title: PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations.
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.
authors.affiliation: School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel.
authors.forename: Nadav
authors.initials: N
authors.lastname: Rappoport
authors.forename: Menachem
authors.initials: M
authors.lastname: Fromer
authors.forename: Regev
authors.initials: R
authors.lastname: Schweiger
authors.forename: Michal
authors.initials: M
authors.lastname: Linial
mesh_terms: D000818:Animals; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D013058:Mass Spectrometry; D051379:Mice; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism* / Q000502:physiology; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism* / Q000502:physiology; D040901:Proteomics; D051381:Rats; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D010455:Peptides; D011506:Proteins
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