Knowledge Integration for Gene Target Selection

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Knowledge Integration for Gene Target Selection

• Graciela Gonzalez, PhD
• Juan C. Uribe
• Contact graciela.gonzalez_at_asu.edu

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GeneRanker in a Nutshell

• Integration of knowledge from
• biomedical literature
• curated PPI databases, and
• protein network topology
• Seeks to prioritize lists of genes on their
  association to specific diseases and phenotypes
  1,
• Such associations may or may not have been
  published (thus, not text mining)

1 Gonzalez G, Uribe JC, Tari L, Brophy C, Baral
C. Mining Gene-Disease relationships from
Biomedical Literature Incorporating
Interactions, Connectivity, Confidence, and
Context Measures. Pacific Symposium in
Biocomputing 2007 Maui, Hawaii 2007.
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GeneRanker Interface

1. The user types a disease or biological process
   to be searched.
2. Genes found to be in association to the disease
   are extracted from the literature.
3. Protein-protein interactions involving those
   genes are then pulled from the literature
   curated sources
4. The protein network is built and each gene ranked

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GeneRanker Interface
Collaboration Application of GeneRanker to a
biological context, with Dr. Michael Berens,
Director of the Brain Tumor Unit at the
Translational Genomics Institute (TGen).
GeneRanker is available as an online
application at http//www.generanker.org.

• Each gene is scored and can be annotated (count
  of co-occurrences and statistical representation)

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Evaluation of GeneRanker

• Contextual (PubMed search) based shows gt 20 jump
  in precision over NLP based extraction.
• Synthetic network results show AUC gt 0.984
• Empirical validation against a glioma dataset
  shows consistent results (118 vs 22
  differentially expressed probes from top vs
  bottom of list)

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Complementary Work

• CBioC www.cbioc.org shows PPIs, gene-disease,
  and gene-bioprocess associations extracted from
  abstracts
• BANNER sourceforge.banner.org (presenting a
  poster on this one). An open source entity
  recognizer available now.
• Gene normalization a similar open source system
  soon to be available.