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 B. Bajic

doi:10.1016/j.ygeno.2006.11.009

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 B. Bajic

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-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 language	English (US)
Pages (from-to)	378-384
Number of pages	7
Journal	Genomics
Volume	89
Issue number	3
DOIs	https://doi.org/10.1016/j.ygeno.2006.11.009
State	Published - Mar 2007
Externally published	Yes

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

Access to Document

10.1016/j.ygeno.2006.11.009

Cite this

@article{9a5434e867324acdaef22d9855632c1d,

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

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.",

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)",

author = "Allen Chong and Zhuo Zhang and Choi, {Kwok Pui} and Vidhu Choudhary and Djamgoz, {Mustafa B.A.} and Guanglan Zhang and Bajic, {Vladimir B.}",

year = "2007",

month = mar,

doi = "10.1016/j.ygeno.2006.11.009",

language = "English (US)",

volume = "89",

pages = "378--384",

journal = "Genomics",

issn = "0888-7543",

publisher = "Academic Press Inc.",

number = "3",

}

TY - JOUR

T1 - Promoter profiling and coexpression data analysis identifies 24 novel genes that are coregulated with AMPA receptor genes, GRIAs

AU - Chong, Allen

AU - Zhang, Zhuo

AU - Choi, Kwok Pui

AU - Choudhary, Vidhu

AU - Djamgoz, Mustafa B.A.

AU - Zhang, Guanglan

AU - Bajic, Vladimir B.

PY - 2007/3

Y1 - 2007/3

N2 - 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.

AB - 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.

KW - Computational biology

KW - 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)

KW - Genome

KW - Ionotropic AMPA glutamate receptor (GRIA/GluR1-4)

KW - Mammal

KW - Microarray

KW - Transcription factor binding sites (CDP CR1, Sp3, BACH2, GKLF, PU.1, MZF1, GATA2, STAT1, STAT3, STAT6, ELF1, Pax4)

UR - http://www.scopus.com/inward/record.url?scp=33846786924&partnerID=8YFLogxK

U2 - 10.1016/j.ygeno.2006.11.009

DO - 10.1016/j.ygeno.2006.11.009

M3 - Article

C2 - 17208408

AN - SCOPUS:33846786924

SN - 0888-7543

VL - 89

SP - 378

EP - 384

JO - Genomics

JF - Genomics

IS - 3

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this