{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T02:16:47Z","timestamp":1775960207496,"version":"3.50.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Identifying candidate genes associated with a given phenotype or trait is an important problem in biological and biomedical studies. Prioritizing genes based on the accumulated information from several data sources is of fundamental importance. Several integrative methods have been developed when a set of candidate genes for the phenotype is available. However, how to prioritize genes for phenotypes when no candidates are available is still a challenging problem.<\/jats:p><jats:p>Results: We develop a new method for prioritizing genes associated with a phenotype by Combining Gene expression and protein Interaction data (CGI). The method is applied to yeast gene expression data sets in combination with protein interaction data sets of varying reliability. We found that our method outperforms the intuitive prioritizing method of using either gene expression data or protein interaction data only and a recent gene ranking algorithm GeneRank. We then apply our method to prioritize genes for Alzheimer's disease.<\/jats:p><jats:p>Availability: The code in this paper is available upon request.<\/jats:p><jats:p>Contact: \u00a0fsun@usc.edu<\/jats:p><jats:p>Supplementary data: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl569","type":"journal-article","created":{"date-parts":[[2006,11,14]],"date-time":"2006-11-14T01:18:26Z","timestamp":1163467106000},"page":"215-221","source":"Crossref","is-referenced-by-count":92,"title":["CGI: a new approach for prioritizing genes by combining gene expression and protein\u2013protein interaction data"],"prefix":"10.1093","volume":"23","author":[{"given":"Xiaotu","family":"Ma","sequence":"first","affiliation":[{"name":"Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California 1 \u00a0 1 \u00a0 \u00a0 Los Angeles, CA 90089-2910, USA"}]},{"given":"Hyunju","family":"Lee","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California 1 \u00a0 1 \u00a0 \u00a0 Los Angeles, CA 90089-2910, USA"},{"name":"Department of Computer Science, University of Southern California 2 \u00a0 2 \u00a0 \u00a0 Los Angeles, CA 90089-2910, USA"}]},{"given":"Li","family":"Wang","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California 1 \u00a0 1 \u00a0 \u00a0 Los Angeles, CA 90089-2910, USA"}]},{"given":"Fengzhu","family":"Sun","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California 1 \u00a0 1 \u00a0 \u00a0 Los Angeles, CA 90089-2910, USA"}]}],"member":"286","published-online":{"date-parts":[[2006,11,10]]},"reference":[{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/nbt1203","article-title":"Gene prioritization through genomic data fusion","volume":"24","author":"Aerts","year":"2006","journal-title":"Nat. Biotechnol."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"2173","DOI":"10.1073\/pnas.0308512100","article-title":"Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumor suppressor responses","volume":"101","author":"Blalock","year":"2004","journal-title":"Proc Natl. Acad. Sci. USA"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1126\/science.1069516","article-title":"Genetic dissection of transcriptional regulation in budding yeast","volume":"296","author":"Brem","year":"2002","journal-title":"Science"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/nature03865","article-title":"Genetic interactions between polymorphisms that affect gene expression in yeast","volume":"436","author":"Brem","year":"2005","journal-title":"Nature"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1002\/jnr.10389","article-title":"Role of mitochondrial dysfunction in Alzheimer's disease","volume":"70","author":"Castellani","year":"2002","journal-title":"J. Neurosci. Res."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/S1097-2765(00)80114-8","article-title":"A genome-wide transcriptional analysis of the mitotic cell cycle","volume":"2","author":"Cho","year":"1998","journal-title":"Mol. Cell"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1093\/biomet\/36.3-4.394","article-title":"The moments of the z and F distributions","volume":"36","author":"David","year":"1949","journal-title":"Biometrika"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1074\/mcp.M100037-MCP200","article-title":"Protein interactions: Two methods for assessment of the reliability of high-throughput observation","volume":"1","author":"Deane","year":"2002","journal-title":"Mol. Cell. Proteom."},{"key":"2023041107034561200_","first-page":"140","article-title":"Assessment of the reliability of protein\u2013protein interactions and protein function prediction","author":"Deng","year":"2003","journal-title":"Pac. Symp. Biocomput. (PSB2003)"},{"key":"2023041107034561200_","first-page":"111","article-title":"Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments","volume":"12","author":"Dudoit","year":"2002","journal-title":"Statistica Sinica"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1126\/science.276.5309.118","article-title":"Bni1p, a yeast formin linking cdc42p and the actin cytoskeleton during polarized morphogenesis","volume":"276","author":"Evangelista","year":"1997","journal-title":"Science"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1086\/504300","article-title":"Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes","volume":"78","author":"Franke","year":"2006","journal-title":"Am. J. Hum. Genet."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"4241","DOI":"10.1091\/mbc.11.12.4241","article-title":"Genomic expression programs in the response of yeast cells to environmental changes","volume":"11","author":"Gasch","year":"2000","journal-title":"Mol. Biol. Cell."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/415141a","article-title":"Functional organization of the yeast proteome by systematic analysis of protein complexes","volume":"415","author":"Gavin","year":"2002","journal-title":"Nature"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1109\/TPAMI.1984.4767596","article-title":"Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images","volume":"6","author":"Geman","year":"1984","journal-title":"IEEE Trans. Patt. Anal. Machine Intell."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"12079","DOI":"10.1073\/pnas.210134797","article-title":"Coupled two-way clustering analysis of gene microarray data","volume":"97","author":"Getz","year":"2000","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/415180a","article-title":"Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry","volume":"415","author":"Ho","year":"2002","journal-title":"Nature"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/S0092-8674(00)00015-5","article-title":"Functional discovery via a compendium of expression profiles","volume":"102","author":"Hughes","year":"2000","journal-title":"Cell"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"S233","DOI":"10.1093\/bioinformatics\/18.suppl_1.S233","article-title":"Discovering regulatory and signalling circuits in molecular interaction networks","volume":"18","author":"Ideker","year":"2002","journal-title":"Bioinformatics"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1073\/pnas.97.3.1143","article-title":"Toward a protein\u2013protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins","author":"Ito","year":"2000","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"4569","DOI":"10.1073\/pnas.061034498","article-title":"A comprehensive two hybrid analysis to explore the yeast protein interactome","volume":"98","author":"Ito","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1101\/gr.205602","article-title":"Relating whole-genome expression data with protein\u2013protein interactions","volume":"12","author":"Jansen","year":"2002","journal-title":"Genome Res."},{"key":"2023041107034561200_","first-page":"315","article-title":"Diffusion kernels on graphs and other discrete inpute spaces","author":"Kondor","year":"2002","journal-title":"Proc. Int. Mach. Learn."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"15148","DOI":"10.1073\/pnas.0404315101","article-title":"Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease","volume":"101","author":"Krauthammer","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1089\/omi.2006.10.40","article-title":"Diffusion kernel based logistic regression models for protein function prediction","volume":"10","author":"Lee","year":"2006","journal-title":"Omics: J. Integr. Biol."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"16875","DOI":"10.1073\/pnas.252466999","article-title":"Genome-wide coexpression dynamics: theory and application","volume":"99","author":"Li","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1016\/j.cell.2006.03.032","article-title":"A protein\u2013protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration","volume":"125","author":"Lim","year":"2006","journal-title":"Cell"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1086\/496902","article-title":"High-resolution whole-genome association study of Parkinson disease","volume":"77","author":"Maraganore","year":"2005","journal-title":"Am. J. Hum. Genet."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1093\/nar\/30.1.31","article-title":"MIPS: a database for genomes and protein sequences","volume":"30","author":"Mewes","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1038\/nature02797","article-title":"Genetic analysis of genome-wide variation in human gene expression","volume":"430","author":"Morley","year":"2004","journal-title":"Nature"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1186\/1471-2105-6-233","article-title":"GeneRank: using search engine technology for the analysis of microarray experiments","volume":"6","author":"Morrison","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"1971","DOI":"10.1101\/gr.206701","article-title":"Is there a bias in proteome research?","volume":"11","author":"Mrowka","year":"2001","journal-title":"Genome Res."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1101\/gr.1680803","article-title":"Development of human protein reference database as an initial platform for approaching systems biology in humans","volume":"13","author":"Peri","year":"2003","journal-title":"Genome Res."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1242\/jcs.113.4.571","article-title":"Polarization of cell growth in yeast","volume":"113(Pt 4)","author":"Pruyne","year":"2000","journal-title":"J. Cell Sci."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1038\/nature04209","article-title":"Towards a proteome-scale map of the human protein\u2013protein interaction network","volume":"437","author":"Rual","year":"2005","journal-title":"Nature"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1093\/bioinformatics\/btg1037","article-title":"Discovering molecular pathways from protein interaction and gene expression data","volume":"19","author":"Segal","year":"2003","journal-title":"Bioinformatics"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","article-title":"Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization","volume":"9","author":"Spellman","year":"1998","journal-title":"Mol. Biol. Cell"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1016\/j.cell.2005.08.029","article-title":"A human protein\u2013protein interaction network: a resource for annotating the proteome","volume":"122","author":"Stelzl","year":"2005","journal-title":"Cell"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"1425","DOI":"10.1101\/gr.180801","article-title":"Creating the gene ontology resource: design and implementation","volume":"11","author":"The Gene Ontology Consortium.","year":"2001","journal-title":"Genome Res."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"6283","DOI":"10.1093\/nar\/gkg838","article-title":"Functional modules by relating protein interaction networks and gene expression","volume":"31","author":"Tornow","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/35001009","article-title":"A comprehensive analysis of protein\u2013protein interactions in Saccharomyces cerevisiae","volume":"403","author":"Uetz","year":"2000","journal-title":"Nature"},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1093\/nar\/30.1.303","article-title":"DIP: The database of interacting proteins: a research tool for studying cellular networks of protein interactions","volume":"30","author":"Xenarios","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023041107034561200_","doi-asserted-by":"crossref","first-page":"12783","DOI":"10.1073\/pnas.192159399","article-title":"Transitive functional annotation by shortest-path analysis of gene expression data","volume":"99","author":"Zhou","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/2\/215\/49820245\/bioinformatics_23_2_215.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/2\/215\/49820245\/bioinformatics_23_2_215.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,9]],"date-time":"2023-05-09T18:27:32Z","timestamp":1683656852000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/2\/215\/204848"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,11,10]]},"references-count":43,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2007,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl569","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,1,15]]},"published":{"date-parts":[[2006,11,10]]}}}