Meta-analysis of cancer gene expression signatures reveals new cancer genes, SAGE tags and tumor associated regions of co-regulation.

Nucleic Acids Research
Ersen KavakAhmet Koman

Abstract

Cancer is among the major causes of human death and its mechanism(s) are not fully understood. We applied a novel meta-analysis approach to multiple sets of merged serial analysis of gene expression and microarray cancer data in order to analyze transcriptome alterations in human cancer. Our methodology, which we denote 'COgnate Gene Expression patterNing in tumours' (COGENT), unmasked numerous genes that were differentially expressed in multiple cancers. COGENT detected well-known tumor-associated (TA) genes such as TP53, EGFR and VEGF, as well as many multi-cancer, but not-yet-tumor-associated genes. In addition, we identified 81 co-regulated regions on the human genome (RIDGEs) by using expression data from all cancers. Some RIDGEs (28%) consist of paralog genes while another subset (30%) are specifically dysregulated in tumors but not in normal tissues. Furthermore, a significant number of RIDGEs are associated with GC-rich regions on the genome. All assembled data is freely available online (www.oncoreveal.org) as a tool implementing COGENT analysis of multi-cancer genes and RIDGEs. These findings engender a deeper understanding of cancer biology by demonstrating the existence of a pool of under-studied multi-cancer genes ...Continue Reading

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Citations

Jan 3, 2012·Briefings in Bioinformatics·Matthew N McCall, Anthony Almudevar
Jan 11, 2013·BMC Systems Biology·Meeta P PradhanMathew J Palakal
Nov 20, 2014·Cancer Biotherapy & Radiopharmaceuticals·Chen ZhangLongpo Zheng
Nov 14, 2014·Journal of Cellular Physiology·Alzenira Costa, Octavio Luiz Franco
May 16, 2014·Nature Reviews. Cancer·Daniele M GilkesDenis Wirtz
Oct 20, 2017·Epigenetics & Chromatin·Saikat BhattacharyaSanjay Gupta
Oct 16, 2020·Animal Genetics·E JaraE Armstrong

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Datasets Mentioned

BETA
X03205
GSE8401

Methods Mentioned

BETA
RNA-Seq
tag-Seq

Software Mentioned

scipy
SAGE
Oncomine
UCSC genome browser
RIDGE
TA
DGED
PHP
Mammaprint
oncoreveal

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