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[]\T1/ptm/m/n/10 For "pri-mary_therapy_outcome_success": com-pletere-sponse|par
tialresponse|progressivedisease|stabledisease:
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[]\T1/ptm/m/n/10 For "site_of_tumor_first_recurrence": (metas-ta-sis / lo-core-
gional / none / lo-core-gional_plus_metastatic).
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Angiogenic mRNA and microRNA gene expression signatu
re predicts a novel subtype of serous ovarian cancer.[]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Expression analysis of stage III serous ovarian aden
ocarcinoma distinguishes a sub-group of survivors.[]
[6]
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[]\T1/fi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[7] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/fi4/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.[]
[8]
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[] \T1/fi4/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.[]
[9] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [10]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Survival-related profile, pathways, and transcriptio
n factors in ovarian cancer.[]
[11] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [12]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: A prognostic gene expression index in ovarian cancer
- validation across different independent data sets.[]
[13] [14] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
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[]\T1/ptm/m/n/10 Advanced-stage ovar-ian can-cer pa-tients are gen-er-ally trea
ted with platinum/taxane-based chemother-
[15]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Gene expression profile for predicting survival in a
dvanced-stage serous ovarian cancer across two independent datasets.[]
[16]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: A gene signature predictive for outcome in advanced
ovarian cancer identifies a survival factor: microfibril-associated glycoprotei
n 2.[]
[18] [19] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [20]
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[] \T1/fi4/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.[]
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[] \T1/fi4/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.[]
[21] [22] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/fi4/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.[]
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[] \T1/fi4/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] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/fi4/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.[]
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[] \T1/fi4/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.[]
[25] [26] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/fi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[27] [28] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [29]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: A gene signature predicting for survival in suboptim
ally debulked patients with ovarian cancer.[]
[30] [31] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [32]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Multidrug resistance-linked gene signature predicts
overall survival of patients with primary ovarian serous carcinoma.[]
[33] [34] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/fi4/m/n/10 Experimenter name: Ferriss JS, Kim Y, Duska L, Birrer M, Le
vine DA, Moskaluk C,Theodorescu D, Lee JK[]
[35]
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[] \T1/fi4/m/n/10 Title: Multi-gene expression predictors of single drug resp
onses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resist
ance.[]
[36]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
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[] \T1/fi4/m/n/10 Agilent-014850 Whole Human Genome Microarray 4x44K G411
2F (Probe Name vers[]
[39]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
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[] \T1/fi4/m/n/10 Agilent-014850 Whole Human Genome Microarray 4x44K G411
2F (Probe Name vers[]
[41] [42] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/ptm/m/it/10 Lysophos-pha-tidic acid-induced tran-scrip-tional pro-file r
ep-re-sents
[43]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Lysophosphatidic acid-induced transcriptional profil
e represents serous epithelial ovarian carcinoma and worsened prognosis.[]
[44] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [45]
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[] \T1/fi4/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.[]
[46] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [47]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Novel molecular subtypes of serous and endometrioid
ovarian cancer linked to clinical outcome.[]
[48] [49]
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[] \T1/fi4/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.[
]
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[] \T1/fi4/m/n/10 Title: Patterns of gene expression that characterize long-t
erm survival in advanced stage serous ovarian cancers.[]
[51]
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[]\T1/fi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[52] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [53]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: An integrated genomic-based approach to individualiz
ed treatment of patients with advanced-stage ovarian cancer.[]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Microarray analysis of early stage serous ovarian ca
ncers shows profiles predictive of favorable outcome.[]
[57]
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[] \T1/fi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[59] [60]
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[] \T1/fi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
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[] \T1/fi4/m/n/10 The following samples are likely from specimens also us
ed in GSE26712: TCG[]
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[]\T1/ptm/m/n/10 For "pri-mary_therapy_outcome_success": com-pletere-sponse|par
tialresponse|progressivedisease|stabledisease:
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[]\T1/ptm/m/n/10 For "site_of_tumor_first_recurrence": (metas-ta-sis / lo-core-
gional / none / lo-core-gional_plus_metastatic).
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Angiogenic mRNA and microRNA gene expression signatu
re predicts a novel subtype of serous ovarian cancer.[]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Expression analysis of stage III serous ovarian aden
ocarcinoma distinguishes a sub-group of survivors.[]
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[]\T1/fi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[7] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [8]
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[] \T1/fi4/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.[]
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[] \T1/fi4/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.[]
[9] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [10]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Survival-related profile, pathways, and transcriptio
n factors in ovarian cancer.[]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: A prognostic gene expression index in ovarian cancer
- validation across different independent data sets.[]
[14]
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[]\T1/ptm/m/n/10 Advanced-stage ovar-ian can-cer pa-tients are gen-er-ally trea
ted with platinum/taxane-based chemother-
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[] \T1/fi4/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.[]
[16]
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[] \T1/fi4/m/n/10 Title: Gene expression profile for predicting survival in a
dvanced-stage serous ovarian cancer across two independent datasets.[]
[17]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: A gene signature predictive for outcome in advanced
ovarian cancer identifies a survival factor: microfibril-associated glycoprotei
n 2.[]
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[] \T1/fi4/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.[]
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[] \T1/fi4/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.[]
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[] \T1/fi4/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.[]
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[] \T1/fi4/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] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [25]
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[] \T1/fi4/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.[]
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[] \T1/fi4/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.[]
[26] [27] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/fi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[28] [29] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [30]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: A gene signature predicting for survival in suboptim
ally debulked patients with ovarian cancer.[]
[31]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Multidrug resistance-linked gene signature predicts
overall survival of patients with primary ovarian serous carcinoma.[]
[34] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [35]
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[] \T1/fi4/m/n/10 Experimenter name: Ferriss JS, Kim Y, Duska L, Birrer M, Le
vine DA, Moskaluk C,Theodorescu D, Lee JK[]
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[] \T1/fi4/m/n/10 Title: Multi-gene expression predictors of single drug resp
onses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resist
ance.[]
[36] [37] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [38]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
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[] \T1/fi4/m/n/10 Agilent-014850 Whole Human Genome Microarray 4x44K G411
2F (Probe Name vers[]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
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[] \T1/fi4/m/n/10 Agilent-014850 Whole Human Genome Microarray 4x44K G411
2F (Probe Name vers[]
[42]
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[] \T1/ptm/m/it/10 Lysophos-pha-tidic acid-induced tran-scrip-tional pro-file r
ep-re-sents
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Lysophosphatidic acid-induced transcriptional profil
e represents serous epithelial ovarian carcinoma and worsened prognosis.[]
[44] [45] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/fi4/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.[]
[46] [47] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [48]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Novel molecular subtypes of serous and endometrioid
ovarian cancer linked to clinical outcome.[]
[49]
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[] \T1/fi4/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.[
]
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[] \T1/fi4/m/n/10 Title: Patterns of gene expression that characterize long-t
erm survival in advanced stage serous ovarian cancers.[]
[52]
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[]\T1/fi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: An integrated genomic-based approach to individualiz
ed treatment of patients with advanced-stage ovarian cancer.[]
[55]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Microarray analysis of early stage serous ovarian ca
ncers shows profiles predictive of favorable outcome.[]
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[] \T1/fi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[60] [61]
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[] \T1/fi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[63]
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[] \T1/fi4/m/n/10 The following samples are likely from specimens also us
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[]\T1/ptm/m/n/10 For "pri-mary_therapy_outcome_success": com-pletere-sponse|par
tialresponse|progressivedisease|stabledisease:
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[]\T1/ptm/m/n/10 For "site_of_tumor_first_recurrence": (metas-ta-sis / lo-core-
gional / none / lo-core-gional_plus_metastatic).
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Angiogenic mRNA and microRNA gene expression signatu
re predicts a novel subtype of serous ovarian cancer.[]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Expression analysis of stage III serous ovarian aden
ocarcinoma distinguishes a sub-group of survivors.[]
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[]\T1/fi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[7] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [8]
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[] \T1/fi4/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.[]
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[] \T1/fi4/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.[]
[9] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [10]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Survival-related profile, pathways, and transcriptio
n factors in ovarian cancer.[]
[11] [12] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [13]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: A prognostic gene expression index in ovarian cancer
- validation across different independent data sets.[]
[14]
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[]\T1/ptm/m/n/10 Advanced-stage ovar-ian can-cer pa-tients are gen-er-ally trea
ted with platinum/taxane-based chemother-
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[] \T1/fi4/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.[]
[16]
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[] \T1/fi4/m/n/10 Title: Gene expression profile for predicting survival in a
dvanced-stage serous ovarian cancer across two independent datasets.[]
[17]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: A gene signature predictive for outcome in advanced
ovarian cancer identifies a survival factor: microfibril-associated glycoprotei
n 2.[]
[19] [20] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [21]
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[] \T1/fi4/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.[]
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[] \T1/fi4/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.[]
[22] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [23]
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[] \T1/fi4/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.[]
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[] \T1/fi4/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] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [25]
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[] \T1/fi4/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.[]
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[] \T1/fi4/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.[]
[26] [27] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/fi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[28] [29] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [30]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: A gene signature predicting for survival in suboptim
ally debulked patients with ovarian cancer.[]
[31]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Multidrug resistance-linked gene signature predicts
overall survival of patients with primary ovarian serous carcinoma.[]
[34] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [35]
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[] \T1/fi4/m/n/10 Experimenter name: Ferriss JS, Kim Y, Duska L, Birrer M, Le
vine DA, Moskaluk C,Theodorescu D, Lee JK[]
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[] \T1/fi4/m/n/10 Title: Multi-gene expression predictors of single drug resp
onses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resist
ance.[]
[36] [37] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [38]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
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[] \T1/fi4/m/n/10 Agilent-014850 Whole Human Genome Microarray 4x44K G411
2F (Probe Name vers[]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
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[] \T1/fi4/m/n/10 Agilent-014850 Whole Human Genome Microarray 4x44K G411
2F (Probe Name vers[]
[42]
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[] \T1/ptm/m/it/10 Lysophos-pha-tidic acid-induced tran-scrip-tional pro-file r
ep-re-sents
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Lysophosphatidic acid-induced transcriptional profil
e represents serous epithelial ovarian carcinoma and worsened prognosis.[]
[44] [45] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/fi4/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.[]
[46] [47] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [48]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Novel molecular subtypes of serous and endometrioid
ovarian cancer linked to clinical outcome.[]
[49]
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[] \T1/fi4/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.[
]
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[] \T1/fi4/m/n/10 Title: Patterns of gene expression that characterize long-t
erm survival in advanced stage serous ovarian cancers.[]
[52]
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[]\T1/fi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: An integrated genomic-based approach to individualiz
ed treatment of patients with advanced-stage ovarian cancer.[]
[55]
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[] \T1/fi4/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.[]
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[] \T1/fi4/m/n/10 Title: Microarray analysis of early stage serous ovarian ca
ncers shows profiles predictive of favorable outcome.[]
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[] \T1/fi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[60] [61]
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[] \T1/fi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[63]
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[] \T1/fi4/m/n/10 The following samples are likely from specimens also us
ed in GSE26712: TCG[]
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Saving output to ‘/private/tmp/Rtmpmg71dC/Rbuild2949170bdb39/curatedOvarianData/build/curatedOvarianData.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘curatedOvarianData_1.0.5.tar.gz’