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Chapter 3: Small Molecules and Disease
[…] Molecule Pathway Databases or SMPDB and the Medical Biochemistry Page [http://themedicalbiochemistrypage.org/]. Several commercial pathway databases also exist such as TransPath (from BioBase Inc.), PathArt (from Jubilant Biosys Inc.), MetaBase (from GeneGo Inc.) and Ingenuity Pathways Analysis (Ingenuity Systems Inc.), many of which provide nicely illustrated metabolic pathway diagrams. Most of […]
Overrepresentation of transcription factor families in the genesets underlying breast cancer subtypes
[…] lied to extract biological associations by mining PubMed to build pathways from extracted facts using data from recent publications and public and commercial databases such as KEGG, BIND, GO, and the PathArt database of curated signaling and disease pathways. The algorithm for building Correlation Network in Pathway Studio is based on Pearson Correlation. Genes with similar expression profiles are […]
Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator activated receptor α agonists
[…] interpretation of gene expression data. For example, pathway analysis is based on the Pathway Library in ArrayTrack, which contains pathways from Kyoto Encyclopedia of Genes and Genomes (KEGG)  and PathArt (Jubilant Biosys Ltd., Columbia, MD). The Fisher Exact Test  is implemented in ArrayTrack to assess the statistical significance of identified pathways. Ingenuity Pathway Analysis software ( […]
Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms
[…] ein phosphorylation, B-cell-and antibody-mediated immunity.In a similar fashion, we also analyzed which cellular pathways played critical roles for defining the two distinct subtypes using Jubilant's PathArt™ database. Table (lower panel) shows the top five PathArt™ pathways over-represented (p < 0.01) by the genes characteristic for luminal A and the basal-like subtypes, respectively. Again, qui […]
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