Search: onr:"swepub:oai:gup.ub.gu.se/61627" >
Predictive screenin...
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals
-
- Nelander, Sven, 1974 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för medicinsk och fysiologisk kemi,Institute of Medical Biochemistry,University of Gothenburg,Sahlgrenska Academy
-
- Larsson, Erik, 1975 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för medicinsk och fysiologisk kemi,Institute of Medical Biochemistry,University of Gothenburg,Sahlgrenska Academy
-
- Kristiansson, Erik, 1978 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper, matematisk statistik,Department of Mathematical Sciences, Mathematical Statistics,Chalmers tekniska högskola,Chalmers University of Technology,University of Gothenburg,Chalmers Technical University
-
show more...
-
- Månsson, Robert (author)
- Lund Strategic Research Center for Stem Cell Biology and Cell Therapy
-
- Nerman, Olle, 1951 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper, matematisk statistik,Department of Mathematical Sciences, Mathematical Statistics,Chalmers tekniska högskola,Chalmers University of Technology,University of Gothenburg,Chalmers Technical University
-
- Sigvardsson, Mikael (author)
- Lund University,Lunds universitet,Stamcellscentrum (SCC),Avdelningen för stamcellsforskning,Institutionen för laboratoriemedicin,Medicinska fakulteten,Stem Cell Center,Division of stem cell research,Department of Laboratory Medicine,Faculty of Medicine,Lund Strategic Research Center for Stem Cell Biology and Cell Therapy
-
- Mostad, Petter, 1964 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper, matematisk statistik,Department of Mathematical Sciences, Mathematical Statistics,Chalmers tekniska högskola,Chalmers University of Technology,University of Gothenburg,Chalmers Technical University
-
- Lindahl, Per, 1967 (author)
- Gothenburg University,Göteborgs universitet,Wallenberglaboratoriet,Institutionen för medicinsk och fysiologisk kemi,Wallenberg Laboratory,Institute of Medical Biochemistry,University of Gothenburg,Sahlgrenska Academy
-
show less...
-
(creator_code:org_t)
- 2005-05-09
- 2005
- English.
-
In: BMC genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 6:1
- Related links:
-
https://bmcgenomics....
-
show more...
-
https://research.cha... (primary) (free)
-
http://dx.doi.org/10...
-
https://liu.diva-por... (primary) (Raw object)
-
https://gup.ub.gu.se...
-
https://doi.org/10.1...
-
https://research.cha...
-
https://lup.lub.lu.s...
-
https://urn.kb.se/re...
-
show less...
Abstract
Subject headings
Close
- 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 approximately 40 percent 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 approximately 10% of all testis specific genes, and HNF-1 and 4 binding sites that were detected in approximately 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Keyword
- Amino Acid Motifs
- Animals
- B-Lymphocytes
- cytology
- Binding Sites
- Cluster Analysis
- Computational Biology
- Conserved Sequence
- Endoplasmic Reticulum
- metabolism
- Exons
- Gene Expression Profiling
- methods
- Gene Expression Regulation
- Genome
- Human
- Genomics
- methods
- Humans
- Male
- Mice
- Models
- Statistical
- Models
- Theoretical
- Multigene Family
- NF-kappa B
- metabolism
- Phylogeny
- RNA
- Messenger
- metabolism
- Regulatory Sequences
- Nucleic Acid
- Ribosomes
- metabolism
- Software
- Species Specificity
- Testis
- metabolism
- Transcription Factors
- metabolism
- Software
- NETWORK
- DATABASE
- MUSCLE-CELL-DIFFERENTIATION
- TRANSCRIPT PROFILING ANALYSIS
- SEQUENCES
- MICROARRAY
- PROTEIN
- EXPRESSION
- KAPPA-B
- MOLECULAR-CLONING
- TECHNOLOGY
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
To the university's database
- By the author/editor
-
Nelander, Sven, ...
-
Larsson, Erik, 1 ...
-
Kristiansson, Er ...
-
Månsson, Robert
-
Nerman, Olle, 19 ...
-
Sigvardsson, Mik ...
-
show more...
-
Mostad, Petter, ...
-
Lindahl, Per, 19 ...
-
show less...
- About the subject
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Biochemistry and ...
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Genetics
- Articles in the publication
-
BMC genomics
- By the university
-
University of Gothenburg
-
Chalmers University of Technology
-
Lund University
-
Linköping University