dataOvarian1: Data on time-to-recurrence and 158 gene expressions for 912...

Description Usage Format Details Source References Examples

Description

Meta-analytic data containing 158 gene expressions and time-to-relapse information for ovarian cancer patients. The data include time-to-recurrence, residual tumour size (>=1cm> vs. <1cm), and associated 158 gene expressions. The dataset is a subset of the curated ovarian data of Ganzfried et al (2013). We prepared the dataset by using "patientselection.config" in "Curated ovarian data" around October 2016.

Usage

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data("dataOvarian1")

Format

A data frame with 912 observations on the following 162 variables.

t.event

: time-to-recurrence in days

event

: event indicator (1=recurrence, 0=no recurrence)

group

: study ID; group=4, 9, 12, or 16

debulk

: residual tumour size (>=1cm> vs. <1cm)

ABI3BP

a numeric vector

ADAM12

a numeric vector

ADORA3

a numeric vector

ANKRD27

a numeric vector

AP2M1

a numeric vector

AP3S1

a numeric vector

ARHGAP28

a numeric vector

ARHGAP29

a numeric vector

ARTN

a numeric vector

ASAP3

a numeric vector

B4GALT5

a numeric vector

BCAP31

a numeric vector

BRD4

a numeric vector

C1QTNF3

a numeric vector

CALD1

a numeric vector

CCNE1

a numeric vector

CCNL1

a numeric vector

CDC42

a numeric vector

CDV3

a numeric vector

CEBPB

a numeric vector

CLIC4

a numeric vector

COL10A1

a numeric vector

COL11A1

a numeric vector

COL16A1

a numeric vector

COL3A1

a numeric vector

COL5A1

a numeric vector

COL5A2

a numeric vector

COMP

a numeric vector

CRISPLD2

a numeric vector

CRYAB

a numeric vector

CSE1L

a numeric vector

CTSK

a numeric vector

CXCL12

a numeric vector of gene expressions. The CXCL12 gene expression is a predictive biomarker of survival in ovarian cancer (Popple et al. 2012). It has been known that CXCL12 promotes tumour growth, participates in tumour metastasis, and suppresses tumour immunity (Kryczek et al. 2007). The statistical significance of the CXCL12 expression on survival is first examined by Popple et al. (2012), and is further confirmed by Ganzfried et al. (2013) based on the meta-analysis of 14 independent studies. A meta-analysis using a joint model further confirmed that the expression of CXCL12 gene is predictive of both cancer relapse and death (Emura et al. 2017; 2018).

CYR61

a numeric vector

DCUN1D1

a numeric vector

DDX27

a numeric vector

DIAPH3

a numeric vector

DNAJB4

a numeric vector

DNAJC13

a numeric vector

DNAJC8

a numeric vector

DPYSL3

a numeric vector

DVL3

a numeric vector

EFNB2

a numeric vector

EIF3K

a numeric vector

ELK1

a numeric vector

ENPP1

a numeric vector

EPYC

a numeric vector

FABP4

a numeric vector

FAM69A

a numeric vector

FAP

a numeric vector

FERMT2

a numeric vector

FGF1

a numeric vector

FN1

a numeric vector

FOSL2

a numeric vector

FSTL1

a numeric vector

GABRG3

a numeric vector

GAS1

a numeric vector

GFRA1

a numeric vector

GFRA3

a numeric vector

GJC1

a numeric vector

GLIPR1

a numeric vector

GPATCH1

a numeric vector

HLTF

a numeric vector

HP1BP3

a numeric vector

HSD17B6

a numeric vector

INHBA

a numeric vector

ITGB1

a numeric vector

JUN

a numeric vector

KIAA0226

a numeric vector

KIAA0355

a numeric vector

KIAA1598

a numeric vector

KIN

a numeric vector

KLHL25

a numeric vector

KPNA6

a numeric vector

KRT7

a numeric vector

KRTAP5.8

a numeric vector

L2HGDH

a numeric vector

LGALS1

a numeric vector

LOX

a numeric vector

LPP

a numeric vector

LUM

a numeric vector

LUZP1

a numeric vector

MAP7D1

a numeric vector

MAPRE1

a numeric vector

MCL1

a numeric vector

MEOX2

a numeric vector

METTL9

a numeric vector

MFN1

a numeric vector

MICAL2

a numeric vector

MMP12

a numeric vector

MRPS22

a numeric vector

MXD1

a numeric vector

MXRA8

a numeric vector

N4BP2L2

a numeric vector

NCOA3

a numeric vector of gene expressions. The NCOA3 gene encodes a nuclear receptor coactivator, and amplification of the gene occurs in breast and ovarian cancers (Anzick et al. 1997). The overexpression of NCOA3 is associated with tumor size (Spears et al. 2012) and tamoxifen resistance (Osborne et al. 2003), which are involved in the progression. Yoshida et al. (2005) reported that NCOA3 could contribute to ovarian cancer progression by promoting cell migration. In Emura et al. (2018), the overexpression of the gene was highly associated with time-to-relapse (Coefficient=0.194, P-value<0.00001) and time-to-death (Coefficient=0.237, P-value<0.00001). This result is consistent with the function of these reports.

NDRG3

a numeric vector

NINJ1

a numeric vector

NNMT

a numeric vector

NOTCH2

a numeric vector

NPY

a numeric vector

NTM

a numeric vector

NUAK1

a numeric vector

OAT

a numeric vector

OLFML2B

a numeric vector

PARD3

a numeric vector

PCYT1A

a numeric vector

PDE1A

a numeric vector

PDGFD

a numeric vector

PDPN

a numeric vector of gene expressions. The PDPN gene encodes the podoplanin protein. It is reported that cancer cells with higher PDPN expression have higher malignant potential due to enhanced platelet aggregation, which promotes alteration of metastasis, cell motility, and epithelial-mesenchymal transition (Shindo et al. 2013). Zhang et al. (2011) reported that overexpression of PDPN in fibroblasts is significantly associated with a poor prognosis in ovarian carcinoma. In Emura et al. (2018), the overexpression of the gene was highly associated with time-to-relapse (Coefficient=0.222, P-value<0.00001) and time-to-death (Coefficient=0.161, P-value<0.0001).

PGRMC1

a numeric vector

PLAU

a numeric vector

PLOD2

a numeric vector

PLSCR4

a numeric vector

POSTN

a numeric vector

PPIC

a numeric vector

PRDM2

a numeric vector

PSMC4

a numeric vector

RAB22A

a numeric vector

RAB31

a numeric vector

RAB32

a numeric vector

RARRES1

a numeric vector

RPS16

a numeric vector

SERPINE1

a numeric vector

SGK1

a numeric vector

SH3PXD2A

a numeric vector

SKIL

a numeric vector

SLC12A8

a numeric vector

SPARC

a numeric vector

SPHK1

a numeric vector

STAU1

a numeric vector

SULF1

a numeric vector

SUPT5H

a numeric vector

TAGLN

a numeric vector

TBCB

a numeric vector

TEAD1

a numeric vector of gene expressions. TEAD1 encodes a ubiquitous transcriptional enhancer factor that is a member of the TEA/ATTS domain family. It is reported that the protein level of TEAD1 was associated with poor prognosis in prostate cancer patients (Knight et al. 2008). In Emura et al. (2018), the overexpression of the gene was highly associated with time-to-relapse (Coefficient=0.195, P-value<0.00001) and time-to-death (Coefficient=0.223, P-value<0.00001).

TESK1

a numeric vector

TGM5

a numeric vector

THEMIS2

a numeric vector

TIMP2

a numeric vector of gene expressions. TIMP2 is a member of the TIMP gene family. The proteins encoded by this gene family are natural inhibitors of the matrix metalloproteinases (MMPs). MMPs and their inhibitors (TIMP gene family) play an important regulatory role in the homeostasis of the extracellular matrix (Halon et al. 2012). In addition to inhibitors of MMPs, TIMP2 has additional functions that are associated with cell proliferation and survival (Bourboulia et al., 2011). In Emura et al. (2018), the overexpression of the gene was highly associated with time-to-relapse (Coefficient=0.235, P-value<0.00001).

TIMP3

a numeric vector

TJP1

a numeric vector

TP73.AS1

a numeric vector

TPM2

a numeric vector

TPM4

a numeric vector

TSC22D2

a numeric vector

TUBB2A

a numeric vector

TUBB6

a numeric vector

TUFT1

a numeric vector

URI1

a numeric vector

USP48

a numeric vector

VCAN

a numeric vector

VSIG4

a numeric vector

YWHAB

a numeric vector of gene expressions. YWHAB encodes a protein belonging to the 14-3-3 family of proteins, members of which mediate signal transduction by binding to phosphoserine-containing proteins. It is reported that the protein of YWHAB can regulate cell survival, proliferation, and motility (Tzivion 2006). Actually, it is reported that overexpression of this gene promotes tumor progression and was associated with extrahepatic metastasis and worse survival in hepatocellular carcinoma (Liu et al. 2011). In Emura et al. (2018), the overexpression of the gene was highly associated with time-to-relapse (Coefficient=0.169, P-value<0.0001) and time-to-death (Coefficient=0.263, P-value<0.00001)

ZFP36

a numeric vector

ZFP36L2

a numeric vector

ZMYM1

a numeric vector

ZNF148

a numeric vector

ZNF79

a numeric vector

Details

4 studies are combined (group=4, 9, 12, and 16). The numbers 4, 9, 12 and 16 corresponds to the IDs from the original data of Ganzfried et al. (2013).

Source

Ganzfried BF et al. (2013), Curated ovarian data: clinically annotated data for the ovarian cancer transcriptome, Database, Article ID bat013.

References

Bourboulia D, et al. (2011), Endogenous angiogenesis inhibitor blocks tumor growth via direct and indirect effects on tumor microenvironment. Am J Pathol 179:2589-600

Emura T, Nakatochi M, Murotani K, Rondeau V (2017), A joint frailty-copula model between tumour progression and death for meta-analysis, Stat Methods Med Res 26(6):2649-66

Emura T, Nakatochi M, Matsui S, Michimae H, Rondeau V (2018), Personalized dynamic prediction of death according to tumour progression and high-dimensional genetic factors: meta-analysis with a joint model, Stat Methods Med Res 27(9):2842-58

Ganzfried BF et al. (2013), Curated ovarian data: clinically annotated data for the ovarian cancer transcriptome, Database, Article ID bat013.

Halon A, et al. (2012), Enhanced immunoreactivity of TIMP-2 in the stromal compartment of tumor as a marker of favorable prognosis in ovarian cancer patients. J Histochem Cytochem 60:491-501

Knight JF, et al. (2008), TEAD1 and c-Cbl are novel prostate basal cell markers that correlate with poor clinical outcome in prostate cancer. Br J Cancer 99:1849-58

Kryczek I, et al. (2007), Stroma-derived factor (SDF-1/CXCL12) and human tumor pathogenesis. Am J Physiol 292:987-95

Liu TA, et al. (2011), Increased expression of 14-3-3beta promotes tumor progression and predicts extrahepatic metastasis and worse survival in hepatocellular carcinoma. Am J Pathol 179:2698-708

Osborne CK, et al. (2003), Role of the estrogen receptor coactivator AIB1 (SRC-3) and HER-2/neu in tamoxifen resistance in breast cancer. J Natl Cancer Inst 95:353-61

Popple A, et al. (2012), The chemokine, CXCL12, is an independent predictor of poor survival in ovarian cancer. Br J Cancer 106:1306-13

Shindo K, et al. (2013), Podoplanin expression in cancer-associated fibroblasts enhances tumor progression of invasive ductal carcinoma of the pancreas. Mol Cancer 12:168

Tzivion G, et al. (2006), 14-3-3 proteins as potential oncogenes. Semin Cancer Biol 16:203-13

Yoshida H, et al. (2005), Steroid receptor coactivator-3, a homolog of Taiman that controls cell migration in the Drosophila ovary, regulates migration of human ovarian cancer cells. Mol Cell Endocrinol 245:77-85

Zhang Y, et al. (2011), Ovarian cancer-associated fibroblasts contribute to epithelial ovarian carcinoma metastasis by promoting angiogenesis, lymphangiogenesis and tumor cell invasion. Cancer Lett 303:47-55

Examples

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data(dataOvarian1)
######## univariate Cox ##########
t.event=dataOvarian1$t.event
event=dataOvarian1$event
X.mat=dataOvarian1[,-c(1,2,3,4)] ## gene expression
Symbol=colnames(dataOvarian1)[-c(1,2,3,4)] ## gene symbol

p=ncol(X.mat)
P_value=coef=NULL
for(j in 1:p){
  res=summary(coxph(Surv(t.event,event)~X.mat[,j]))$coefficients
  P_value=c(P_value,res[5])
  coef=c(coef,res[1])
}
data.frame( gene=Symbol[order(P_value)], P=P_value[order(P_value)], 
coef=round(coef[order(P_value)],3) )

joint.Cox documentation built on Feb. 4, 2022, 5:08 p.m.