PaLS: Filtering common literature, biological terms and pathway information.
Entity
UAM. Departamento de BioquímicaPublisher
Oxford University PressDate
2008-07-01Citation
10.1093/nar/gkn251
Nucleic Acids Research 36.Web Server issue (2008): W364-367
ISSN
0305-1048 (print); 1362-4962 (online)DOI
10.1093/nar/gkn251Funded by
Funding provided by Fundación de Investigación Médica Mutua Madrileña and Project TIC2003-09331-C02-02 of the Spanish Ministry of Education and Science (MEC).Project
Gobierno de España. TIC2003-09331-C02-02Editor's Version
http://dx.doi.org/10.1093/nar/gkn251Subjects
Biological experiment; Information; Function in common; Pathway; PaLS; MedicinaRights
© 2008 The Author(s)Abstract
Many biological experiments and their subsequent analysis yield lists of genes or proteins that can potentially be important to the prognosis or diagnosis of certain diseases (e.g. cancer). Nowadays, information about the function of those genes or proteins may be already gathered in some databases, but it is essential to understand if some of the members of those lists have a function in common or if they belong to the same metabolic pathway. To help researchers filter those genes or proteins that have such information in common, we have developed PaLS (pathway and literature strainer, http://pals.bioinfo.cnio.es). PaLS takes a list or a set of lists of gene or protein identifiers and shows which ones share certain descriptors. Four publicly available databases have been used for this purpose: PubMed, which links genes with those articles that make reference to them; Gene Ontology, an annotated ontology of terms related to the cellular component, biological process or molecular function where those genes or proteins are involved; KEGG pathways and Reactome pathways. Those descriptors among these four sources of information that are shared by more members of the list (or lists) are highlighted by PaLS.
Files in this item
Google Scholar:Alibés, Andreu
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Cañada, Andrés
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Díaz Uriarte, Ramón
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