Network Analysis of Functional Genomics Data: Application to Avian Sex-Biased Gene Expression
2012 (English)In: Scientific World Journal, ISSN 1537-744X, 130491- p.Article in journal (Refereed) Published
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.
Place, publisher, year, edition, pages
2012. 130491- p.
Functional Interaction Networks, Protein Networks, Gene Ontology, Database, Alignment, Unification, Integration, Server, Tool
IdentifiersURN: urn:nbn:se:kth:diva-117580DOI: 10.1100/2012/130491ISI: 000313179900001ScopusID: 2-s2.0-84872791228OAI: oai:DiVA.org:kth-117580DiVA: diva2:602362
FunderSwedish Research CouncilEU, European Research Council, 260233Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish e‐Science Research Center
QC 201302012013-02-012013-01-312013-02-01Bibliographically approved