Name
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 similar to 200 000 different annotation terms associated with similar to 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. |
Year | DOI | Venue |
|---|---|---|
2010 | 10.1093/nar/gkq320 | NUCLEIC ACIDS RESEARCH |
Field | DocType | Volume |
Genome,Annotation,Proteomics,Biology,UniProt,Genetics,Hierarchical INTegration,DNA microarray,Statistical hypothesis testing,InterPro | Journal | 38 |
Issue | ISSN | Citations |
SUPnan | 0305-1048 | 6 |
PageRank | References | Authors |
0.47 | 4 | 4 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Nadav Rappoport | 1 | 21 | 3.08 |
| Menachem Fromer | 2 | 143 | 10.47 |
| Regev Schweiger | 3 | 15 | 2.36 |
| Michal Linial | 4 | 1502 | 149.92 |