Pathway Analysis of Differential Gene Expression

The differentially expressed gene set was input into pathway analysis package GeneGo MetaCore (https://portal.genego.com/) to build biological networks and list the associated biological processes and diseases. A p-value of 0.05 was used as a cut off to determine significant enrichment of a pathway or annotated gene grouping present in the Metacore database. Gene Set Enrichment Analysis software (https://software.broadinstitute.org/software/cprg/?q=node/14) was also used to enrich gene sets or groups from these differentially expressed genes that share common biological function, chromosomal location, or regulation [55 (link)]. As a freely available software package together with an initial database of 1,325 biologically defined gene sets, GSEA is a computational method that determines whether a pre-defined set of genes shows statistically significant, concordant differences between two biological states. GSEA-enriched genes were then externally validated in The Cancer Genome Atlas (TCGA) breast cancer database and the web-based Oncomine cDNA microarray database (http://www.oncomine.org) were also used to identify the clinical significance and expression level of these TCGA-validated genes in other cancer types. Published microarray data sets of TECs from 13 colon cancer patients (GSE89287) and 4 lymphoma patients (GSE8852) were downloaded from Gene Expression Omnibus (GEO). Microarray gene expression values were then calculated by global median normalization.

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Sun Z., Wang C.Y., Lawson D.A., Kwek S., Velozo H.G., Owyong M., Lai M.D., Fong L., Wilson M., Su H., Werb Z, & Cooke D.L. (2017). Single-cell RNA sequencing reveals gene expression signatures of breast cancer-associated endothelial cells. Oncotarget, 9(13), 10945-10961.

Publication 2017

Biological Biological function Breast cancer Cancer Cdna microarray Chromosomal Colon cancer Cprg Gene expression Genes Genome Lymphoma Microarray Patients Tecs

Corresponding Organization :

Other organizations : University of California, San Francisco, National Cheng Kung University, University of California, Irvine

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Protocol cited in 7 other protocols

Variable analysis

independent variables

Differentially expressed gene set

dependent variables

Biological networks
Biological processes
Diseases
Gene sets or groups that share common biological function, chromosomal location, or regulation
Clinical significance and expression level of TCGA-validated genes in other cancer types

control variables

A p-value of 0.05 was used as a cut off to determine significant enrichment of a pathway or annotated gene grouping present in the Metacore database
Published microarray data sets of TECs from 13 colon cancer patients (GSE89287) and 4 lymphoma patients (GSE8852) were downloaded from Gene Expression Omnibus (GEO) and microarray gene expression values were then calculated by global median normalization

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