Gene characterization index: Assessing the depth of gene annotation

Danielle Kemmer, Raf M. Podowski, Dimas Yusuf, Jochen Brumm, Warren Cheung, Claes Wahlestedt, Boris Lenhard, Wyeth W. Wasserman

Research output: Contribution to journalArticle

8 Scopus citations

Abstract

Background. We introduce the Gene Characterization Index, a bioinformatics method scoring the extent to which a protein-encoding gene is functionally described. Inherently a reflection of human perception, the Gene Characterization Index is applied for assessing the characterization status of individual genes, thus serving the advancement of both genome annotation and applied genomics research by rapid and unbiased identification of groups of uncharacterized genes for diverse applications such as directed functional studies and delineation of novel drug targets. Methodology/Principal Findings. The scoring procedure is based on a global survey of researchers, who assigned characterization scores from 1 (poor) to 10 (extensive) for a sample of genes based on major online resources. By evaluating the survey as training data, we developed a bioinformatics procedure to assign gene characterization scores to all genes in the human genome. We analyzed snapshots of functional genome annotation over a period of 6 years to assess temporal changes reflected by the increase of the average Gene Characterization Index. Applying the Gene Characterization Index to genes within pharmaceutically relevant classes, we confirmed known drug targets as high-scoring genes and revealed potentially interesting novel targets with low characterization indexes. Removing known drug targets and genes linked to sequence-related patent filings from the entirety of indexed genes, we identified sets of low-scoring genes particularly suited for further experimental investigation. Conclusions/Significance. The Gene Characterization Index is intended to serve as a tool to the scientific community and granting agencies for focusing resources and efforts on unexplored areas of the genome. The Gene Characterization Index is available from.

Original languageEnglish (US)
Article numbere1440
JournalPloS one
Volume3
Issue number1
DOIs
StatePublished - Jan 23 2008
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Kemmer, D., Podowski, R. M., Yusuf, D., Brumm, J., Cheung, W., Wahlestedt, C., Lenhard, B., & Wasserman, W. W. (2008). Gene characterization index: Assessing the depth of gene annotation. PloS one, 3(1), [e1440]. https://doi.org/10.1371/journal.pone.0001440