148
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[71] [72]
Overfull \hbox (1221.25671pt too wide) in paragraph at lines 3230--3230
[] \T1/zi4/m/n/10 Experimenter name: Dressman HK, Berchuck A, Chan G, Zhai J,
Bild A, Sayer R, Cragun J, Clarke J, Whitaker RS, Li L, Gray J, Marks J, Ginsb
urg GS, Potti A, West M, Nevins JR, Lancaster JM.An integrated genomic-based ap
proach to individualized treatment of patients with advanced-stage ovarian canc
er. J Clin Oncol. 2007 Feb 10; 25(5):517-25.[]
Overfull \hbox (184.72977pt too wide) in paragraph at lines 3233--3233
[] \T1/zi4/m/n/10 Title: An integrated genomic-based approach to individualiz
ed treatment of patients with advanced-stage ovarian cancer.[]
[73] [74] [75]
Overfull \hbox (1237.92679pt too wide) in paragraph at lines 3358--3358
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Luo J, Clarke JP
, Horne H, Levine DA, Boyd J, Alonso MA, Secord AA, Bernardini MQ, Barnett JC,
Boren T, Murphy SK, Dressman HK, Marks JR, Lancaster JM.Microarray analysis of
early stage serous ovarian cancers shows profiles predictive of favorable outco
me. Clin Cancer Res. 2009 Apr 1; 15(7):2448-55.[]
Overfull \hbox (148.0597pt too wide) in paragraph at lines 3361--3361
[] \T1/zi4/m/n/10 Title: Microarray analysis of early stage serous ovarian ca
ncers shows profiles predictive of favorable outcome.[]
[76] [77] [78]
Overfull \hbox (64.73999pt too wide) in paragraph at lines 3490--3490
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[79]
Underfull \vbox (badness 10000) has occurred while \output is active [80]
Underfull \vbox (badness 10000) has occurred while \output is active [81]
[82]
Overfull \hbox (64.73999pt too wide) in paragraph at lines 3666--3666
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[83]
Underfull \vbox (badness 10000) has occurred while \output is active [84]
Underfull \vbox (badness 10000) has occurred while \output is active [85]
Overfull \hbox (64.73999pt too wide) in paragraph at lines 3839--3839
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[86] [87]
Underfull \vbox (badness 10000) has occurred while \output is active [88]
Underfull \vbox (badness 10000) has occurred while \output is active [89]
No file Rd2.ind.
[90]
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.aux
) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (90 pages, 224197 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (92 entries accepted, 0 rejected).
Sorting entries....done (616 comparisons).
Generating output file Rd2.ind....done (146 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 2
L3 programming layer <2020-02-14>
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 378.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 378.
) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.aux
) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.out
)
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.out
) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.toc
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Underfull \vbox (badness 10000) has occurred while \output is active [2]
Overfull \hbox (42.89548pt too wide) in paragraph at lines 99--102
[]\T1/ptm/m/n/10 For "pri-mary_therapy_outcome_success": com-pletere-sponse|par
tialresponse|progressivedisease|stabledisease:
Overfull \hbox (14.36601pt too wide) in paragraph at lines 120--122
[]\T1/ptm/m/n/10 For "site_of_tumor_first_recurrence": (metas-ta-sis / lo-core-
gional / none / lo-core-gional_plus_metastatic).
[3] [4]
Overfull \hbox (1107.93701pt too wide) in paragraph at lines 192--192
[] \T1/zi4/m/n/10 Experimenter name: Bentink S, Haibe-Kains B, Risch T, Fan J
-B, Hirsch MS, Holton K, Rubio R, April C, Chen J, Wickham-Garcia E, Liu J, Cul
hane A, Drapkin R, Quackenbush J, Matulonis UA: Angiogenic mRNA and microRNA ge
ne expression signature predicts a novel subtype of serous ovarian cancer. PLoS
ONE 2012, 7:e30269.[]
Overfull \hbox (146.38962pt too wide) in paragraph at lines 195--195
[] \T1/zi4/m/n/10 Title: Angiogenic mRNA and microRNA gene expression signatu
re predicts a novel subtype of serous ovarian cancer.[]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [5]
Underfull \vbox (badness 10000) has occurred while \output is active [6]
Overfull \hbox (591.34872pt too wide) in paragraph at lines 314--314
[] \T1/zi4/m/n/10 Experimenter name: Partheen K, Levan K, Osterberg L, Horvat
h G.Expression analysis of stage III serous ovarian adenocarcinoma distinguishe
s a sub-group of survivors. Eur J Cancer. 2006 Nov; 42(16):2846-54.[]
Overfull \hbox (134.72977pt too wide) in paragraph at lines 317--317
[] \T1/zi4/m/n/10 Title: Expression analysis of stage III serous ovarian aden
ocarcinoma distinguishes a sub-group of survivors.[]
[7]
Overfull \hbox (34.73999pt too wide) in paragraph at lines 353--353
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[8] [9]
Overfull \hbox (1299.59686pt too wide) in paragraph at lines 431--431
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Komata D, Yamamot
o T, Kodama S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H,
Kudo Y, Inoue I, Tanaka K.Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis. Cancer Sci. 2009 Aug; 100(8):1421-8.[]
Overfull \hbox (379.70932pt too wide) in paragraph at lines 434--434
[] \T1/zi4/m/n/10 Title: Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis.[]
[10] [11]
Overfull \hbox (861.2976pt too wide) in paragraph at lines 523--523
[] \T1/zi4/m/n/10 Experimenter name: Crijns AP, Fehrmann RS, de Jong S, Gerbe
ns F, Meersma GJ, Klip HG, Hollema H, Hofstra RM, te Meerman GJ, de Vries EG, v
an der Zee AG.Survival-related profile, pathways, and transcription factors in
ovarian cancer. PLoS Med. 2009 Feb 3; 6(2):e24.[]
Overfull \hbox (31.41006pt too wide) in paragraph at lines 526--526
[] \T1/zi4/m/n/10 Title: Survival-related profile, pathways, and transcriptio
n factors in ovarian cancer.[]
[12] [13] [14]
Overfull \hbox (636.3385pt too wide) in paragraph at lines 641--641
[] \T1/zi4/m/n/10 Experimenter name: Denkert C, Budczies J, Darb-Esfahani S,
Gy??rffy B et al. A prognostic gene expression index in ovarian cancer - valida
tion across different independent data sets. J Pathol 2009 Jun;218(2):273-80.[]
Overfull \hbox (146.38962pt too wide) in paragraph at lines 644--644
[] \T1/zi4/m/n/10 Title: A prognostic gene expression index in ovarian cancer
- validation across different independent data sets.[]
[15] [16]
Overfull \hbox (3.12666pt too wide) in paragraph at lines 754--755
[]\T1/ptm/m/n/10 Advanced-stage ovar-ian can-cer pa-tients are gen-er-ally trea
ted with platinum/taxane-based chemother-
[17]
Overfull \hbox (1289.58664pt too wide) in paragraph at lines 767--767
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Yahata T, Kodama
S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H, Kudo Y, Kot
era K, Masuzaki H, Tashiro H, Katabuchi H, Inoue I, Tanaka K.Gene expression pr
ofile for predicting survival in advanced-stage serous ovarian cancer across tw
o independent datasets. PLoS One. 2010 Mar 12; 5(3):e9615.[]
Overfull \hbox (221.38962pt too wide) in paragraph at lines 770--770
[] \T1/zi4/m/n/10 Title: Gene expression profile for predicting survival in a
dvanced-stage serous ovarian cancer across two independent datasets.[]
[18] [19] [20]
Overfull \hbox (1551.22604pt too wide) in paragraph at lines 905--905
[] \T1/zi4/m/n/10 Experimenter name: Mok SC, Bonome T, Vathipadiekal V, Bell
A, Johnson ME, Wong KK, Park DC, Hao K, Yip DK, Donninger H, Ozbun L, Samimi G,
Brady J, Randonovich M, Pise-Masison CA, Barrett JC, Wong WH, Welch WR, Berkow
itz RS, Birrer MJ.A gene signature predictive for outcome in advanced ovarian c
ancer identifies a survival factor: microfibril-associated glycoprotein 2. Canc
er Cell. 2009 Dec 8; 16(6):521-32.[]
Overfull \hbox (293.04947pt too wide) in paragraph at lines 908--908
[] \T1/zi4/m/n/10 Title: A gene signature predictive for outcome in advanced
ovarian cancer identifies a survival factor: microfibril-associated glycoprotei
n 2.[]
[21] [22] [23]
Overfull \hbox (904.64798pt too wide) in paragraph at lines 1040--1040
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (353.03925pt too wide) in paragraph at lines 1043--1043
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[24] [25]
Overfull \hbox (904.64798pt too wide) in paragraph at lines 1138--1138
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (353.03925pt too wide) in paragraph at lines 1141--1141
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[26] [27] [28]
Overfull \hbox (1481.23627pt too wide) in paragraph at lines 1236--1236
[] \T1/zi4/m/n/10 Experimenter name: Meyniel JP, Cottu PH, Decraene C, Stern
MH, Couturier J, Lebigot I, Nicolas A, Weber N, Fourchotte V, Alran S, Rapinat
A, Gentien D, Roman-Roman S, Mignot L, Sastre-Garau X.A genomic and transcripto
mic approach for a differential diagnosis between primary and secondary ovarian
carcinomas in patients with a previous history of breast cancer. BMC Cancer. 2
010 May 21; 10:222.[]
Overfull \hbox (451.35895pt too wide) in paragraph at lines 1239--1239
[] \T1/zi4/m/n/10 Title: A genomic and transcriptomic approach for a differen
tial diagnosis between primary and secondary ovarian carcinomas in patients wit
h a previous history of breast cancer.[]
[29] [30]
Overfull \hbox (101.41006pt too wide) in paragraph at lines 1344--1344
[] \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[31] [32]
Overfull \hbox (126.38962pt too wide) in paragraph at lines 1456--1456
[] \T1/zi4/m/n/10 Experimenter name: Mateescu B, Batista L, Mariani O, Meynie
l J, Cottu PH, Sastre-Garau X, Mechta-Grigoriou F[]
Overfull \hbox (81.39984pt too wide) in paragraph at lines 1459--1459
[] \T1/zi4/m/n/10 Title: miR-141 and miR-200a act on ovarian tumorigenesis by
controlling oxidative stress response.[]
[33] [34] [35]
Overfull \hbox (917.96768pt too wide) in paragraph at lines 1582--1582
[] \T1/zi4/m/n/10 Experimenter name: Bonome T, Levine DA, Shih J, Randonovich
M, Pise-Masison CA, Bogomolniy F, Ozbun L, Brady J, Barrett JC, Boyd J, Birrer
MJ: A Gene Signature Predicting for Survival in Suboptimally Debulked Patients
with Ovarian Cancer. Cancer Research 2008, 68:5478 -5486.[]
Overfull \hbox (99.72977pt too wide) in paragraph at lines 1585--1585
[] \T1/zi4/m/n/10 Title: A gene signature predicting for survival in suboptim
ally debulked patients with ovarian cancer.[]
[36] [37] [38]
Overfull \hbox (724.66843pt too wide) in paragraph at lines 1725--1725
[] \T1/zi4/m/n/10 Experimenter name: Gillet JP, Calcagno AM, Varma S, Davidso
n B et al. Multidrug resistance-linked gene signature predicts overall survival
of patients with primary ovarian serous carcinoma. Clin Cancer Res 2012 Jun 1;
18(11):3197-206.[]
Overfull \hbox (218.0597pt too wide) in paragraph at lines 1728--1728
[] \T1/zi4/m/n/10 Title: Multidrug resistance-linked gene signature predicts
overall survival of patients with primary ovarian serous carcinoma.[]
[39] [40] [41]
Overfull \hbox (84.71954pt too wide) in paragraph at lines 1847--1847
[] \T1/zi4/m/n/10 Experimenter name: Ferriss JS, Kim Y, Duska L, Birrer M, Le
vine DA, Moskaluk C,Theodorescu D, Lee JK[]
Overfull \hbox (299.71954pt too wide) in paragraph at lines 1850--1850
[] \T1/zi4/m/n/10 Title: Multi-gene expression predictors of single drug resp
onses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resist
ance.[]
[42] [43] [44]
Overfull \hbox (834.6582pt too wide) in paragraph at lines 1993--1993
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (318.04947pt too wide) in paragraph at lines 1996--1996
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[45] [46] [47]
Overfull \hbox (834.6582pt too wide) in paragraph at lines 2120--2120
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (318.04947pt too wide) in paragraph at lines 2123--2123
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[48] [49] [50]
Overfull \hbox (66.39984pt too wide) in paragraph at lines 2250--2250
[] \T1/zi4/m/n/10 Title: COL11A1 promotes tumor progression and predicts poor
clinical outcome in ovarian cancer.[]
[51]
Overfull \hbox (34.73999pt too wide) in paragraph at lines 2286--2286
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[52]
Overfull \hbox (456.32828pt too wide) in paragraph at lines 2356--2356
[] \T1/zi4/m/n/10 Experimenter name: Pils D1, Hager G, Tong D, Aust S, Heinze
G, Kohl M, Schuster E, Wolf A, Sehouli J, Braicu I, Vergote I, Cadron I, Mahne
r S, Hofstetter G, Speiser P, Zeillinger R[]
Overfull \hbox (156.3794pt too wide) in paragraph at lines 2359--2359
[] \T1/zi4/m/n/10 Title: Validating the impact of a molecular subtype in ovar
ian cancer on outcomes: a study of the OVCAD Consortium.[]
[53] [54]
Underfull \vbox (badness 10000) has occurred while \output is active [55]
Overfull \hbox (139.70932pt too wide) in paragraph at lines 2483--2483
[] \T1/zi4/m/n/10 Experimenter name: Karlan BY, Dering J, Walsh C, Orsulic S,
Lester J, Anderson LA, Ginther CL, Fejzo M, Slamon D[]
Overfull \hbox (133.06992pt too wide) in paragraph at lines 2486--2486
[] \T1/zi4/m/n/10 Title: POSTN/TGFBI-associated stromal signature predicts po
or prognosis in serous epithelial ovarian cancer.[]
[56] [57]
Underfull \vbox (badness 10000) has occurred while \output is active [58]
Underfull \hbox (badness 1337) in paragraph at lines 2604--2604
[] \T1/ptm/m/it/10 Lysophos-pha-tidic acid-induced tran-scrip-tional pro-file r
ep-re-sents
Overfull \hbox (1007.96768pt too wide) in paragraph at lines 2622--2622
[] \T1/zi4/m/n/10 Experimenter name: Murph MM, Liu W, Yu S, Lu Y, Hall H, Hen
nessy BT, Lahad J, Schaner M, Helland A, Kristensen G, Brresen-Dale AL, Mills G
B. Lysophosphatidic acid-induced transcriptional profile represents serous epit
helial ovarian carcinoma and worsened prognosis. PLoS One. 2009; 4(5):e5583.[]
[59]
Overfull \hbox (246.39984pt too wide) in paragraph at lines 2625--2625
[] \T1/zi4/m/n/10 Title: Lysophosphatidic acid-induced transcriptional profil
e represents serous epithelial ovarian carcinoma and worsened prognosis.[]
[60] [61]
Overfull \hbox (972.96768pt too wide) in paragraph at lines 2730--2730
[] \T1/zi4/m/n/10 Experimenter name: Ouellet V, Provencher DM, Maugard CM, Le
Page C, Ren F, Lussier C, Novak J, Ge B, Hudson TJ, Tonin PN, Mes-Masson A-M:
Discrimination between serous low malignant potential and invasive epithelial o
varian tumors using molecular profiling. Oncogene 2005, 24:4672-4687.[]
[62] [63]
Overfull \hbox (929.62753pt too wide) in paragraph at lines 2826--2826
[] \T1/zi4/m/n/10 Experimenter name: Marchini S, Mariani P, Chiorino G, Marra
zzo E, Bonomi R, Fruscio R, Clivio L, Garbi A, Torri V, Cinquini M, Dell\TS1/zi
4/m/n/10 '\T1/zi4/m/n/10 Anna T, Apolone G, Broggini M, D\TS1/zi4/m/n/10 '\T1/z
i4/m/n/10 Incalci M.Analysis of gene expression in early-stage ovarian cancer.
Clin Cancer Res. 2008 Dec 1; 14(23):7850-60.[]
[64] [65] [66]
Overfull \hbox (1302.91656pt too wide) in paragraph at lines 2952--2952
[] \T1/zi4/m/n/10 Experimenter name: Tothill RW, Tinker AV, George J, Brown R
, Fox SB, Lade S, Johnson DS, Trivett MK, Etemadmoghadam D, Locandro B, Trafica
nte N, Fereday S, Hung JA, Chiew YE, Haviv I, Gertig D, DeFazio A, Bowtell DD.N
ovel molecular subtypes of serous and endometrioid ovarian cancer linked to cli
nical outcome. Clin Cancer Res. 2008 Aug 15; 14(16):5198-208.[]
Overfull \hbox (94.72977pt too wide) in paragraph at lines 2955--2955
[] \T1/zi4/m/n/10 Title: Novel molecular subtypes of serous and endometrioid
ovarian cancer linked to clinical outcome.[]
[67]
Underfull \vbox (badness 10000) has occurred while \output is active [68]
[69]
Overfull \hbox (1011.28738pt too wide) in paragraph at lines 3107--3107
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Lancaster JM, Pi
ttman J, Luo J, Lee P, Murphy S, Dressman HK, Febbo PG, West M, Nevins JR, Mark
s JR.Patterns of gene expression that characterize long-term survival in advanc
ed stage serous ovarian cancers. Clin Cancer Res. 2005 May 15; 11(10):3686-96.[
]
Overfull \hbox (153.0597pt too wide) in paragraph at lines 3110--3110
[] \T1/zi4/m/n/10 Title: Patterns of gene expression that characterize long-t
erm survival in advanced stage serous ovarian cancers.[]
[70]
Overfull \hbox (34.73999pt too wide) in paragraph at lines 3148--3148
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[71] [72]
Overfull \hbox (1221.25671pt too wide) in paragraph at lines 3230--3230
[] \T1/zi4/m/n/10 Experimenter name: Dressman HK, Berchuck A, Chan G, Zhai J,
Bild A, Sayer R, Cragun J, Clarke J, Whitaker RS, Li L, Gray J, Marks J, Ginsb
urg GS, Potti A, West M, Nevins JR, Lancaster JM.An integrated genomic-based ap
proach to individualized treatment of patients with advanced-stage ovarian canc
er. J Clin Oncol. 2007 Feb 10; 25(5):517-25.[]
Overfull \hbox (184.72977pt too wide) in paragraph at lines 3233--3233
[] \T1/zi4/m/n/10 Title: An integrated genomic-based approach to individualiz
ed treatment of patients with advanced-stage ovarian cancer.[]
[73] [74] [75]
Overfull \hbox (1237.92679pt too wide) in paragraph at lines 3358--3358
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Luo J, Clarke JP
, Horne H, Levine DA, Boyd J, Alonso MA, Secord AA, Bernardini MQ, Barnett JC,
Boren T, Murphy SK, Dressman HK, Marks JR, Lancaster JM.Microarray analysis of
early stage serous ovarian cancers shows profiles predictive of favorable outco
me. Clin Cancer Res. 2009 Apr 1; 15(7):2448-55.[]
Overfull \hbox (148.0597pt too wide) in paragraph at lines 3361--3361
[] \T1/zi4/m/n/10 Title: Microarray analysis of early stage serous ovarian ca
ncers shows profiles predictive of favorable outcome.[]
[76] [77] [78]
Overfull \hbox (64.73999pt too wide) in paragraph at lines 3490--3490
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[79]
Underfull \vbox (badness 10000) has occurred while \output is active [80]
Underfull \vbox (badness 10000) has occurred while \output is active [81]
[82]
Overfull \hbox (64.73999pt too wide) in paragraph at lines 3666--3666
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[83]
Underfull \vbox (badness 10000) has occurred while \output is active [84]
Underfull \vbox (badness 10000) has occurred while \output is active [85]
Overfull \hbox (64.73999pt too wide) in paragraph at lines 3839--3839
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[86] [87]
Underfull \vbox (badness 10000) has occurred while \output is active [88]
Underfull \vbox (badness 10000) has occurred while \output is active [89]
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.ind
[90]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 37.
[91] [92])
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.aux
)
Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb
></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on Rd2.pdf (92 pages, 236724 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (92 entries accepted, 0 rejected).
Sorting entries....done (616 comparisons).
Generating output file Rd2.ind....done (146 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 2
L3 programming layer <2020-02-14>
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty)))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 378.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 378.
) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.aux
) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.out
)
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.out
) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.toc
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Underfull \vbox (badness 10000) has occurred while \output is active [2]
Overfull \hbox (42.89548pt too wide) in paragraph at lines 99--102
[]\T1/ptm/m/n/10 For "pri-mary_therapy_outcome_success": com-pletere-sponse|par
tialresponse|progressivedisease|stabledisease:
Overfull \hbox (14.36601pt too wide) in paragraph at lines 120--122
[]\T1/ptm/m/n/10 For "site_of_tumor_first_recurrence": (metas-ta-sis / lo-core-
gional / none / lo-core-gional_plus_metastatic).
[3] [4]
Overfull \hbox (1107.93701pt too wide) in paragraph at lines 192--192
[] \T1/zi4/m/n/10 Experimenter name: Bentink S, Haibe-Kains B, Risch T, Fan J
-B, Hirsch MS, Holton K, Rubio R, April C, Chen J, Wickham-Garcia E, Liu J, Cul
hane A, Drapkin R, Quackenbush J, Matulonis UA: Angiogenic mRNA and microRNA ge
ne expression signature predicts a novel subtype of serous ovarian cancer. PLoS
ONE 2012, 7:e30269.[]
Overfull \hbox (146.38962pt too wide) in paragraph at lines 195--195
[] \T1/zi4/m/n/10 Title: Angiogenic mRNA and microRNA gene expression signatu
re predicts a novel subtype of serous ovarian cancer.[]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [5]
Underfull \vbox (badness 10000) has occurred while \output is active [6]
Overfull \hbox (591.34872pt too wide) in paragraph at lines 314--314
[] \T1/zi4/m/n/10 Experimenter name: Partheen K, Levan K, Osterberg L, Horvat
h G.Expression analysis of stage III serous ovarian adenocarcinoma distinguishe
s a sub-group of survivors. Eur J Cancer. 2006 Nov; 42(16):2846-54.[]
Overfull \hbox (134.72977pt too wide) in paragraph at lines 317--317
[] \T1/zi4/m/n/10 Title: Expression analysis of stage III serous ovarian aden
ocarcinoma distinguishes a sub-group of survivors.[]
[7]
Overfull \hbox (34.73999pt too wide) in paragraph at lines 353--353
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[8] [9]
Overfull \hbox (1299.59686pt too wide) in paragraph at lines 431--431
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Komata D, Yamamot
o T, Kodama S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H,
Kudo Y, Inoue I, Tanaka K.Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis. Cancer Sci. 2009 Aug; 100(8):1421-8.[]
Overfull \hbox (379.70932pt too wide) in paragraph at lines 434--434
[] \T1/zi4/m/n/10 Title: Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis.[]
[10] [11]
Overfull \hbox (861.2976pt too wide) in paragraph at lines 523--523
[] \T1/zi4/m/n/10 Experimenter name: Crijns AP, Fehrmann RS, de Jong S, Gerbe
ns F, Meersma GJ, Klip HG, Hollema H, Hofstra RM, te Meerman GJ, de Vries EG, v
an der Zee AG.Survival-related profile, pathways, and transcription factors in
ovarian cancer. PLoS Med. 2009 Feb 3; 6(2):e24.[]
Overfull \hbox (31.41006pt too wide) in paragraph at lines 526--526
[] \T1/zi4/m/n/10 Title: Survival-related profile, pathways, and transcriptio
n factors in ovarian cancer.[]
[12] [13] [14]
Overfull \hbox (636.3385pt too wide) in paragraph at lines 641--641
[] \T1/zi4/m/n/10 Experimenter name: Denkert C, Budczies J, Darb-Esfahani S,
Gy??rffy B et al. A prognostic gene expression index in ovarian cancer - valida
tion across different independent data sets. J Pathol 2009 Jun;218(2):273-80.[]
Overfull \hbox (146.38962pt too wide) in paragraph at lines 644--644
[] \T1/zi4/m/n/10 Title: A prognostic gene expression index in ovarian cancer
- validation across different independent data sets.[]
[15] [16]
Overfull \hbox (3.12666pt too wide) in paragraph at lines 754--755
[]\T1/ptm/m/n/10 Advanced-stage ovar-ian can-cer pa-tients are gen-er-ally trea
ted with platinum/taxane-based chemother-
[17]
Overfull \hbox (1289.58664pt too wide) in paragraph at lines 767--767
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Yahata T, Kodama
S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H, Kudo Y, Kot
era K, Masuzaki H, Tashiro H, Katabuchi H, Inoue I, Tanaka K.Gene expression pr
ofile for predicting survival in advanced-stage serous ovarian cancer across tw
o independent datasets. PLoS One. 2010 Mar 12; 5(3):e9615.[]
Overfull \hbox (221.38962pt too wide) in paragraph at lines 770--770
[] \T1/zi4/m/n/10 Title: Gene expression profile for predicting survival in a
dvanced-stage serous ovarian cancer across two independent datasets.[]
[18] [19] [20]
Overfull \hbox (1551.22604pt too wide) in paragraph at lines 905--905
[] \T1/zi4/m/n/10 Experimenter name: Mok SC, Bonome T, Vathipadiekal V, Bell
A, Johnson ME, Wong KK, Park DC, Hao K, Yip DK, Donninger H, Ozbun L, Samimi G,
Brady J, Randonovich M, Pise-Masison CA, Barrett JC, Wong WH, Welch WR, Berkow
itz RS, Birrer MJ.A gene signature predictive for outcome in advanced ovarian c
ancer identifies a survival factor: microfibril-associated glycoprotein 2. Canc
er Cell. 2009 Dec 8; 16(6):521-32.[]
Overfull \hbox (293.04947pt too wide) in paragraph at lines 908--908
[] \T1/zi4/m/n/10 Title: A gene signature predictive for outcome in advanced
ovarian cancer identifies a survival factor: microfibril-associated glycoprotei
n 2.[]
[21] [22] [23]
Overfull \hbox (904.64798pt too wide) in paragraph at lines 1040--1040
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (353.03925pt too wide) in paragraph at lines 1043--1043
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[24] [25]
Overfull \hbox (904.64798pt too wide) in paragraph at lines 1138--1138
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (353.03925pt too wide) in paragraph at lines 1141--1141
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[26] [27] [28]
Overfull \hbox (1481.23627pt too wide) in paragraph at lines 1236--1236
[] \T1/zi4/m/n/10 Experimenter name: Meyniel JP, Cottu PH, Decraene C, Stern
MH, Couturier J, Lebigot I, Nicolas A, Weber N, Fourchotte V, Alran S, Rapinat
A, Gentien D, Roman-Roman S, Mignot L, Sastre-Garau X.A genomic and transcripto
mic approach for a differential diagnosis between primary and secondary ovarian
carcinomas in patients with a previous history of breast cancer. BMC Cancer. 2
010 May 21; 10:222.[]
Overfull \hbox (451.35895pt too wide) in paragraph at lines 1239--1239
[] \T1/zi4/m/n/10 Title: A genomic and transcriptomic approach for a differen
tial diagnosis between primary and secondary ovarian carcinomas in patients wit
h a previous history of breast cancer.[]
[29] [30]
Overfull \hbox (101.41006pt too wide) in paragraph at lines 1344--1344
[] \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[31] [32]
Overfull \hbox (126.38962pt too wide) in paragraph at lines 1456--1456
[] \T1/zi4/m/n/10 Experimenter name: Mateescu B, Batista L, Mariani O, Meynie
l J, Cottu PH, Sastre-Garau X, Mechta-Grigoriou F[]
Overfull \hbox (81.39984pt too wide) in paragraph at lines 1459--1459
[] \T1/zi4/m/n/10 Title: miR-141 and miR-200a act on ovarian tumorigenesis by
controlling oxidative stress response.[]
[33] [34] [35]
Overfull \hbox (917.96768pt too wide) in paragraph at lines 1582--1582
[] \T1/zi4/m/n/10 Experimenter name: Bonome T, Levine DA, Shih J, Randonovich
M, Pise-Masison CA, Bogomolniy F, Ozbun L, Brady J, Barrett JC, Boyd J, Birrer
MJ: A Gene Signature Predicting for Survival in Suboptimally Debulked Patients
with Ovarian Cancer. Cancer Research 2008, 68:5478 -5486.[]
Overfull \hbox (99.72977pt too wide) in paragraph at lines 1585--1585
[] \T1/zi4/m/n/10 Title: A gene signature predicting for survival in suboptim
ally debulked patients with ovarian cancer.[]
[36] [37] [38]
Overfull \hbox (724.66843pt too wide) in paragraph at lines 1725--1725
[] \T1/zi4/m/n/10 Experimenter name: Gillet JP, Calcagno AM, Varma S, Davidso
n B et al. Multidrug resistance-linked gene signature predicts overall survival
of patients with primary ovarian serous carcinoma. Clin Cancer Res 2012 Jun 1;
18(11):3197-206.[]
Overfull \hbox (218.0597pt too wide) in paragraph at lines 1728--1728
[] \T1/zi4/m/n/10 Title: Multidrug resistance-linked gene signature predicts
overall survival of patients with primary ovarian serous carcinoma.[]
[39] [40] [41]
Overfull \hbox (84.71954pt too wide) in paragraph at lines 1847--1847
[] \T1/zi4/m/n/10 Experimenter name: Ferriss JS, Kim Y, Duska L, Birrer M, Le
vine DA, Moskaluk C,Theodorescu D, Lee JK[]
Overfull \hbox (299.71954pt too wide) in paragraph at lines 1850--1850
[] \T1/zi4/m/n/10 Title: Multi-gene expression predictors of single drug resp
onses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resist
ance.[]
[42] [43] [44]
Overfull \hbox (834.6582pt too wide) in paragraph at lines 1993--1993
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (318.04947pt too wide) in paragraph at lines 1996--1996
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[45] [46] [47]
Overfull \hbox (834.6582pt too wide) in paragraph at lines 2120--2120
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (318.04947pt too wide) in paragraph at lines 2123--2123
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[48] [49] [50]
Overfull \hbox (66.39984pt too wide) in paragraph at lines 2250--2250
[] \T1/zi4/m/n/10 Title: COL11A1 promotes tumor progression and predicts poor
clinical outcome in ovarian cancer.[]
[51]
Overfull \hbox (34.73999pt too wide) in paragraph at lines 2286--2286
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[52]
Overfull \hbox (456.32828pt too wide) in paragraph at lines 2356--2356
[] \T1/zi4/m/n/10 Experimenter name: Pils D1, Hager G, Tong D, Aust S, Heinze
G, Kohl M, Schuster E, Wolf A, Sehouli J, Braicu I, Vergote I, Cadron I, Mahne
r S, Hofstetter G, Speiser P, Zeillinger R[]
Overfull \hbox (156.3794pt too wide) in paragraph at lines 2359--2359
[] \T1/zi4/m/n/10 Title: Validating the impact of a molecular subtype in ovar
ian cancer on outcomes: a study of the OVCAD Consortium.[]
[53] [54]
Underfull \vbox (badness 10000) has occurred while \output is active [55]
Overfull \hbox (139.70932pt too wide) in paragraph at lines 2483--2483
[] \T1/zi4/m/n/10 Experimenter name: Karlan BY, Dering J, Walsh C, Orsulic S,
Lester J, Anderson LA, Ginther CL, Fejzo M, Slamon D[]
Overfull \hbox (133.06992pt too wide) in paragraph at lines 2486--2486
[] \T1/zi4/m/n/10 Title: POSTN/TGFBI-associated stromal signature predicts po
or prognosis in serous epithelial ovarian cancer.[]
[56] [57]
Underfull \vbox (badness 10000) has occurred while \output is active [58]
Underfull \hbox (badness 1337) in paragraph at lines 2604--2604
[] \T1/ptm/m/it/10 Lysophos-pha-tidic acid-induced tran-scrip-tional pro-file r
ep-re-sents
Overfull \hbox (1007.96768pt too wide) in paragraph at lines 2622--2622
[] \T1/zi4/m/n/10 Experimenter name: Murph MM, Liu W, Yu S, Lu Y, Hall H, Hen
nessy BT, Lahad J, Schaner M, Helland A, Kristensen G, Brresen-Dale AL, Mills G
B. Lysophosphatidic acid-induced transcriptional profile represents serous epit
helial ovarian carcinoma and worsened prognosis. PLoS One. 2009; 4(5):e5583.[]
[59]
Overfull \hbox (246.39984pt too wide) in paragraph at lines 2625--2625
[] \T1/zi4/m/n/10 Title: Lysophosphatidic acid-induced transcriptional profil
e represents serous epithelial ovarian carcinoma and worsened prognosis.[]
[60] [61]
Overfull \hbox (972.96768pt too wide) in paragraph at lines 2730--2730
[] \T1/zi4/m/n/10 Experimenter name: Ouellet V, Provencher DM, Maugard CM, Le
Page C, Ren F, Lussier C, Novak J, Ge B, Hudson TJ, Tonin PN, Mes-Masson A-M:
Discrimination between serous low malignant potential and invasive epithelial o
varian tumors using molecular profiling. Oncogene 2005, 24:4672-4687.[]
[62] [63]
Overfull \hbox (929.62753pt too wide) in paragraph at lines 2826--2826
[] \T1/zi4/m/n/10 Experimenter name: Marchini S, Mariani P, Chiorino G, Marra
zzo E, Bonomi R, Fruscio R, Clivio L, Garbi A, Torri V, Cinquini M, Dell\TS1/zi
4/m/n/10 '\T1/zi4/m/n/10 Anna T, Apolone G, Broggini M, D\TS1/zi4/m/n/10 '\T1/z
i4/m/n/10 Incalci M.Analysis of gene expression in early-stage ovarian cancer.
Clin Cancer Res. 2008 Dec 1; 14(23):7850-60.[]
[64] [65] [66]
Overfull \hbox (1302.91656pt too wide) in paragraph at lines 2952--2952
[] \T1/zi4/m/n/10 Experimenter name: Tothill RW, Tinker AV, George J, Brown R
, Fox SB, Lade S, Johnson DS, Trivett MK, Etemadmoghadam D, Locandro B, Trafica
nte N, Fereday S, Hung JA, Chiew YE, Haviv I, Gertig D, DeFazio A, Bowtell DD.N
ovel molecular subtypes of serous and endometrioid ovarian cancer linked to cli
nical outcome. Clin Cancer Res. 2008 Aug 15; 14(16):5198-208.[]
Overfull \hbox (94.72977pt too wide) in paragraph at lines 2955--2955
[] \T1/zi4/m/n/10 Title: Novel molecular subtypes of serous and endometrioid
ovarian cancer linked to clinical outcome.[]
[67]
Underfull \vbox (badness 10000) has occurred while \output is active [68]
[69]
Overfull \hbox (1011.28738pt too wide) in paragraph at lines 3107--3107
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Lancaster JM, Pi
ttman J, Luo J, Lee P, Murphy S, Dressman HK, Febbo PG, West M, Nevins JR, Mark
s JR.Patterns of gene expression that characterize long-term survival in advanc
ed stage serous ovarian cancers. Clin Cancer Res. 2005 May 15; 11(10):3686-96.[
]
Overfull \hbox (153.0597pt too wide) in paragraph at lines 3110--3110
[] \T1/zi4/m/n/10 Title: Patterns of gene expression that characterize long-t
erm survival in advanced stage serous ovarian cancers.[]
[70]
Overfull \hbox (34.73999pt too wide) in paragraph at lines 3148--3148
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[71] [72]
Overfull \hbox (1221.25671pt too wide) in paragraph at lines 3230--3230
[] \T1/zi4/m/n/10 Experimenter name: Dressman HK, Berchuck A, Chan G, Zhai J,
Bild A, Sayer R, Cragun J, Clarke J, Whitaker RS, Li L, Gray J, Marks J, Ginsb
urg GS, Potti A, West M, Nevins JR, Lancaster JM.An integrated genomic-based ap
proach to individualized treatment of patients with advanced-stage ovarian canc
er. J Clin Oncol. 2007 Feb 10; 25(5):517-25.[]
Overfull \hbox (184.72977pt too wide) in paragraph at lines 3233--3233
[] \T1/zi4/m/n/10 Title: An integrated genomic-based approach to individualiz
ed treatment of patients with advanced-stage ovarian cancer.[]
[73] [74] [75]
Overfull \hbox (1237.92679pt too wide) in paragraph at lines 3358--3358
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Luo J, Clarke JP
, Horne H, Levine DA, Boyd J, Alonso MA, Secord AA, Bernardini MQ, Barnett JC,
Boren T, Murphy SK, Dressman HK, Marks JR, Lancaster JM.Microarray analysis of
early stage serous ovarian cancers shows profiles predictive of favorable outco
me. Clin Cancer Res. 2009 Apr 1; 15(7):2448-55.[]
Overfull \hbox (148.0597pt too wide) in paragraph at lines 3361--3361
[] \T1/zi4/m/n/10 Title: Microarray analysis of early stage serous ovarian ca
ncers shows profiles predictive of favorable outcome.[]
[76] [77] [78]
Overfull \hbox (64.73999pt too wide) in paragraph at lines 3490--3490
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[79]
Underfull \vbox (badness 10000) has occurred while \output is active [80]
Underfull \vbox (badness 10000) has occurred while \output is active [81]
[82]
Overfull \hbox (64.73999pt too wide) in paragraph at lines 3666--3666
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[83]
Underfull \vbox (badness 10000) has occurred while \output is active [84]
Underfull \vbox (badness 10000) has occurred while \output is active [85]
Overfull \hbox (64.73999pt too wide) in paragraph at lines 3839--3839
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[86] [87]
Underfull \vbox (badness 10000) has occurred while \output is active [88]
Underfull \vbox (badness 10000) has occurred while \output is active [89]
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.ind
[90]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 37.
[91] [92])
(/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/.Rd2pdf2018565/Rd2.aux
)
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb
></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on Rd2.pdf (92 pages, 237209 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmpapsAvB/Rbuild1ecd0572bd84dc/curatedOvarianData/build/curatedOvarianData.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘curatedOvarianData_1.32.0.tar.gz’
