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Nucleic Acids Res. 2010 Jul;38(Web Server issue):W84-9. doi: 10.1093/nar/gkq320. Epub 2010 May 5.

PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations.

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  • 1School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel.

Abstract

Derivation of biological meaning from large sets of proteins or genes is a frequent task in genomic and proteomic studies. Such sets often arise from experimental methods including large-scale gene expression experiments and mass spectrometry (MS) proteomics. Large sets of genes or proteins are also the outcome of computational methods such as BLAST search and homology-based classifications. We have developed the PANDORA web server, which functions as a platform for the advanced biological analysis of sets of genes, proteins, or proteolytic peptides. First, the input set is mapped to a set of corresponding proteins. Then, an analysis of the protein set produces a graph-based hierarchy which highlights intrinsic relations amongst biological subsets, in light of their different annotations from multiple annotation resources. PANDORA integrates a large collection of annotation sources (GO, UniProt Keywords, InterPro, Enzyme, SCOP, CATH, Gene-3D, NCBI taxonomy and more) that comprise approximately 200,000 different annotation terms associated with approximately 3.2 million sequences from UniProtKB. Statistical enrichment based on a binomial approximation of the hypergeometric distribution and corrected for multiple hypothesis tests is calculated using several background sets, including major gene-expression DNA-chip platforms. Users can also visualize either standard or user-defined binary and quantitative properties alongside the proteins. PANDORA 4.2 is available at http://www.pandora.cs.huji.ac.il.

PMID:
20444873
[PubMed - indexed for MEDLINE]
PMCID:
PMC2896089
Free PMC Article
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