CPG: SRC Signaling Pathway CpG Methylation Data in TCGA

In iNOTE: Integrative Network Omnibus Total Effect Test

Description

TCGA lung cancer patient Illumina 450K CpG methylation data for genes in the SRC signaling pathway geneset identified Gautschi et al (2008).

Usage

data(CPG)

Format

A list object with eight indices, containing the matrix of CpG methylation levels for sites associated with each individual gene in the SRC Signaling pathway for 249 TCGA subjects.

ID1

A named matrix with 249 subject rows and 14 CpG columns.

ID2

A named matrix with 249 subject rows and 15 CpG columns.

ID3

A named matrix with 249 subject rows and 14 CpG columns.

ID4

A named matrix with 249 subject rows and 8 CpG columns.

SERPINE1

A named matrix with 249 subject rows and 14 CpG columns.

SMAD6

A named matrix with 249 subject rows and 36 CpG columns.

SMAD7

A named matrix with 249 subject rows and 24 CpG columns.

TGFB1

A named matrix with 249 subject rows and 21 CpG columns.

Details

Genomic data were extracted from lung cancer patients (adenocarcinoma or squamous cell carcinoma) in The Cancer Genome Atlas and adjusted for batch effects. The CPG dataset represents a subset of the CpG methylation data for patients with non-missing survival status at one year after initial diagnosis in genes identified by Gautschi et al (2008) in the Molecular Signatures Database (MsigDB; Subramanian et al (2005)) as lung-cancer associated members of the SRC signaling pathway.

Source

TCGA

http://cancergenome.nih.gov/

MsigDB

http://software.broadinstitute.org/gsea/msigdb/

References

Gautschi O, Tepper CG, Purnell PR, Izumiya Y, Evans CP, Green TP, et al. (2008) Regulation of Id1 expression by SRC: implications for targeting of the bone morphogenetic protein pathway in cancer. Cancer Research. 68(7):2250<e2><80><93>8.

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 102(43):15545<e2><80><93>50.

Examples

data(CPG)
str(CPG)

iNOTE documentation built on May 2, 2019, 11:44 a.m.