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Network Analysis of...
Network Analysis of Functional Genomics Data : Application to Avian Sex-Biased Gene Expression
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- Frings, Oliver (author)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),Stockholm Univ, Science for life laboratory
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Mank, Judith E. (author)
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- Alexeyenko, Andrey (author)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Sonnhammer, Erik L. L. (author)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)
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(creator_code:org_t)
- Hindawi Limited, 2012
- 2012
- English.
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In: Scientific World Journal. - : Hindawi Limited. - 1537-744X. ; , s. 130491-
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Abstract
Subject headings
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- Gene expression analysis is often used to investigate the molecular and functional underpinnings of a phenotype. However, differential expression of individual genes is limited in that it does not consider how the genes interact with each other in networks. To address this shortcoming we propose a number of network-based analyses that give additional functional insights into the studied process. These were applied to a dataset of sex-specific gene expression in the chicken gonad and brain at different developmental stages. We first constructed a global chicken interaction network. Combining the network with the expression data showed that most sex-biased genes tend to have lower network connectivity, that is, act within local network environments, although some interesting exceptions were found. Genes of the same sex bias were generally more strongly connected with each other than expected. We further studied the fates of duplicated sex-biased genes and found that there is a significant trend to keep the same pattern of sex bias after duplication. We also identified sex-biased modules in the network, which reveal pathways or complexes involved in sex-specific processes. Altogether, this work integrates evolutionary genomics with systems biology in a novel way, offering new insights into the modular nature of sex-biased genes.
Subject headings
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Keyword
- Functional Interaction Networks
- Protein Networks
- Gene Ontology
- Database
- Alignment
- Unification
- Integration
- Server
- Tool
- biokemi, inriktning teoretisk kemi
Publication and Content Type
- ref (subject category)
- art (subject category)
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