{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T22:11:43Z","timestamp":1775167903655,"version":"3.50.1"},"reference-count":96,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2013,3,14]],"date-time":"2013-03-14T00:00:00Z","timestamp":1363219200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002957","type":"journal-article","created":{"date-parts":[[2013,3,14]],"date-time":"2013-03-14T23:39:22Z","timestamp":1363304362000},"page":"e1002957","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":60,"title":["Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes"],"prefix":"10.1371","volume":"9","author":[{"given":"Christopher Y.","family":"Park","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aaron K.","family":"Wong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Casey S.","family":"Greene","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica","family":"Rowland","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuanfang","family":"Guan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lars A.","family":"Bongo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rebecca D.","family":"Burdine","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olga G.","family":"Troyanskaya","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2013,3,14]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1186\/gb-2008-9-s1-s3","article-title":"Predicting gene function in a hierarchical context with an ensemble of classifiers","volume":"9","author":"Y Guan","year":"2008","journal-title":"Genome Biology"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/gb-2008-9-s1-s4","article-title":"GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function","volume":"9","author":"S Mostafavi","year":"2008","journal-title":"Genome Biology"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1101\/gr.9.12.1198","article-title":"Prediction of Gene Function by Genome-Scale Expression Analysis: Prostate Cancer-Associated Genes","volume":"9","author":"MG Walker","year":"1999","journal-title":"Genome Research"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/ng906","article-title":"Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters","volume":"31","author":"LF Wu","year":"2002","journal-title":"Nat Genet"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"2005.0026","DOI":"10.1038\/msb4100034","article-title":"Gene function prediction from congruent synthetic lethal interactions in yeast","volume":"1","author":"P Ye","year":"2005","journal-title":"Mol Syst Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1186\/gb-2008-9-s1-s5","article-title":"Inferring mouse gene functions from genomic-scale data using a combined functional network\/classification strategy","volume":"9","author":"W Kim","year":"2008","journal-title":"Genome Biology"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/gb-2008-9-s1-s2","article-title":"A critical assessment of Mus musculus gene function prediction using integrated genomic evidence","volume":"9","author":"L Pena-Castillo","year":"2008","journal-title":"Genome Biology"},{"key":"ref8","doi-asserted-by":"crossref","unstructured":"Pavlidis P, Weston J, Cai J, Grundy WN (2001) Gene functional classification from heterogeneous data. Proceedings of the fifth annual international conference on Computational biology. Montreal, Quebec, Canada: ACM. pp. 249\u2013255.","DOI":"10.1145\/369133.369228"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"R114","DOI":"10.1186\/gb-2005-6-13-r114","article-title":"Discovery of biological networks from diverse functional genomic data","volume":"6","author":"CL Myers","year":"2005","journal-title":"Genome Biol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1759","DOI":"10.1093\/bioinformatics\/btq262","article-title":"Fast integration of heterogeneous data sources for predicting gene function with limited annotation","volume":"26","author":"S Mostafavi","year":"2010","journal-title":"Bioinformatics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"W368","DOI":"10.1093\/nar\/gkr440","article-title":"PILGRM: an interactive data-driven discovery platform for expert biologists","volume":"39","author":"CS Greene","year":"2011","journal-title":"Nucleic Acids Research"},{"key":"ref12","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":"TR Hughes","year":"2000","journal-title":"Cell"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/47048","article-title":"A combined algorithm for genome-wide prediction of protein function","volume":"402","author":"EM Marcotte","year":"1999","journal-title":"Nature"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1016\/S0022-2836(02)00379-0","article-title":"Prediction of Human Protein Function from Post-translational Modifications and Localization Features","volume":"319","author":"LJ Jensen","year":"2002","journal-title":"Journal of Molecular Biology"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1093\/bioinformatics\/btk048","article-title":"Hierarchical multi-label prediction of gene function","volume":"22","author":"Z Barutcuoglu","year":"2006","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1038\/nbt825","article-title":"Global protein function prediction from protein-protein interaction networks","volume":"21","author":"A Vazquez","year":"2003","journal-title":"Nat Biotech"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"e1000407","DOI":"10.1371\/journal.pgen.1000407","article-title":"Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis","volume":"5","author":"DC Hess","year":"2009","journal-title":"PLoS Genet"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1038\/nbt.1603","article-title":"Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana","volume":"28","author":"I Lee","year":"2010","journal-title":"Nat Biotech"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","article-title":"Cluster analysis and display of genome-wide expression patterns","volume":"95","author":"MB Eisen","year":"1998","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref20","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":"A Subramanian","year":"2005","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1101\/gr.8.3.163","article-title":"Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis","volume":"8","author":"JA Eisen","year":"1998","journal-title":"Genome Research"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"D572","DOI":"10.1093\/nar\/gkj118","article-title":"TreeFam: a curated database of phylogenetic trees of animal gene families","volume":"34","author":"H Li","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"D476","DOI":"10.1093\/nar\/gki107","article-title":"Inparanoid: a comprehensive database of eukaryotic orthologs","volume":"33","author":"KP O'Brien","year":"2005","journal-title":"Nucleic Acids Research"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1904","DOI":"10.1073\/pnas.96.5.1904","article-title":"Angiopoietins 3 and 4: Diverging gene counterparts in mice and humans","volume":"96","author":"DM Valenzuela","year":"1999","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"e1001074","DOI":"10.1371\/journal.pcbi.1001074","article-title":"Accurate quantification of functional analogy among close homologs","volume":"7","author":"MD Chikina","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"W484","DOI":"10.1093\/nar\/gks458","article-title":"IMP: A multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks","volume":"40","author":"AK Wong","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1038\/nbt1206-1565","article-title":"What is a support vector machine?","volume":"24","author":"WS Noble","year":"2006","journal-title":"Nat Biotech"},{"key":"ref28","first-page":"1871","article-title":"LIBLINEAR: A Library for Large Linear Classification","volume":"9","author":"R-E Fan","year":"2008","journal-title":"J Mach Learn Res"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random Forests","volume":"45","author":"L Breiman","year":"2001","journal-title":"Machine Learning"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1038\/nprot.2011.372","article-title":"Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network","volume":"6","author":"S Hwang","year":"2011","journal-title":"Nat Protocols"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"4851","DOI":"10.1093\/emboj\/cdf481","article-title":"A role for cell polarity proteins in mitotic exit","volume":"21","author":"T Hofken","year":"2002","journal-title":"EMBO J"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1002\/dvdy.20551","article-title":"Smaller inner ear sensory epithelia in Neurog1 null mice are related to earlier hair cell cycle exit","volume":"234","author":"V Matei","year":"2005","journal-title":"Developmental Dynamics"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1595","DOI":"10.1016\/S0960-9822(01)00483-3","article-title":"mei-41 and bub1 block mitosis at two distinct steps in response to incomplete DNA replication in Drosophila embryos","volume":"11","author":"M Garner","year":"2001","journal-title":"Current Biology"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.mod.2010.03.004","article-title":"Mutations in N-cadherin and a Stardust homolog, Nagie oko, affect cell-cycle exit in zebrafish retina","volume":"127","author":"M Yamaguchi","year":"2010","journal-title":"Mechanisms of Development"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1126\/science.2683079","article-title":"Checkpoints: controls that ensure the order of cell cycle events","volume":"246","author":"L Hartwell","year":"1989","journal-title":"Science"},{"key":"ref37","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":"AP Gasch","year":"2000","journal-title":"Mol Biol Cell"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1242\/dev.117.1.97","article-title":"Changing patterns of gene expression define four stages of cerebellar granule neuron differentiation","volume":"117","author":"SG Kuhar","year":"1993","journal-title":"Development"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1629","DOI":"10.1126\/science.1062660","article-title":"Patterns of Gene Expression During Drosophila Mesoderm Development","volume":"293","author":"EEM Furlong","year":"2001","journal-title":"Science"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.neuron.2004.12.036","article-title":"Neuronal Subtype-Specific Genes that Control Corticospinal Motor Neuron Development In Vivo","volume":"45","author":"P Arlotta","year":"2005","journal-title":"Neuron"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1678","DOI":"10.4161\/cc.7.11.6011","article-title":"A global genomic view of MIF knockdown-mediated cell cycle arrest","volume":"7","author":"L Liu","year":"2008","journal-title":"Cell Cycle"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1042\/BJ20060057","article-title":"Phenotypic responses to mechanical stress in fibroblasts from tendon, cornea and skin","volume":"396","author":"JR Mackley","year":"2006","journal-title":"Biochemical Journal"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"e237","DOI":"10.1371\/journal.pbio.0050237","article-title":"High-Throughput In Vivo Analysis of Gene Expression in <italic>Caenorhabditis elegans<\/italic>","volume":"5","author":"R Hunt-Newbury","year":"2007","journal-title":"PLoS Biol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1038\/nature04250","article-title":"Glyoxalase 1 and glutathione reductase 1 regulate anxiety in mice","volume":"438","author":"I Hovatta","year":"2005","journal-title":"Nature"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"R48","DOI":"10.1186\/gb-2005-6-6-r48","article-title":"Mechanisms of aging in senescence-accelerated mice","volume":"6","author":"T Carter","year":"2005","journal-title":"Genome Biology"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ydbio.2005.07.038","article-title":"Left\u2013right asymmetry and congenital cardiac defects: Getting to the heart of the matter in vertebrate left\u2013right axis determination","volume":"288","author":"AF Ramsdell","year":"2005","journal-title":"Developmental Biology"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"2241","DOI":"10.1016\/j.jacc.2011.08.025","article-title":"Birth Prevalence of Congenital Heart Disease Worldwide: A Systematic Review and Meta-Analysis","volume":"58","author":"D van der Linde","year":"2011","journal-title":"Journal of the American College of Cardiology"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"13924","DOI":"10.1073\/pnas.0802159105","article-title":"Direct and indirect roles for Nodal signaling in two axis conversions during asymmetric morphogenesis of the zebrafish heart","volume":"105","author":"K Baker","year":"2008","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1016\/j.devcel.2007.11.015","article-title":"Rotation and Asymmetric Development of the Zebrafish Heart Requires Directed Migration of Cardiac Progenitor Cells","volume":"14","author":"KA Smith","year":"2008","journal-title":"Developmental Cell"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"e12","DOI":"10.1161\/CIRCRESAHA.107.165241","article-title":"Asymmetric Involution of the Myocardial Field Drives Heart Tube Formation in Zebrafish","volume":"102","author":"S Rohr","year":"2008","journal-title":"Circulation Research"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"3624","DOI":"10.1002\/dvdy.21777","article-title":"Nodal signaling promotes the speed and directional movement of cardiomyocytes in zebrafish","volume":"237","author":"MIM de Campos-Baptista","year":"2008","journal-title":"Developmental Dynamics"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"3640","DOI":"10.1002\/dvdy.21771","article-title":"Initiation and propagation of posterior to anterior (PA) waves in zebrafish left\u2013right development","volume":"237","author":"X Wang","year":"2008","journal-title":"Developmental Dynamics"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"5101","DOI":"10.1242\/dev.127.23.5101","article-title":"Asymmetric nodal signaling in the zebrafish diencephalon positions the pineal organ","volume":"127","author":"JO Liang","year":"2000","journal-title":"Development"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1242\/dev.01663","article-title":"Kupffer&apos;s vesicle is a ciliated organ of asymmetry in the zebrafish embryo that initiates left-right development of the brain, heart and gut","volume":"132","author":"JJ Essner","year":"2005","journal-title":"Development"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1006\/dbio.1999.9441","article-title":"casanova Plays an Early and Essential Role in Endoderm Formation in Zebrafish","volume":"215","author":"J Alexander","year":"1999","journal-title":"Developmental Biology"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1006\/dbio.1998.8935","article-title":"Zebrafish Nodal-Related Genes Are Implicated in Axial Patterning and Establishing Left\u2013Right Asymmetry","volume":"199","author":"MR Rebagliati","year":"1998","journal-title":"Developmental Biology"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"2389","DOI":"10.1242\/dev.061473","article-title":"Zebrafish cardiac development requires a conserved secondary heart field","volume":"138","author":"D Hami","year":"2011","journal-title":"Development"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"2129","DOI":"10.1016\/S0960-9822(02)01361-1","article-title":"Lefty Antagonism of Squint Is Essential for Normal Gastrulation","volume":"12","author":"B Feldman","year":"2002","journal-title":"Current Biology"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"4405","DOI":"10.1242\/dev.071092","article-title":"Two additional midline barriers function with midline lefty1 expression to maintain asymmetric Nodal signaling during left-right axis specification in zebrafish","volume":"138","author":"KF Lenhart","year":"2011","journal-title":"Development"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"e1002289","DOI":"10.1371\/journal.pgen.1002289","article-title":"Bmp and Nodal Independently Regulate <italic>lefty1<\/italic> Expression to Maintain Unilateral Nodal Activity during Left-Right Axis Specification in Zebrafish","volume":"7","author":"KA Smith","year":"2011","journal-title":"PLoS Genet"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"e26548","DOI":"10.1371\/journal.pone.0026548","article-title":"Def6 Is Required for Convergent Extension Movements during Zebrafish Gastrulation Downstream of Wnt5b Signaling","volume":"6","author":"K Goudevenou","year":"2011","journal-title":"PLoS ONE"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"reviews1015.1011","DOI":"10.1186\/gb-2001-2-5-reviews1015","article-title":"Morpholino antisense oligonucleotides: tools for investigating vertebrate development","volume":"2","author":"D Corey","year":"2001","journal-title":"Genome Biology"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1242\/jcs.077156","article-title":"Centriolar satellites are assembly points for proteins implicated in human ciliopathies, including oral-facial-digital syndrome 1","volume":"124","author":"CAM Lopes","year":"2011","journal-title":"Journal of Cell Science"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.ydbio.2009.10.025","article-title":"The Zn Finger protein Iguana impacts Hedgehog signaling by promoting ciliogenesis","volume":"337","author":"AM Glazer","year":"2010","journal-title":"Developmental Biology"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"2980","DOI":"10.1002\/dvdy.22431","article-title":"Sox17 and chordin are required for formation of Kupffer&apos;s vesicle and left-right asymmetry determination in zebrafish","volume":"239","author":"E Aamar","year":"2010","journal-title":"Developmental Dynamics"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"8348","DOI":"10.1073\/pnas.0832373100","article-title":"A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)","volume":"100","author":"OG Troyanskaya","year":"2003","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1126\/science.1099511","article-title":"A Probabilistic Functional Network of Yeast Genes","volume":"306","author":"I Lee","year":"2004","journal-title":"Science"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1038\/nbt1103","article-title":"Probabilistic model of the human protein-protein interaction network","volume":"23","author":"DR Rhodes","year":"2005","journal-title":"Nat Biotech"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1101\/gr.082214.108","article-title":"Exploring the human genome with functional maps","volume":"19","author":"C Huttenhower","year":"2009","journal-title":"Genome Research"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"D698","DOI":"10.1093\/nar\/gkq1116","article-title":"The BioGRID Interaction Database: 2011 update","volume":"39","author":"C Stark","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"D841","DOI":"10.1093\/nar\/gkr1088","article-title":"The IntAct molecular interaction database in 2012","volume":"40","author":"S Kerrien","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"D857","DOI":"10.1093\/nar\/gkr930","article-title":"MINT, the molecular interaction database: 2012 update","volume":"40","author":"L Licata","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/nar\/28.1.37","article-title":"MIPS: a database for genomes and protein sequences","volume":"28","author":"HW Mewes","year":"2000","journal-title":"Nucleic Acids Research"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkq964","article-title":"YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface","volume":"39","author":"D Abdulrehman","year":"2011","journal-title":"Nucleic Acids Research"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"D91","DOI":"10.1093\/nar\/gkh012","article-title":"JASPAR: an open access database for eukaryotic transcription factor binding profiles","volume":"32","author":"A Sandelin","year":"2004","journal-title":"Nucleic Acids Research"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1093\/bioinformatics\/btr064","article-title":"FIMO: scanning for occurrences of a given motif","volume":"27","author":"CE Grant","year":"2011","journal-title":"Bioinformatics"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1093\/nar\/26.1.73","article-title":"SGD: Saccharomyces Genome Database","volume":"26","author":"JM Cherry","year":"1998","journal-title":"Nucleic Acids Research"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"D724","DOI":"10.1093\/nar\/gkm961","article-title":"The Mouse Genome Database (MGD): mouse biology and model systems","volume":"36","author":"CJ Bult","year":"2008","journal-title":"Nucleic Acids Research"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1093\/nar\/29.1.82","article-title":"WormBase: network access to the genome and biology of Caenorhabditis elegans","volume":"29","author":"L Stein","year":"2001","journal-title":"Nucleic Acids Research"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"D390","DOI":"10.1093\/nar\/gki046","article-title":"FlyBase: genes and gene models","volume":"33","author":"RA Drysdale","year":"2005","journal-title":"Nucleic Acids Research"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1093\/nar\/gkg027","article-title":"The Zebrafish Information Network (ZFIN): the zebrafish model organism database","volume":"31","author":"J Sprague","year":"2003","journal-title":"Nucleic Acids Research"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"bar049","DOI":"10.1093\/database\/bar049","article-title":"BioMart: driving a paradigm change in biological data management","volume":"2011","author":"A Kasprzyk","year":"2011","journal-title":"Database"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"D138","DOI":"10.1093\/nar\/gkh121","article-title":"The Pfam protein families database","volume":"32","author":"A Bateman","year":"2004","journal-title":"Nucleic Acids Research"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"D227","DOI":"10.1093\/nar\/gkj063","article-title":"The PROSITE database","volume":"34","author":"N Hulo","year":"2006","journal-title":"Nucleic Acids Research"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1186\/1471-2164-7-187","article-title":"Finding function: evaluation methods for functional genomic data","volume":"7","author":"C Myers","year":"2006","journal-title":"BMC Genomics"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/978-1-61779-400-1_2","article-title":"The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals","volume":"802","author":"M Kotera","year":"2012","journal-title":"Methods Mol Biol"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"D674","DOI":"10.1093\/nar\/gkn653","article-title":"PID: the Pathway Interaction Database","volume":"37","author":"CF Schaefer","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"D742","DOI":"10.1093\/nar\/gkr1014","article-title":"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway\/genome databases","volume":"40","author":"R Caspi","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"e1000991","DOI":"10.1371\/journal.pcbi.1000991","article-title":"Functional genomics complements quantitative genetics in identifying disease-gene associations","volume":"6","author":"Y Guan","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref90","unstructured":"John CP (1999) Probabilistic Outputs for Support Vector Machines and Comparisons to Regularized Likelihood Methods. MIT Press."},{"key":"ref91","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1080\/00401706.2000.10485983","article-title":"Ridge regression: biased estimation for nonorthogonal problems","volume":"42","author":"AE Hoerl","year":"2000","journal-title":"Technometrics"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1111\/j.1467-9868.2011.00771.x","article-title":"Regression shrinkage and selection via the lasso","volume":"73","author":"R Tibshirani","year":"1994","journal-title":"J R Statist Soc B"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1471-2105-7-3","article-title":"Gene selection and classification of microarray data using random forest","volume":"7","author":"R Diaz-Uriarte","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1093\/bioinformatics\/btn237","article-title":"The Sleipnir library for computational functional genomics","volume":"24","author":"C Huttenhower","year":"2008","journal-title":"Bioinformatics"},{"key":"ref95","doi-asserted-by":"crossref","unstructured":"Joachims T (2006) Training linear SVMs in linear time. Proceedings of the 12th ACM SIGKDD international conference on Knowledge discovery and data mining. Philadelphia, PA, USA: ACM. pp. 217\u2013226.","DOI":"10.1145\/1150402.1150429"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1002\/dvdy.10356","article-title":"Germ-line transmission of a myocardium-specific GFP transgene reveals critical regulatory elements in the cardiac myosin light chain 2 promoter of zebrafish","volume":"228","author":"C-J Huang","year":"2003","journal-title":"Developmental Dynamics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002957","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T09:03:12Z","timestamp":1688115792000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002957"}},"subtitle":[],"editor":[{"given":"Greg","family":"Tucker-Kellogg","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2013,3,14]]},"references-count":96,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2013,3,14]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002957","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,3,14]]}}}