PaLS: filtering common literature, biological terms and pathway information.

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.