Promoter profiling and coexpression data analysis identifies 24 novel genes that are coregulated with AMPA receptor genes, GRIAs

Allen Chong*, Zhuo Zhang, Kwok Pui Choi, Vidhu Choudhary, Mustafa B.A. Djamgoz, Guanglan Zhang, Vladimir Bajic

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

We identified a set of transcriptional elements that are conserved and overrepresented within the promoters of human, mouse, and rat GRIAs by comparing these promoters against a collection of 10,741 gene promoters. Cells regulate functional groups of genes by coordinating the transcriptional and/or posttranscriptional mRNA levels of interacting genes. As such, it is expected that functional groups of genes share the same transcriptional features within their promoters. We found 47 genes whose promoters contain the same combination of transcriptional elements that are overrepresented within the promoters of the GRIA gene family. Coexpressed genes may be transcriptionally coregulated, which in turn suggests that these genes may play complementary roles within a particular functional context. Using microarray expression data, we found 24 (of the 47) genes that share not only a similar promoter profile with GRIAs but also a well-correlated gene expression profile and, thus, we believe these to be coregulated with GRIAs.

Original languageEnglish (US)
Pages (from-to)378-384
Number of pages7
JournalGenomics
Volume89
Issue number3
DOIs
StatePublished - Mar 1 2007

Keywords

  • Computational biology
  • Gene expression regulation (KLK6, CLSTN3, RAB3B, IL16, BAI2, FAM107A, KLHL18, BEX1, DSN1, PIGC, DKKL1, VAMP4, NFKBIB, CD1C, FLT3LG, CAPN11, ARMC8, SETD4, CASZ1, FLJ10847, ADAMTS9, ARL6IP2, ALDH8A1, WDR71)
  • Genome
  • Ionotropic AMPA glutamate receptor (GRIA/GluR1-4)
  • Mammal
  • Microarray
  • Transcription factor binding sites (CDP CR1, Sp3, BACH2, GKLF, PU.1, MZF1, GATA2, STAT1, STAT3, STAT6, ELF1, Pax4)

ASJC Scopus subject areas

  • Genetics

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