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Transcriptome and proteome derived networks reveal distinct and complementary gene relationships

ABSTRACT: Co-expression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting the functional roles of individual genes at a system-wide scale. To enable network reconstructions we built a large-scale gene expression atlas comprised of 62,547 mRNAs, 17,862 non-modified proteins, and 6,227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development. There was little edge conservation in co-expression and GRNs reconstructed using transcriptome versus proteome data yet networks from either data type were enriched in ontological categories and effective in predicting known regulatory relationships. This integrated gene expression atlas provides a valuable community resource. The networks should facilitate plant biology research and they provide a conceptual framework for future systems biology studies highlighting the importance of studying gene regulation at several levels.

INSTRUMENT(S): LTQ Velos

ORGANISM(S): Zea Mays (ncbitaxon:4577)

SUBMITTER: Steven P. Briggs

PROVIDER: MSV000079290 | MassIVE |

SECONDARY ACCESSION(S): PXD002853

REPOSITORIES: MassIVE

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