Improved modulon identification from bacterial gene expression array data using operon-based correlation reference set
✍ Scribed by S. Hedge; E.A. Permina; Y.A. Medvedeva; S.C. Mande; V.J. Makeev
- Publisher
- Elsevier
- Year
- 2010
- Tongue
- English
- Weight
- 69 KB
- Volume
- 27
- Category
- Article
- ISSN
- 1871-6784
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✦ Synopsis
is usually characterized by an increase in functionally paralogous proteins or an increase in combinations of functional domains. Large scale phylogenetic analysis can shed light on the relative amounts of functional domains or their combinations and interactions involved in certain regulatory networks.
Methods: We performed comparative and functional analysis of three regulatory mechanisms: (1) transcriptional regulation by transcription factors, (2) post-transcriptional regulation by miR-NAs, and (3) chromatin regulation across all domains of life. All of these methods are evolutionarily old and passed through several major innovations. We calculated single domain distributions and domain co-occurrences from SUPERFAMILY domain annotations or about 900 genomes. Functional annotation from GeneOnthology and protein domain descriptions was integrated into our comparative analysis.
Results: Functional domains and their combinations show increasing complexity with the complexity of the organism. Sudden expansions of the regulatory networks fall together with major innovations and potential changes to the regulatory concepts. This is clearly shown by the massive expansion of transcription factor families and the pervasive combinatorial control of genes by multiple transcription factors. In chromatin regulation, binding of histone modification seems to be a eukaryotic innovation, enabling propagation, inheritance, and context dependent interpretation of histone modifications. The overall scenario will be presented.