Accentuate the negative

Proteome comparisons using the negative proteome database

Lawrence Reiter, Long H. Do, Michael S. Fischer, Nancy A. Hong, Ethan Bier

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The availability of complete genome sequence information for diverse organisms including model genetic organisms has ushered in a new era of protein sequence comparisons making it possible to search for commonalities among entire proteomes using the Basic Local Alignment Search Tool (BLAST). Although the identification and analysis of proteins shared by humans and model organisms has proven an invaluable tool to understanding gene function, the sets of proteins unique to a given model organism's proteome have remained largely unexplored. We have constructed a searchable database that allows biologists to identify proteins unique to a given proteome. The Negative Proteome Database (NPD) is populated with pair-wise protein sequence comparisons between each of the following proteomes: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Dictyostelium discoideum, Chlamydomonus reinhardti, Escherichia coli K12, Arabidopsis thaliana and Methanoscarcina acetivorans. Our analysis of negative proteome datasets using the NPD has thus far revealed 107 proteins in humans that may be involved in motile cilia function, 1628 potential pesticide target proteins in flies, 659 proteins shared by flies and humans that are not represented in the less neurologically complex worm proteome, and 180 nuclear encoded human disease associated proteins that are absent from the fly proteome. The NPD is the only online resource where users can quickly perform complex negative and positive comparisons of model organism proteomes. We anticipate that the NPD and the adaptable algorithm which can readily be used to duplicate this analysis on custom sets of proteomes will be an invaluable tool in the investigation of organism specific protein sets.

Original languageEnglish (US)
Pages (from-to)164-171
Number of pages8
JournalFly
Volume1
Issue number3
DOIs
StatePublished - Jan 1 2007

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proteome
organisms
proteins
amino acid sequences
Escherichia coli K12
Dictyostelium discoideum
Mus musculus
cilia
Caenorhabditis elegans
human diseases
biologists
Drosophila melanogaster
Saccharomyces cerevisiae
pesticides
Arabidopsis thaliana

All Science Journal Classification (ASJC) codes

  • Insect Science

Cite this

Accentuate the negative : Proteome comparisons using the negative proteome database. / Reiter, Lawrence; Do, Long H.; Fischer, Michael S.; Hong, Nancy A.; Bier, Ethan.

In: Fly, Vol. 1, No. 3, 01.01.2007, p. 164-171.

Research output: Contribution to journalArticle

Reiter, Lawrence ; Do, Long H. ; Fischer, Michael S. ; Hong, Nancy A. ; Bier, Ethan. / Accentuate the negative : Proteome comparisons using the negative proteome database. In: Fly. 2007 ; Vol. 1, No. 3. pp. 164-171.
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