These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


Pubmed for Handhelds

PUBMED FOR HANDHELDS

Search MEDLINE/PubMed

  • Title: Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts.
    Author: Taylor RC, Sanfilippo A, McDermott JE, Baddeley B, Riensche R, Jensen R, Verhagen M, Pustejovsky J.
    Journal: Int J Comput Biol Drug Des; 2011; 4(1):56-82. PubMed ID: 21330694.
    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.
    [Abstract] [Full Text] [Related] [New Search]