Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts.
| Title: | Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts. |
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| Authors: | Taylor RC; Pacific Northwest National Laboratory, Richland, WA 99352, USA. Ronald.Taylor@pnl.gov; Sanfilippo A; McDermott JE; Baddeley B; Riensche R; Jensen R; Verhagen M; Pustejovsky J |
| Source: | International journal of computational biology and drug design [Int J Comput Biol Drug Des] 2011; Vol. 4 (1), pp. 56-82. Date of Electronic Publication: 2011 Feb 17. |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: Inderscience Enterprise Country of Publication: England NLM ID: 101479540 Publication Model: Print-Electronic Cited Medium: Print ISSN: 1756-0756 (Print) Linking ISSN: 17560756 NLM ISO Abbreviation: Int J Comput Biol Drug Des Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: [Olney] : Inderscience Enterprise, 2008- |
| MeSH Terms: | Algorithms* ; Cluster Analysis* ; Gene Regulatory Networks*; Computational Biology/*methods; Genes, Bacterial/genetics ; Genes, Bacterial/physiology ; Data Mining ; Databases, Genetic ; Escherichia coli ; Gene Expression Profiling ; Models, Genetic ; PubMed |
| Abstract: | Increasingly, reverse engineering methods have been employed to infer transcriptional regulatory networks from gene expression data. Enrichment with independent evidence from sources such as the biomedical literature and the Gene Ontology (GO) is desirable to corroborate, annotate and expand these networks as well as manually constructed networks. In this paper, we explore a novel approach for computer-assisted enrichment of regulatory networks. GO-based gene similarity is first tuned to an initial network augmented with gene links mined from PubMed and then used to drive network construction using a bootstrapping algorithm. We describe two applications of this approach and discuss its added value in terms of corroboration, annotation and expansion of manually constructed and reversed engineered networks. |
| Entry Date(s): | Date Created: 20110219 Date Completed: 20110511 Latest Revision: 20110218 |
| Update Code: | 20260130 |
| DOI: | 10.1504/IJCBDD.2011.038657 |
| PMID: | 21330694 |
| Database: | MEDLINE |
Journal Article