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Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals

Nelander, S.; Larsson, E.; Kristiansson, E.; Mansson, R.; Nerman, O.; Sigvardsson, Mikael LU ; Mostad, P. and Lindahl, P. (2005) In BMC Genomics 6. p.21-21
Abstract
Background: The expression of gene batteries, genomic units of functionally linked genes which are activated by similar sets of cis- and trans-acting regulators, has been proposed as a major determinant of cell specialization in metazoans. We developed a predictive procedure to screen the mouse and human genomes and transcriptomes for cases of gene-battery-like regulation. Results: In a screen that covered ∼ 40 per cent of all annotated protein-coding genes, we identified 21 co-expressed gene clusters with statistically supported sharing of cis- regulatory sequence elements. 66 predicted cases of over-represented transcription factor binding motifs were validated against the literature and fell into three categories: (i) previously... (More)
Background: The expression of gene batteries, genomic units of functionally linked genes which are activated by similar sets of cis- and trans-acting regulators, has been proposed as a major determinant of cell specialization in metazoans. We developed a predictive procedure to screen the mouse and human genomes and transcriptomes for cases of gene-battery-like regulation. Results: In a screen that covered ∼ 40 per cent of all annotated protein-coding genes, we identified 21 co-expressed gene clusters with statistically supported sharing of cis- regulatory sequence elements. 66 predicted cases of over-represented transcription factor binding motifs were validated against the literature and fell into three categories: (i) previously described cases of gene battery-like regulation, (ii) previously unreported cases of gene battery-like regulation with some support in a limited number of genes, and (iii) predicted cases that currently lack experimental support. The novel predictions include for example Sox 17 and RFX transcription factor binding sites that were detected in ∼ 10% of all testis specific genes, and HNF-1 and 4 binding sites that were detected in ∼ 30% of all kidney specific genes respectively. The results are publicly available at http://www.wlab.gu.se/lindahl/genebatteries. Conclusion: 21 co-expressed gene clusters were enriched for a total of 66 shared cis-regulatory sequence elements. A majority of these predictions represent novel cases of potential co-regulation of functionally coupled proteins. Critical technical parameters were evaluated, and the results and the methods provide a valuable resource for future experimental design. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
NETWORK, DATABASE, MUSCLE-CELL-DIFFERENTIATION, TRANSCRIPT PROFILING ANALYSIS, SEQUENCES, MICROARRAY, PROTEIN, EXPRESSION, KAPPA-B, MOLECULAR-CLONING
in
BMC Genomics
volume
6
pages
21 - 21
publisher
BioMed Central
external identifiers
  • wos:000229170300002
  • scopus:25444503796
ISSN
1471-2164
DOI
10.1186/1471-2164-6-68
language
English
LU publication?
yes
id
c30bd5a9-d17b-4ef8-92b2-2cd015579795 (old id 1417443)
date added to LUP
2009-06-12 10:01:29
date last changed
2017-08-20 04:32:57
@article{c30bd5a9-d17b-4ef8-92b2-2cd015579795,
  abstract     = {Background: The expression of gene batteries, genomic units of functionally linked genes which are activated by similar sets of cis- and trans-acting regulators, has been proposed as a major determinant of cell specialization in metazoans. We developed a predictive procedure to screen the mouse and human genomes and transcriptomes for cases of gene-battery-like regulation. Results: In a screen that covered ∼ 40 per cent of all annotated protein-coding genes, we identified 21 co-expressed gene clusters with statistically supported sharing of cis- regulatory sequence elements. 66 predicted cases of over-represented transcription factor binding motifs were validated against the literature and fell into three categories: (i) previously described cases of gene battery-like regulation, (ii) previously unreported cases of gene battery-like regulation with some support in a limited number of genes, and (iii) predicted cases that currently lack experimental support. The novel predictions include for example Sox 17 and RFX transcription factor binding sites that were detected in ∼ 10% of all testis specific genes, and HNF-1 and 4 binding sites that were detected in ∼ 30% of all kidney specific genes respectively. The results are publicly available at http://www.wlab.gu.se/lindahl/genebatteries. Conclusion: 21 co-expressed gene clusters were enriched for a total of 66 shared cis-regulatory sequence elements. A majority of these predictions represent novel cases of potential co-regulation of functionally coupled proteins. Critical technical parameters were evaluated, and the results and the methods provide a valuable resource for future experimental design.},
  author       = {Nelander, S. and Larsson, E. and Kristiansson, E. and Mansson, R. and Nerman, O. and Sigvardsson, Mikael and Mostad, P. and Lindahl, P.},
  issn         = {1471-2164},
  keyword      = {NETWORK,DATABASE,MUSCLE-CELL-DIFFERENTIATION,TRANSCRIPT PROFILING ANALYSIS,SEQUENCES,MICROARRAY,PROTEIN,EXPRESSION,KAPPA-B,MOLECULAR-CLONING},
  language     = {eng},
  pages        = {21--21},
  publisher    = {BioMed Central},
  series       = {BMC Genomics},
  title        = {Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals},
  url          = {http://dx.doi.org/10.1186/1471-2164-6-68},
  volume       = {6},
  year         = {2005},
}