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BioC experimental data: BUILD report for curatedCRCData on petty

This page was generated on 2014-10-04 17:43:49 -0700 (Sat, 04 Oct 2014).

Package 49/197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
curatedCRCData 1.0.0
Princy Parsana
Snapshot Date: 2014-10-04 07:15:22 -0700 (Sat, 04 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs/curatedCRCData
Last Changed Rev: 2799 / Revision: 3055
Last Changed Date: 2014-04-11 14:27:08 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded [ OK ] OK  OK 

Summary

Package: curatedCRCData
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data curatedCRCData
StartedAt: 2014-10-04 08:39:09 -0700 (Sat, 04 Oct 2014)
EndedAt: 2014-10-04 08:44:03 -0700 (Sat, 04 Oct 2014)
EllapsedTime: 293.9 seconds
RetCode: 0
Status:  OK 
PackageFile: curatedCRCData_1.0.0.tar.gz
PackageFileSize: 390.8 MiB

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data curatedCRCData
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* checking for file ‘curatedCRCData/DESCRIPTION’ ... OK
* preparing ‘curatedCRCData’:
* 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 ...

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(/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (929.78088pt too wide) in paragraph at lines 86--86
 []  \T1/zi4/m/n/10 Experimenter name: Auman JT, Church R, Lee SY, Watson MA, F
leshman JW, Mcleod HL.??Celecoxib pre-treatment in human colorectal adenocarcin
oma patients is associated with gene expression alterations suggestive of dimin
ished cellular proliferation.??Eur J Cancer??2008 Aug[] 
[2]
Overfull \hbox (444.78088pt too wide) in paragraph at lines 89--89
 []  \T1/zi4/m/n/10 Title: Celecoxib pre-treatment in human colorectal adenocar
cinoma patients is associated with gene expression alterations suggestive of di
minished cellular proliferation.[] 
(/usr/local/texlive/2014/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3]
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Overfull \hbox (541.78088pt too wide) in paragraph at lines 212--212
 []  \T1/zi4/m/n/10 Experimenter name: Lips EH, van Eijk R, de Graaf EJ, Oostin
g J et al.??Integrating chromosomal aberrations and gene expression profiles to
 dissect rectal tumorigenesis.BMC Cancer??2008 Oct 29[] 

Overfull \hbox (121.78088pt too wide) in paragraph at lines 215--215
 []  \T1/zi4/m/n/10 Title: Integrating chromosomal aberrations and gene express
ion profiles to dissect rectal tumorigenesis.[] 
[5] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [6]
Overfull \hbox (633.78088pt too wide) in paragraph at lines 298--298
 []  \T1/zi4/m/n/10 Experimenter name: Staub E, Groene J, Heinze M, Mennerich D
 et al.??An expression module of WIPF1-coexpressed genes identifies patients wi
th favorable prognosis in three tumor types.??J Mol Med (Berl)??2009 Jun[] 

Overfull \hbox (202.78088pt too wide) in paragraph at lines 301--301
 []  \T1/zi4/m/n/10 Title: An expression module of WIPF1-coexpressed genes iden
tifies patients with favorable prognosis in three tumor types.[] 
[7] [8] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [9]
Overfull \hbox (5.87547pt too wide) in paragraph at lines 433--434
\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-

Overfull \hbox (714.78088pt too wide) in paragraph at lines 446--446
 []  \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman 
M et al.??DNA copy-number alterations underlie gene expression differences betw
een microsatellite stable and unstable colorectal cancers.??Clin Cancer Res??20
08 Dec 15[] 

Overfull \hbox (268.78088pt too wide) in paragraph at lines 449--449
 []  \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
 differences between microsatellite stable and unstable colorectal cancers.[] 
[10] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (5.87547pt too wide) in paragraph at lines 523--524
\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
[11]
Overfull \hbox (696.78088pt too wide) in paragraph at lines 536--536
 []  \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman 
M et al. DNA copy-number alterations underlie gene expression differences betwe
en microsatellite stable and unstable colorectal cancers. Clin Cancer Res 2008 
Dec 15[] 

Overfull \hbox (268.78088pt too wide) in paragraph at lines 539--539
 []  \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
 differences between microsatellite stable and unstable colorectal cancers.[] 
[12] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [13]
Overfull \hbox (707.78088pt too wide) in paragraph at lines 626--626
 []  \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Yamamoto Y, Matsu
da K et al.??Gene expression signature and response to the use of leucovorin, f
luorouracil and oxaliplatin in colorectal cancer patients.??Clin Transl Oncol??
2011 Jun[] 

Overfull \hbox (250.78088pt too wide) in paragraph at lines 629--629
 []  \T1/zi4/m/n/10 Title: Gene expression signature and response to the use of
 leucovorin, fluorouracil and oxaliplatin in colorectal cancer patients.[] 
[14] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [15]
Overfull \hbox (701.78088pt too wide) in paragraph at lines 700--700
 []  \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Gibbs P, Christie M, Prakas
h S et al.??Metastasis-Associated Gene Expression Changes Predict Poor Outcomes
 in Patients with Dukes Stage B and C Colorectal Cancer.??Clin Cancer Res??2009
 Dec 15[] 

Overfull \hbox (245.78088pt too wide) in paragraph at lines 703--703
 []  \T1/zi4/m/n/10 Title: Metastasis-Associated Gene Expression Changes Predic
t Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer.[] 
[16] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [17]
Overfull \hbox (519.78088pt too wide) in paragraph at lines 810--810
 []  \T1/zi4/m/n/10 Experimenter name: Reid JF, Gariboldi M, Sokolova V, Capobi
anco P et al.??Integrative approach for prioritizing cancer genes in sporadic c
olon cancer.??Genes Chromosomes Cancer??2009 Nov[] 

Overfull \hbox (17.78088pt too wide) in paragraph at lines 813--813
 []  \T1/zi4/m/n/10 Title: Integrative approach for prioritizing cancer genes i
n sporadic colon cancer.[] 
[18] [19] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (641.78088pt too wide) in paragraph at lines 928--928
 []  \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
 al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[] 
[20]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 931--931
 []  \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[] 
[21] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [22]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1048--1048
 []  \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
 al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[] 

Overfull \hbox (222.78088pt too wide) in paragraph at lines 1051--1051
 []  \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[] 
[23] [24] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [25]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1172--1172
 []  \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
 al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[] 

Overfull \hbox (222.78088pt too wide) in paragraph at lines 1175--1175
 []  \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[] 
[26]
Underfull \vbox (badness 10000) has occurred while \output is active [27]
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Overfull \hbox (601.78088pt too wide) in paragraph at lines 1297--1297
 []  \T1/zi4/m/n/10 Experimenter name: Matsuyama T, Ishikawa T, Mogushi K, Yosh
ida T et al.??MUC12 mRNA expression is an independent marker of prognosis in st
age II and stage III colorectal cancer.??Int J Cancer??2010 Nov 15[] 

Overfull \hbox (150.78088pt too wide) in paragraph at lines 1300--1300
 []  \T1/zi4/m/n/10 Title: MUC12 mRNA expression is an independent marker of pr
ognosis in stage II and stage III colorectal cancer.[] 
[28] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [29]
Overfull \hbox (108.78088pt too wide) in paragraph at lines 1383--1383
 []  \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[] 
[30]
Underfull \vbox (badness 10000) has occurred while \output is active [31]
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[]\T1/ptm/m/n/10 This study aimed to iden-tify a novel biomarker or a tar-get o
f treat-ment for col-orec-tal can-cer (CRC).The

Overfull \hbox (479.78088pt too wide) in paragraph at lines 1501--1501
 []  \T1/zi4/m/n/10 Experimenter name: Tsukamoto S, Ishikawa T, Iida S, Ishigur
o M et al.??Clinical significance of osteoprotegerin expression in human colore
ctal cancer.??Clin Cancer Res2011 Apr 15[] 

Overfull \hbox (33.78088pt too wide) in paragraph at lines 1504--1504
 []  \T1/zi4/m/n/10 Title: Clinical significance of osteoprotegerin expression 
in human colorectal cancer.[] 
[32] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [33]
Overfull \hbox (742.78088pt too wide) in paragraph at lines 1595--1595
 []  \T1/zi4/m/n/10 Experimenter name: Kogo R, Shimamura T, Mimori K, Kawahara 
K et al.??Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modi
fication and is associated with poor prognosis in colorectal cancers.??Cancer R
es??2011 Oct 15[] 

Overfull \hbox (320.78088pt too wide) in paragraph at lines 1598--1598
 []  \T1/zi4/m/n/10 Title: Long noncoding RNA HOTAIR regulates polycomb-depende
nt chromatin modification and is associated with poor prognosis in colorectal c
ancers.[] 
[34] [35] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (881.78088pt too wide) in paragraph at lines 1702--1702
 []  \T1/zi4/m/n/10 Experimenter name: Sveen A,????esen TH,??Rognum TO,??Lothe 
RA,??Skotheim RI. Transcriptome instability in colorectal cancer identified by 
exon microarray analyses: Associations with splicing factor expression levels a
nd patient survival. Genome Med 2011 May 27[] 

Overfull \hbox (428.78088pt too wide) in paragraph at lines 1705--1705
 []  \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
 levels and patient survival.[] 
[36] [37] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [38]
Overfull \hbox (845.78088pt too wide) in paragraph at lines 1797--1797
 []  \T1/zi4/m/n/10 Experimenter name: Sveen A, Agesen TH, Nesbakken A, Rognum 
TO et al.??Transcriptome instability in colorectal cancer identified by exon mi
croarray analyses: Associations with splicing factor expression levels and pati
ent survival.Genome Med??2011 May 27[] 

Overfull \hbox (428.78088pt too wide) in paragraph at lines 1800--1800
 []  \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
 levels and patient survival.[] 
[39] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [40]
Overfull \hbox (731.78088pt too wide) in paragraph at lines 1896--1896
 []  \T1/zi4/m/n/10 Experimenter name: Bandr??E,??Malumbres R,??Cubedo E,??Sola
 J,??Garc??Foncillas J,??Labarga A. A gene signature of 8 genes could identify 
the risk of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10
 B colon cancer patients. Oncol Rep 2007 May[] 

Overfull \hbox (60.78088pt too wide) in paragraph at lines 1897--1897
 []  \T1/zi4/m/n/10 Laboratory: Bandr??E,??Malumbres R,??Cubedo E,??Sola J,??Ga
rc??Foncillas J,??Labarga A 2005[] 

Overfull \hbox (207.78088pt too wide) in paragraph at lines 1899--1899
 []  \T1/zi4/m/n/10 Title: A gene signature of 8 genes could identify the risk 
of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10 B colon 
cancer patients.[] 
[41] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [42]
Overfull \hbox (1051.78088pt too wide) in paragraph at lines 1998--1998
 []  \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
 

Overfull \hbox (269.78088pt too wide) in paragraph at lines 2001--2001
 []  \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[] 
[43] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [44]
Overfull \hbox (1051.78088pt too wide) in paragraph at lines 2092--2092
 []  \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
 

Overfull \hbox (269.78088pt too wide) in paragraph at lines 2095--2095
 []  \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[] 
[45] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [46]
Overfull \hbox (428.78088pt too wide) in paragraph at lines 2186--2186
 []  \T1/zi4/m/n/10 Experimenter name: Birnbaum DJ, Laibe S, Ferrari A, Lagarde
 A et al.??Expression Profiles in Stage II Colon Cancer According to APC Gene S
tatus.??Transl Oncol??2012 Apr[] 

Overfull \hbox (5.78088pt too wide) in paragraph at lines 2189--2189
 []  \T1/zi4/m/n/10 Title: Expression Profiles in Stage II Colon Cancer Accordi
ng to APC Gene Status.[] 
[47] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [48]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 2296--2296
 []  \T1/zi4/m/n/10 Experimenter name: Bernal M,??Garc??Alcalde F,??Concha ????
Blanco A,??Garrido F,??Ruiz-Cabello F[] 

Overfull \hbox (74.78088pt too wide) in paragraph at lines 2297--2297
 []  \T1/zi4/m/n/10 Laboratory: Bernal M,??Garc??Alcalde F,??Concha ????Blanco 
A,??Garrido F,??Ruiz-Cabello F 2011[] 

Overfull \hbox (240.78088pt too wide) in paragraph at lines 2299--2299
 []  \T1/zi4/m/n/10 Title: Genome-wide profiling characterizes CRCs with geneti
c instability and specific routes to HLA class I loss and immunoescape[] 
[49] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (501.78088pt too wide) in paragraph at lines 2386--2386
 []  \T1/zi4/m/n/10 Experimenter name: Tsuji S, Midorikawa Y, Takahashi T, Yagi
 K et al.??Potential responders to FOLFOX therapy for colorectal cancer by Rand
om Forests analysis.??Br J Cancer??2012 Jan 3[] 
[50]
Overfull \hbox (75.78088pt too wide) in paragraph at lines 2389--2389
 []  \T1/zi4/m/n/10 Title: Potential responders to FOLFOX therapy for colorecta
l cancer by Random Forests analysis.[] 
[51] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [52]
Overfull \hbox (588.78088pt too wide) in paragraph at lines 2480--2480
 []  \T1/zi4/m/n/10 Experimenter name: Bianchini M, Levy E, Zucchini C, Pinski 
V et al.??Comparative study of gene expression by cDNA microarray in human colo
rectal cancer tissues and normal mucosa.??Int J Oncol??2006 Jul[] 

Overfull \hbox (176.78088pt too wide) in paragraph at lines 2483--2483
 []  \T1/zi4/m/n/10 Title: Comparative study of gene expression by cDNA microar
ray in human colorectal cancer tissues and normal mucosa.[] 
[53] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [54]
Overfull \hbox (682.78088pt too wide) in paragraph at lines 2582--2582
 []  \T1/zi4/m/n/10 Experimenter name: de Sousa E Melo F, Colak S, Buikhuisen J
, Koster J et al.??Methylation of cancer-stem-cell-associated Wnt target genes 
predicts poor prognosis in colorectal cancer patients.??Cell Stem Cell??2011 No
v 4[] 

Overfull \hbox (83.78088pt too wide) in paragraph at lines 2585--2585
 []  \T1/zi4/m/n/10 Title: Mutations in the Ras-Raf Axis underlie the prognosti
c value of CD133 in colorectal cancer.[] 
[55] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [56]
Overfull \hbox (622.78088pt too wide) in paragraph at lines 2680--2680
 []  \T1/zi4/m/n/10 Experimenter name: Marisa L, de Reyni??A, Duval A, Selves J
 et al.??Gene expression classification of colon cancer into molecular subtypes
: characterization, validation, and prognostic value.??PLoS Med??2013[] 

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 []  \T1/zi4/m/n/10 Title: Gene expression classification of colon cancer into 
molecular subtypes: characterization, validation, and prognostic value.[] 
[57] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [58]
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 []  \T1/zi4/m/n/10 Experimenter name: Graudens E, Boulanger V, Mollard C, Mari
age-Samson R et al.??Deciphering cellular states of innate tumor drug responses
.??Genome Biol??2006[] 
[59] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [60]
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 []  \T1/zi4/m/n/10 Experimenter name: Laiho P, Kokko A, Vanharanta S, Salovaar
a R et al.??Serrated carcinomas form a subclass of colorectal cancer with disti
nct molecular basis.??Oncogene2007 Jan 11[] 

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 []  \T1/zi4/m/n/10 Title: Serrated carcinomas form a subclass of colorectal ca
ncer with distinct molecular basis.[] 
[61] [62] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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 []  \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Sakamoto E, Yamam
oto Y et al.??Gene expression signature for recurrence in stage III colorectal 
cancers.??Cancer??2009 Jan 15[] 

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 []  \T1/zi4/m/n/10 Title: Gene expression signature for recurrence in stage II
I colorectal cancers.[] 
[63] [64] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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 []  \T1/zi4/m/n/10 Experimenter name: Profiling project of a panel of tubular 
adenoma and serrated adenoma patient material collected in the Academic Medical
 Center[] 

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 []  \T1/zi4/m/n/10 Laboratory: Medema JP,??de Sousa E Melo F,??Vermeulen L,??J
ansen M,??Dekker E,??Van Noesel C,??Fessler E 2013[] 
[65] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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 []  \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
 of human colon and rectal cancer. Nature 2012, 487:330-337[] 

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 []  \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[] 
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 of human colon and rectal cancer. Nature 2012, 487:330-337[] 

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 of human colon and rectal cancer. Nature 2012, 487:330-337[] 

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 []  \T1/zi4/m/n/10 Experimenter name: Auman JT, Church R, Lee SY, Watson MA, F
leshman JW, Mcleod HL.??Celecoxib pre-treatment in human colorectal adenocarcin
oma patients is associated with gene expression alterations suggestive of dimin
ished cellular proliferation.??Eur J Cancer??2008 Aug[] 

Overfull \hbox (444.78088pt too wide) in paragraph at lines 89--89
 []  \T1/zi4/m/n/10 Title: Celecoxib pre-treatment in human colorectal adenocar
cinoma patients is associated with gene expression alterations suggestive of di
minished cellular proliferation.[] 
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[4] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [5]
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 []  \T1/zi4/m/n/10 Experimenter name: Lips EH, van Eijk R, de Graaf EJ, Oostin
g J et al.??Integrating chromosomal aberrations and gene expression profiles to
 dissect rectal tumorigenesis.BMC Cancer??2008 Oct 29[] 

Overfull \hbox (121.78088pt too wide) in paragraph at lines 215--215
 []  \T1/zi4/m/n/10 Title: Integrating chromosomal aberrations and gene express
ion profiles to dissect rectal tumorigenesis.[] 
[6] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [7]
Overfull \hbox (633.78088pt too wide) in paragraph at lines 298--298
 []  \T1/zi4/m/n/10 Experimenter name: Staub E, Groene J, Heinze M, Mennerich D
 et al.??An expression module of WIPF1-coexpressed genes identifies patients wi
th favorable prognosis in three tumor types.??J Mol Med (Berl)??2009 Jun[] 

Overfull \hbox (202.78088pt too wide) in paragraph at lines 301--301
 []  \T1/zi4/m/n/10 Title: An expression module of WIPF1-coexpressed genes iden
tifies patients with favorable prognosis in three tumor types.[] 
[8]
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\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
[10]
Overfull \hbox (714.78088pt too wide) in paragraph at lines 446--446
 []  \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman 
M et al.??DNA copy-number alterations underlie gene expression differences betw
een microsatellite stable and unstable colorectal cancers.??Clin Cancer Res??20
08 Dec 15[] 

Overfull \hbox (268.78088pt too wide) in paragraph at lines 449--449
 []  \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
 differences between microsatellite stable and unstable colorectal cancers.[] 
[11] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
[12]
Overfull \hbox (696.78088pt too wide) in paragraph at lines 536--536
 []  \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman 
M et al. DNA copy-number alterations underlie gene expression differences betwe
en microsatellite stable and unstable colorectal cancers. Clin Cancer Res 2008 
Dec 15[] 

Overfull \hbox (268.78088pt too wide) in paragraph at lines 539--539
 []  \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
 differences between microsatellite stable and unstable colorectal cancers.[] 
[13] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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 []  \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Yamamoto Y, Matsu
da K et al.??Gene expression signature and response to the use of leucovorin, f
luorouracil and oxaliplatin in colorectal cancer patients.??Clin Transl Oncol??
2011 Jun[] 
[14]
Overfull \hbox (250.78088pt too wide) in paragraph at lines 629--629
 []  \T1/zi4/m/n/10 Title: Gene expression signature and response to the use of
 leucovorin, fluorouracil and oxaliplatin in colorectal cancer patients.[] 
[15] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (701.78088pt too wide) in paragraph at lines 700--700
 []  \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Gibbs P, Christie M, Prakas
h S et al.??Metastasis-Associated Gene Expression Changes Predict Poor Outcomes
 in Patients with Dukes Stage B and C Colorectal Cancer.??Clin Cancer Res??2009
 Dec 15[] 

Overfull \hbox (245.78088pt too wide) in paragraph at lines 703--703
 []  \T1/zi4/m/n/10 Title: Metastasis-Associated Gene Expression Changes Predic
t Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer.[] 
[16] [17] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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 []  \T1/zi4/m/n/10 Experimenter name: Reid JF, Gariboldi M, Sokolova V, Capobi
anco P et al.??Integrative approach for prioritizing cancer genes in sporadic c
olon cancer.??Genes Chromosomes Cancer??2009 Nov[] 
[18]
Overfull \hbox (17.78088pt too wide) in paragraph at lines 813--813
 []  \T1/zi4/m/n/10 Title: Integrative approach for prioritizing cancer genes i
n sporadic colon cancer.[] 
[19] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [20]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 928--928
 []  \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
 al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[] 

Overfull \hbox (222.78088pt too wide) in paragraph at lines 931--931
 []  \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[] 
[21] [22] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [23]
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 []  \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
 al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[] 

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 []  \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[] 
[24] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [25]
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 []  \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
 al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[] 

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 []  \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[] 
[26] [27] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [28]
Overfull \hbox (601.78088pt too wide) in paragraph at lines 1297--1297
 []  \T1/zi4/m/n/10 Experimenter name: Matsuyama T, Ishikawa T, Mogushi K, Yosh
ida T et al.??MUC12 mRNA expression is an independent marker of prognosis in st
age II and stage III colorectal cancer.??Int J Cancer??2010 Nov 15[] 

Overfull \hbox (150.78088pt too wide) in paragraph at lines 1300--1300
 []  \T1/zi4/m/n/10 Title: MUC12 mRNA expression is an independent marker of pr
ognosis in stage II and stage III colorectal cancer.[] 
[29] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (108.78088pt too wide) in paragraph at lines 1383--1383
 []  \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[] 
[30] [31] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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[]\T1/ptm/m/n/10 This study aimed to iden-tify a novel biomarker or a tar-get o
f treat-ment for col-orec-tal can-cer (CRC).The
[32]
Overfull \hbox (479.78088pt too wide) in paragraph at lines 1501--1501
 []  \T1/zi4/m/n/10 Experimenter name: Tsukamoto S, Ishikawa T, Iida S, Ishigur
o M et al.??Clinical significance of osteoprotegerin expression in human colore
ctal cancer.??Clin Cancer Res2011 Apr 15[] 

Overfull \hbox (33.78088pt too wide) in paragraph at lines 1504--1504
 []  \T1/zi4/m/n/10 Title: Clinical significance of osteoprotegerin expression 
in human colorectal cancer.[] 
[33] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [34]
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 []  \T1/zi4/m/n/10 Experimenter name: Kogo R, Shimamura T, Mimori K, Kawahara 
K et al.??Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modi
fication and is associated with poor prognosis in colorectal cancers.??Cancer R
es??2011 Oct 15[] 

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 []  \T1/zi4/m/n/10 Title: Long noncoding RNA HOTAIR regulates polycomb-depende
nt chromatin modification and is associated with poor prognosis in colorectal c
ancers.[] 
[35] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [36]
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 []  \T1/zi4/m/n/10 Experimenter name: Sveen A,????esen TH,??Rognum TO,??Lothe 
RA,??Skotheim RI. Transcriptome instability in colorectal cancer identified by 
exon microarray analyses: Associations with splicing factor expression levels a
nd patient survival. Genome Med 2011 May 27[] 

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 []  \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
 levels and patient survival.[] 
[37] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [38]
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 []  \T1/zi4/m/n/10 Experimenter name: Sveen A, Agesen TH, Nesbakken A, Rognum 
TO et al.??Transcriptome instability in colorectal cancer identified by exon mi
croarray analyses: Associations with splicing factor expression levels and pati
ent survival.Genome Med??2011 May 27[] 

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 []  \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
 levels and patient survival.[] 
[39] [40] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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 []  \T1/zi4/m/n/10 Experimenter name: Bandr??E,??Malumbres R,??Cubedo E,??Sola
 J,??Garc??Foncillas J,??Labarga A. A gene signature of 8 genes could identify 
the risk of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10
 B colon cancer patients. Oncol Rep 2007 May[] 

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 []  \T1/zi4/m/n/10 Laboratory: Bandr??E,??Malumbres R,??Cubedo E,??Sola J,??Ga
rc??Foncillas J,??Labarga A 2005[] 

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 []  \T1/zi4/m/n/10 Title: A gene signature of 8 genes could identify the risk 
of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10 B colon 
cancer patients.[] 
[41] [42] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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 []  \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
 

Overfull \hbox (269.78088pt too wide) in paragraph at lines 2001--2001
 []  \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[] 
[43] [44] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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 []  \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
 

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 []  \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[] 
[45] [46] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (428.78088pt too wide) in paragraph at lines 2186--2186
 []  \T1/zi4/m/n/10 Experimenter name: Birnbaum DJ, Laibe S, Ferrari A, Lagarde
 A et al.??Expression Profiles in Stage II Colon Cancer According to APC Gene S
tatus.??Transl Oncol??2012 Apr[] 

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 []  \T1/zi4/m/n/10 Title: Expression Profiles in Stage II Colon Cancer Accordi
ng to APC Gene Status.[] 
[47] [48] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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 []  \T1/zi4/m/n/10 Experimenter name: Bernal M,??Garc??Alcalde F,??Concha ????
Blanco A,??Garrido F,??Ruiz-Cabello F[] 

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 []  \T1/zi4/m/n/10 Laboratory: Bernal M,??Garc??Alcalde F,??Concha ????Blanco 
A,??Garrido F,??Ruiz-Cabello F 2011[] 

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 []  \T1/zi4/m/n/10 Title: Genome-wide profiling characterizes CRCs with geneti
c instability and specific routes to HLA class I loss and immunoescape[] 
[49] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [50]
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 []  \T1/zi4/m/n/10 Experimenter name: Tsuji S, Midorikawa Y, Takahashi T, Yagi
 K et al.??Potential responders to FOLFOX therapy for colorectal cancer by Rand
om Forests analysis.??Br J Cancer??2012 Jan 3[] 

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 []  \T1/zi4/m/n/10 Title: Potential responders to FOLFOX therapy for colorecta
l cancer by Random Forests analysis.[] 
[51] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [52]
Overfull \hbox (588.78088pt too wide) in paragraph at lines 2480--2480
 []  \T1/zi4/m/n/10 Experimenter name: Bianchini M, Levy E, Zucchini C, Pinski 
V et al.??Comparative study of gene expression by cDNA microarray in human colo
rectal cancer tissues and normal mucosa.??Int J Oncol??2006 Jul[] 

Overfull \hbox (176.78088pt too wide) in paragraph at lines 2483--2483
 []  \T1/zi4/m/n/10 Title: Comparative study of gene expression by cDNA microar
ray in human colorectal cancer tissues and normal mucosa.[] 
[53] [54] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (682.78088pt too wide) in paragraph at lines 2582--2582
 []  \T1/zi4/m/n/10 Experimenter name: de Sousa E Melo F, Colak S, Buikhuisen J
, Koster J et al.??Methylation of cancer-stem-cell-associated Wnt target genes 
predicts poor prognosis in colorectal cancer patients.??Cell Stem Cell??2011 No
v 4[] 

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 []  \T1/zi4/m/n/10 Title: Mutations in the Ras-Raf Axis underlie the prognosti
c value of CD133 in colorectal cancer.[] 
[55] [56] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [57]
Overfull \hbox (622.78088pt too wide) in paragraph at lines 2680--2680
 []  \T1/zi4/m/n/10 Experimenter name: Marisa L, de Reyni??A, Duval A, Selves J
 et al.??Gene expression classification of colon cancer into molecular subtypes
: characterization, validation, and prognostic value.??PLoS Med??2013[] 

Overfull \hbox (248.78088pt too wide) in paragraph at lines 2683--2683
 []  \T1/zi4/m/n/10 Title: Gene expression classification of colon cancer into 
molecular subtypes: characterization, validation, and prognostic value.[] 
[58] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [59]
Overfull \hbox (383.78088pt too wide) in paragraph at lines 2778--2778
 []  \T1/zi4/m/n/10 Experimenter name: Graudens E, Boulanger V, Mollard C, Mari
age-Samson R et al.??Deciphering cellular states of innate tumor drug responses
.??Genome Biol??2006[] 
[60] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [61]
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 []  \T1/zi4/m/n/10 Experimenter name: Laiho P, Kokko A, Vanharanta S, Salovaar
a R et al.??Serrated carcinomas form a subclass of colorectal cancer with disti
nct molecular basis.??Oncogene2007 Jan 11[] 

Overfull \hbox (70.78088pt too wide) in paragraph at lines 2871--2871
 []  \T1/zi4/m/n/10 Title: Serrated carcinomas form a subclass of colorectal ca
ncer with distinct molecular basis.[] 
[62] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [63]
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 []  \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Sakamoto E, Yamam
oto Y et al.??Gene expression signature for recurrence in stage III colorectal 
cancers.??Cancer??2009 Jan 15[] 

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 []  \T1/zi4/m/n/10 Title: Gene expression signature for recurrence in stage II
I colorectal cancers.[] 
[64] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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 []  \T1/zi4/m/n/10 Experimenter name: Profiling project of a panel of tubular 
adenoma and serrated adenoma patient material collected in the Academic Medical
 Center[] 

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 []  \T1/zi4/m/n/10 Laboratory: Medema JP,??de Sousa E Melo F,??Vermeulen L,??J
ansen M,??Dekker E,??Van Noesel C,??Fessler E 2013[] 
[65] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [66]
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 []  \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
 of human colon and rectal cancer. Nature 2012, 487:330-337[] 

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 []  \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[] 
[67] [68]
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 of human colon and rectal cancer. Nature 2012, 487:330-337[] 

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[71] [72]
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 of human colon and rectal cancer. Nature 2012, 487:330-337[] 

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 []  \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
 of human colon and rectal cancer. Nature 2012, 487:330-337[] 

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lon and rectal cancer.[] 
[78] [79]
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Overfull \hbox (929.78088pt too wide) in paragraph at lines 86--86
 []  \T1/zi4/m/n/10 Experimenter name: Auman JT, Church R, Lee SY, Watson MA, F
leshman JW, Mcleod HL.??Celecoxib pre-treatment in human colorectal adenocarcin
oma patients is associated with gene expression alterations suggestive of dimin
ished cellular proliferation.??Eur J Cancer??2008 Aug[] 

Overfull \hbox (444.78088pt too wide) in paragraph at lines 89--89
 []  \T1/zi4/m/n/10 Title: Celecoxib pre-treatment in human colorectal adenocar
cinoma patients is associated with gene expression alterations suggestive of di
minished cellular proliferation.[] 
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[4] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [5]
Overfull \hbox (541.78088pt too wide) in paragraph at lines 212--212
 []  \T1/zi4/m/n/10 Experimenter name: Lips EH, van Eijk R, de Graaf EJ, Oostin
g J et al.??Integrating chromosomal aberrations and gene expression profiles to
 dissect rectal tumorigenesis.BMC Cancer??2008 Oct 29[] 

Overfull \hbox (121.78088pt too wide) in paragraph at lines 215--215
 []  \T1/zi4/m/n/10 Title: Integrating chromosomal aberrations and gene express
ion profiles to dissect rectal tumorigenesis.[] 
[6] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [7]
Overfull \hbox (633.78088pt too wide) in paragraph at lines 298--298
 []  \T1/zi4/m/n/10 Experimenter name: Staub E, Groene J, Heinze M, Mennerich D
 et al.??An expression module of WIPF1-coexpressed genes identifies patients wi
th favorable prognosis in three tumor types.??J Mol Med (Berl)??2009 Jun[] 

Overfull \hbox (202.78088pt too wide) in paragraph at lines 301--301
 []  \T1/zi4/m/n/10 Title: An expression module of WIPF1-coexpressed genes iden
tifies patients with favorable prognosis in three tumor types.[] 
[8]
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\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
[10]
Overfull \hbox (714.78088pt too wide) in paragraph at lines 446--446
 []  \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman 
M et al.??DNA copy-number alterations underlie gene expression differences betw
een microsatellite stable and unstable colorectal cancers.??Clin Cancer Res??20
08 Dec 15[] 

Overfull \hbox (268.78088pt too wide) in paragraph at lines 449--449
 []  \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
 differences between microsatellite stable and unstable colorectal cancers.[] 
[11] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
[12]
Overfull \hbox (696.78088pt too wide) in paragraph at lines 536--536
 []  \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman 
M et al. DNA copy-number alterations underlie gene expression differences betwe
en microsatellite stable and unstable colorectal cancers. Clin Cancer Res 2008 
Dec 15[] 

Overfull \hbox (268.78088pt too wide) in paragraph at lines 539--539
 []  \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
 differences between microsatellite stable and unstable colorectal cancers.[] 
[13] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [14]
Overfull \hbox (707.78088pt too wide) in paragraph at lines 626--626
 []  \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Yamamoto Y, Matsu
da K et al.??Gene expression signature and response to the use of leucovorin, f
luorouracil and oxaliplatin in colorectal cancer patients.??Clin Transl Oncol??
2011 Jun[] 

Overfull \hbox (250.78088pt too wide) in paragraph at lines 629--629
 []  \T1/zi4/m/n/10 Title: Gene expression signature and response to the use of
 leucovorin, fluorouracil and oxaliplatin in colorectal cancer patients.[] 
[15] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (701.78088pt too wide) in paragraph at lines 700--700
 []  \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Gibbs P, Christie M, Prakas
h S et al.??Metastasis-Associated Gene Expression Changes Predict Poor Outcomes
 in Patients with Dukes Stage B and C Colorectal Cancer.??Clin Cancer Res??2009
 Dec 15[] 

Overfull \hbox (245.78088pt too wide) in paragraph at lines 703--703
 []  \T1/zi4/m/n/10 Title: Metastasis-Associated Gene Expression Changes Predic
t Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer.[] 
[16] [17] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (519.78088pt too wide) in paragraph at lines 810--810
 []  \T1/zi4/m/n/10 Experimenter name: Reid JF, Gariboldi M, Sokolova V, Capobi
anco P et al.??Integrative approach for prioritizing cancer genes in sporadic c
olon cancer.??Genes Chromosomes Cancer??2009 Nov[] 
[18]
Overfull \hbox (17.78088pt too wide) in paragraph at lines 813--813
 []  \T1/zi4/m/n/10 Title: Integrative approach for prioritizing cancer genes i
n sporadic colon cancer.[] 
[19] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [20]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 928--928
 []  \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
 al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[] 

Overfull \hbox (222.78088pt too wide) in paragraph at lines 931--931
 []  \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[] 
[21] [22] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [23]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1048--1048
 []  \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
 al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[] 

Overfull \hbox (222.78088pt too wide) in paragraph at lines 1051--1051
 []  \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[] 
[24] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [25]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1172--1172
 []  \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
 al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[] 

Overfull \hbox (222.78088pt too wide) in paragraph at lines 1175--1175
 []  \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[] 
[26] [27] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [28]
Overfull \hbox (601.78088pt too wide) in paragraph at lines 1297--1297
 []  \T1/zi4/m/n/10 Experimenter name: Matsuyama T, Ishikawa T, Mogushi K, Yosh
ida T et al.??MUC12 mRNA expression is an independent marker of prognosis in st
age II and stage III colorectal cancer.??Int J Cancer??2010 Nov 15[] 

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 []  \T1/zi4/m/n/10 Title: MUC12 mRNA expression is an independent marker of pr
ognosis in stage II and stage III colorectal cancer.[] 
[29] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
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 []  \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[] 
[30] [31] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (8.67705pt too wide) in paragraph at lines 1488--1489
[]\T1/ptm/m/n/10 This study aimed to iden-tify a novel biomarker or a tar-get o
f treat-ment for col-orec-tal can-cer (CRC).The
[32]
Overfull \hbox (479.78088pt too wide) in paragraph at lines 1501--1501
 []  \T1/zi4/m/n/10 Experimenter name: Tsukamoto S, Ishikawa T, Iida S, Ishigur
o M et al.??Clinical significance of osteoprotegerin expression in human colore
ctal cancer.??Clin Cancer Res2011 Apr 15[] 

Overfull \hbox (33.78088pt too wide) in paragraph at lines 1504--1504
 []  \T1/zi4/m/n/10 Title: Clinical significance of osteoprotegerin expression 
in human colorectal cancer.[] 
[33] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [34]
Overfull \hbox (742.78088pt too wide) in paragraph at lines 1595--1595
 []  \T1/zi4/m/n/10 Experimenter name: Kogo R, Shimamura T, Mimori K, Kawahara 
K et al.??Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modi
fication and is associated with poor prognosis in colorectal cancers.??Cancer R
es??2011 Oct 15[] 

Overfull \hbox (320.78088pt too wide) in paragraph at lines 1598--1598
 []  \T1/zi4/m/n/10 Title: Long noncoding RNA HOTAIR regulates polycomb-depende
nt chromatin modification and is associated with poor prognosis in colorectal c
ancers.[] 
[35] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [36]
Overfull \hbox (881.78088pt too wide) in paragraph at lines 1702--1702
 []  \T1/zi4/m/n/10 Experimenter name: Sveen A,????esen TH,??Rognum TO,??Lothe 
RA,??Skotheim RI. Transcriptome instability in colorectal cancer identified by 
exon microarray analyses: Associations with splicing factor expression levels a
nd patient survival. Genome Med 2011 May 27[] 

Overfull \hbox (428.78088pt too wide) in paragraph at lines 1705--1705
 []  \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
 levels and patient survival.[] 
[37] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [38]
Overfull \hbox (845.78088pt too wide) in paragraph at lines 1797--1797
 []  \T1/zi4/m/n/10 Experimenter name: Sveen A, Agesen TH, Nesbakken A, Rognum 
TO et al.??Transcriptome instability in colorectal cancer identified by exon mi
croarray analyses: Associations with splicing factor expression levels and pati
ent survival.Genome Med??2011 May 27[] 

Overfull \hbox (428.78088pt too wide) in paragraph at lines 1800--1800
 []  \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
 levels and patient survival.[] 
[39] [40] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (731.78088pt too wide) in paragraph at lines 1896--1896
 []  \T1/zi4/m/n/10 Experimenter name: Bandr??E,??Malumbres R,??Cubedo E,??Sola
 J,??Garc??Foncillas J,??Labarga A. A gene signature of 8 genes could identify 
the risk of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10
 B colon cancer patients. Oncol Rep 2007 May[] 

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 []  \T1/zi4/m/n/10 Laboratory: Bandr??E,??Malumbres R,??Cubedo E,??Sola J,??Ga
rc??Foncillas J,??Labarga A 2005[] 

Overfull \hbox (207.78088pt too wide) in paragraph at lines 1899--1899
 []  \T1/zi4/m/n/10 Title: A gene signature of 8 genes could identify the risk 
of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10 B colon 
cancer patients.[] 
[41] [42] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1051.78088pt too wide) in paragraph at lines 1998--1998
 []  \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
 

Overfull \hbox (269.78088pt too wide) in paragraph at lines 2001--2001
 []  \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[] 
[43] [44] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1051.78088pt too wide) in paragraph at lines 2092--2092
 []  \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
 

Overfull \hbox (269.78088pt too wide) in paragraph at lines 2095--2095
 []  \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[] 
[45] [46] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (428.78088pt too wide) in paragraph at lines 2186--2186
 []  \T1/zi4/m/n/10 Experimenter name: Birnbaum DJ, Laibe S, Ferrari A, Lagarde
 A et al.??Expression Profiles in Stage II Colon Cancer According to APC Gene S
tatus.??Transl Oncol??2012 Apr[] 

Overfull \hbox (5.78088pt too wide) in paragraph at lines 2189--2189
 []  \T1/zi4/m/n/10 Title: Expression Profiles in Stage II Colon Cancer Accordi
ng to APC Gene Status.[] 
[47] [48] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (84.78088pt too wide) in paragraph at lines 2296--2296
 []  \T1/zi4/m/n/10 Experimenter name: Bernal M,??Garc??Alcalde F,??Concha ????
Blanco A,??Garrido F,??Ruiz-Cabello F[] 

Overfull \hbox (74.78088pt too wide) in paragraph at lines 2297--2297
 []  \T1/zi4/m/n/10 Laboratory: Bernal M,??Garc??Alcalde F,??Concha ????Blanco 
A,??Garrido F,??Ruiz-Cabello F 2011[] 

Overfull \hbox (240.78088pt too wide) in paragraph at lines 2299--2299
 []  \T1/zi4/m/n/10 Title: Genome-wide profiling characterizes CRCs with geneti
c instability and specific routes to HLA class I loss and immunoescape[] 
[49] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [50]
Overfull \hbox (501.78088pt too wide) in paragraph at lines 2386--2386
 []  \T1/zi4/m/n/10 Experimenter name: Tsuji S, Midorikawa Y, Takahashi T, Yagi
 K et al.??Potential responders to FOLFOX therapy for colorectal cancer by Rand
om Forests analysis.??Br J Cancer??2012 Jan 3[] 

Overfull \hbox (75.78088pt too wide) in paragraph at lines 2389--2389
 []  \T1/zi4/m/n/10 Title: Potential responders to FOLFOX therapy for colorecta
l cancer by Random Forests analysis.[] 
[51] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [52]
Overfull \hbox (588.78088pt too wide) in paragraph at lines 2480--2480
 []  \T1/zi4/m/n/10 Experimenter name: Bianchini M, Levy E, Zucchini C, Pinski 
V et al.??Comparative study of gene expression by cDNA microarray in human colo
rectal cancer tissues and normal mucosa.??Int J Oncol??2006 Jul[] 

Overfull \hbox (176.78088pt too wide) in paragraph at lines 2483--2483
 []  \T1/zi4/m/n/10 Title: Comparative study of gene expression by cDNA microar
ray in human colorectal cancer tissues and normal mucosa.[] 
[53] [54] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (682.78088pt too wide) in paragraph at lines 2582--2582
 []  \T1/zi4/m/n/10 Experimenter name: de Sousa E Melo F, Colak S, Buikhuisen J
, Koster J et al.??Methylation of cancer-stem-cell-associated Wnt target genes 
predicts poor prognosis in colorectal cancer patients.??Cell Stem Cell??2011 No
v 4[] 

Overfull \hbox (83.78088pt too wide) in paragraph at lines 2585--2585
 []  \T1/zi4/m/n/10 Title: Mutations in the Ras-Raf Axis underlie the prognosti
c value of CD133 in colorectal cancer.[] 
[55] [56] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [57]
Overfull \hbox (622.78088pt too wide) in paragraph at lines 2680--2680
 []  \T1/zi4/m/n/10 Experimenter name: Marisa L, de Reyni??A, Duval A, Selves J
 et al.??Gene expression classification of colon cancer into molecular subtypes
: characterization, validation, and prognostic value.??PLoS Med??2013[] 

Overfull \hbox (248.78088pt too wide) in paragraph at lines 2683--2683
 []  \T1/zi4/m/n/10 Title: Gene expression classification of colon cancer into 
molecular subtypes: characterization, validation, and prognostic value.[] 
[58] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [59]
Overfull \hbox (383.78088pt too wide) in paragraph at lines 2778--2778
 []  \T1/zi4/m/n/10 Experimenter name: Graudens E, Boulanger V, Mollard C, Mari
age-Samson R et al.??Deciphering cellular states of innate tumor drug responses
.??Genome Biol??2006[] 
[60] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [61]
Overfull \hbox (483.78088pt too wide) in paragraph at lines 2868--2868
 []  \T1/zi4/m/n/10 Experimenter name: Laiho P, Kokko A, Vanharanta S, Salovaar
a R et al.??Serrated carcinomas form a subclass of colorectal cancer with disti
nct molecular basis.??Oncogene2007 Jan 11[] 

Overfull \hbox (70.78088pt too wide) in paragraph at lines 2871--2871
 []  \T1/zi4/m/n/10 Title: Serrated carcinomas form a subclass of colorectal ca
ncer with distinct molecular basis.[] 
[62] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [63]
Overfull \hbox (425.78088pt too wide) in paragraph at lines 2978--2978
 []  \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Sakamoto E, Yamam
oto Y et al.??Gene expression signature for recurrence in stage III colorectal 
cancers.??Cancer??2009 Jan 15[] 

Overfull \hbox (2.78088pt too wide) in paragraph at lines 2981--2981
 []  \T1/zi4/m/n/10 Title: Gene expression signature for recurrence in stage II
I colorectal cancers.[] 
[64] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (317.78088pt too wide) in paragraph at lines 3060--3060
 []  \T1/zi4/m/n/10 Experimenter name: Profiling project of a panel of tubular 
adenoma and serrated adenoma patient material collected in the Academic Medical
 Center[] 

Overfull \hbox (144.78088pt too wide) in paragraph at lines 3061--3061
 []  \T1/zi4/m/n/10 Laboratory: Medema JP,??de Sousa E Melo F,??Vermeulen L,??J
ansen M,??Dekker E,??Van Noesel C,??Fessler E 2013[] 
[65] (/usr/local/texlive/2014/texmf-dist/tex/latex/base/utf8.def) [66]
Overfull \hbox (189.78088pt too wide) in paragraph at lines 3138--3138
 []  \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
 of human colon and rectal cancer. Nature 2012, 487:330-337[] 

Overfull \hbox (8.78088pt too wide) in paragraph at lines 3141--3141
 []  \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[] 
[67] [68]
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 []  \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
 of human colon and rectal cancer. Nature 2012, 487:330-337[] 

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 []  \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[] 
[71] [72]
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 []  \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
 of human colon and rectal cancer. Nature 2012, 487:330-337[] 

Overfull \hbox (8.78088pt too wide) in paragraph at lines 3559--3559
 []  \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[] 
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 []  \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
 of human colon and rectal cancer. Nature 2012, 487:330-337[] 

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 []  \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[] 
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Saving output to ‘/private/tmp/RtmpZA4uZx/Rbuilda5ca348c2ca4/curatedCRCData/build/curatedCRCData.pdf’ ...
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* 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 ‘curatedCRCData_1.0.0.tar.gz’