{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,5]],"date-time":"2026-04-05T21:03:53Z","timestamp":1775423033761,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: When identifying differentially expressed (DE) genes from high-throughput gene expression measurements, we would like to take both statistical significance (such as P-value) and biological relevance (such as fold change) into consideration. In gene set enrichment analysis (GSEA), a score that can combine fold change and P-value together is needed for better gene ranking.<\/jats:p><jats:p>Results: We defined a gene significance score \u03c0-value by combining expression fold change and statistical significance (P-value), and explored its statistical properties. When compared to various existing methods, \u03c0-value based approach is more robust in selecting DE genes, with the largest area under curve in its receiver operating characteristic curve. We applied \u03c0-value to GSEA and found it comparable to P-value and t-statistic based methods, with added protection against false discovery in certain situations. Finally, in a gene functional study of breast cancer profiles, we showed that using \u03c0-value helps elucidating otherwise overlooked important biological functions.<\/jats:p><jats:p>Availability: \u00a0http:\/\/gccri.uthscsa.edu\/Pi_Value_Supplementary.asp<\/jats:p><jats:p>Contact: \u00a0xy@ieee.org, cheny8@uthscsa.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr671","type":"journal-article","created":{"date-parts":[[2012,2,10]],"date-time":"2012-02-10T01:22:15Z","timestamp":1328836935000},"page":"801-807","source":"Crossref","is-referenced-by-count":302,"title":["A novel significance score for gene selection and ranking"],"prefix":"10.1093","volume":"30","author":[{"given":"Yufei","family":"Xiao","sequence":"first","affiliation":[{"name":"1 Department of Epidemiology and Biostatistics, 2Computational Biology and Bioinformatics Division, Greehey Children's Cancer Research Institute, 3Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, 4United States Army Institute of Surgical Research, Fort Sam Houston, TX 78234 and 5Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"},{"name":"1 Department of Epidemiology and Biostatistics, 2Computational Biology and Bioinformatics Division, Greehey Children's Cancer Research Institute, 3Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, 4United States Army Institute of Surgical Research, Fort Sam Houston, TX 78234 and 5Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Tzu-Hung","family":"Hsiao","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Biostatistics, 2Computational Biology and Bioinformatics Division, Greehey Children's Cancer Research Institute, 3Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, 4United States Army Institute of Surgical Research, Fort Sam Houston, TX 78234 and 5Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Uthra","family":"Suresh","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Biostatistics, 2Computational Biology and Bioinformatics Division, Greehey Children's Cancer Research Institute, 3Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, 4United States Army Institute of Surgical Research, Fort Sam Houston, TX 78234 and 5Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Hung-I Harry","family":"Chen","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Biostatistics, 2Computational Biology and Bioinformatics Division, Greehey Children's Cancer Research Institute, 3Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, 4United States Army Institute of Surgical Research, Fort Sam Houston, TX 78234 and 5Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Xiaowu","family":"Wu","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Biostatistics, 2Computational Biology and Bioinformatics Division, Greehey Children's Cancer Research Institute, 3Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, 4United States Army Institute of Surgical Research, Fort Sam Houston, TX 78234 and 5Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"},{"name":"1 Department of Epidemiology and Biostatistics, 2Computational Biology and Bioinformatics Division, Greehey Children's Cancer Research Institute, 3Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, 4United States Army Institute of Surgical Research, Fort Sam Houston, TX 78234 and 5Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Steven E.","family":"Wolf","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Biostatistics, 2Computational Biology and Bioinformatics Division, Greehey Children's Cancer Research Institute, 3Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, 4United States Army Institute of Surgical Research, Fort Sam Houston, TX 78234 and 5Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"},{"name":"1 Department of Epidemiology and Biostatistics, 2Computational Biology and Bioinformatics Division, Greehey Children's Cancer Research Institute, 3Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, 4United States Army Institute of Surgical Research, Fort Sam Houston, TX 78234 and 5Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Yidong","family":"Chen","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Biostatistics, 2Computational Biology and Bioinformatics Division, Greehey Children's Cancer Research Institute, 3Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, 4United States Army Institute of Surgical Research, Fort Sam Houston, TX 78234 and 5Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, 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