Nucleic Acids Research Advance Access originally published online on May 8, 2008
Nucleic Acids Research 2008 36(Web Server issue):W364-W367; doi:10.1093/nar/gkn251
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W364-W367
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
PaLS: filtering common literature, biological terms and pathway information
Statistical Computing Team, Structural and Computational Biology Programme, Spanish National Cancer Center (CNIO), Melchor Fernández Almagro 3, Madrid, 28029, Spain
*To whom correspondence should be addressed. Tel: +34 93 316 0258; Fax: +34 93 396 9983; Email: aalibes{at}gmail.com Correspondence may also be addressed to Andrés Cañada, Tel: +34 91 224 6900; Fax: +34 91 224 6980; Email: acanada{at}cnio.es
Received January 31, 2008. Revised April 15, 2008. Accepted April 20, 2008.
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.
Present address: Andreu Alibés: EMBL-CRG Systems Biology Unit, Center for Genomic Regulation, Dr Aiguader 88, 08003 Barcelona, Spain
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  E. R. Morrissey and R. Diaz-Uriarte Pomelo II: finding differentially expressed genes Nucleic Acids Res., July 1, 2009; 37(suppl_2): W581 - W586. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Hu, J.-H. Hung, Y. Wang, Y.-C. Chang, C.-L. Huang, M. Huyck, and C. DeLisi VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology Nucleic Acids Res., July 1, 2009; 37(suppl_2): W115 - W121. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. W. Huang, B. T. Sherman, and R. A. Lempicki Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists Nucleic Acids Res., January 1, 2009; 37(1): 1 - 13. [Abstract] [Full Text] [PDF]
|
|