{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T08:57:16Z","timestamp":1769849836581,"version":"3.49.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: Extracting biological insight from microarray data is important but challenging. Here we describe TAPPA, a java-based tool, for identification of phenotype-associated genetic pathways utilizing the pathway topological measures. This is achieved by first calculating a Pathway Connectivity Index (PCI) for each pathway, followed by evaluating its correlation to the phenotypic variation. Our PCI definition not only efficiently captures the contributions from genes that show subtle but consistent changes in expression, but also naturally overweighs the hub genes that interact with a large number of other genes in the pathway. TAPPA also allows evaluation of sub-modules within a pathway and their association to phenotypes.<\/jats:p><jats:p>Availability: TAPPA and data for Figure 1 are freely available from http:\/\/watson.mcgee.mcw.edu:8080\/~sgao<\/jats:p><jats:p>Contact: \u00a0sgao@mcw.edu<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm460","type":"journal-article","created":{"date-parts":[[2007,9,22]],"date-time":"2007-09-22T00:33:25Z","timestamp":1190421205000},"page":"3100-3102","source":"Crossref","is-referenced-by-count":55,"title":["TAPPA: topological analysis of pathway phenotype association"],"prefix":"10.1093","volume":"23","author":[{"given":"Shouguo","family":"Gao","sequence":"first","affiliation":[{"name":"The Max McGee National Research Center for Juvenile Diabetes & The Human and Molecular Genetics Center, The Medical College of Wisconsin and Children's Hospital of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA"}]},{"given":"Xujing","family":"Wang","sequence":"additional","affiliation":[{"name":"The Max McGee National Research Center for Juvenile Diabetes & The Human and Molecular Genetics Center, The Medical College of Wisconsin and Children's Hospital of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,9,21]]},"reference":[{"key":"2023041208452756200_","doi-asserted-by":"crossref","first-page":"2730","DOI":"10.1093\/bioinformatics\/bti398","article-title":"Correlation between gene expression profiles and protein\u2013protein interactions within and across genomes","volume":"21","author":"Bhardwaj","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041208452756200_","doi-asserted-by":"crossref","first-page":"2242","DOI":"10.1093\/bioinformatics\/bth234","article-title":"Gene co-expression network topology provides a framework for molecular characterization of cellular state","volume":"20","author":"Carter","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041208452756200_","doi-asserted-by":"crossref","first-page":"361","DOI":"10.6339\/JDS.2003.01(4).172","article-title":"The matrix expression, topological index and atomic attribute of molecular topological structure","volume":"1","author":"Hu","year":"2003","journal-title":"J. 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Biol."},{"key":"2023041208452756200_","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2003","journal-title":"Proc. Natl Acad. Sci. 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