Data Sources

BIND
(Biomolecular IN teraction Database) is now a component of the Biomolecular Object Network Databank
www.unleashedinformatics.com

UNIPROT
(Universal Protein Resource)
www.pir.uniprot.org

Pubmed
www.nlm.nih.gov

GO
(Gene Ontology)
www.godatabase.org

GOA
(Gene Ontology Annotation)
www.ebi.ac.uk/GOA

Entrez Gene
www.nlm.nih.gov

KOG
(Eukaryotic section of Clusters of Orthologous Groups)
www.ncbi.nlm.nih.gov

KEGG
(Kyoto Encyclopedia of Genes and Genomes)
www.pathway.jp/mosaic/

TRANSFAC®
www.biobase-international.com

Note

Medline is free but requires the user to have a license.

KEGG and TRANSFAC® are commercially distributed products for which customer licenses are required.

KEGG, integrated into genTELLECT™, may be purchased at a substantial savings.

genTELLECT™ is a data integration platform that maximizes the usefulness of a widely-used set of data sources. The list of public and commercial data sources in common use by researchers and that normally reside on different servers may include: KEGG, TRANSFAC®, BIND, Medline, UNIPROT, Entrez Gene, Gene Ontology and KOG. UMLS Metathesaurus terms have been mapped to Medline abstracts yielding associations which are unique to genTELLECT™

genTELLECT™ places a framework around these sources that puts them into a common information space, allowing researchers to ask complex questions that span database boundaries. It is aimed at researchers doing proteomics and gene expression studies. Although diverse in nature, these experiments usually have similar output, which is a list of genes or proteins of interest. Researchers usually then wish to know things such as:

• How are the members of the list inter-related?
• Do they have common transcriptional regulators?
• Are they found in the same pathways?
• Are they referenced in the same articles?
• Are they related in clinical ontologies?

genTELLECT™ can currently load UNIPROT IDs, Entrez Gene IDs, and Affymetrix ProbeSet IDs, and then identify every known fact about each gene in each of the data sources. These facts are displayed as either tables or interactive graphs. In tabular format, facts of greater importance rise to the top of the list. For example, a pathway containing 10 members of the input list will appear higher than pathways containing fewer members. The graph provides an intuitive way of looking at these sets of related facts, and can be edited and rearranged manually. Items in the tables and graphs are connected to detailed reports, compiled from the original data sources.