A Resource of Quantitative Functional Annotation forHomo sapiensGenes
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Barrell, 2009, The GOA database in 2009–an integrated Gene Ontology Annotation resource, Nucleic Acids Res., 37, 396, 10.1093/nar/gkn803
Barrett, 2009, NCBI GEO: archive for high-throughput functional genomic data, Nucleic Acids Res., 37, D885, 10.1093/nar/gkn764
Beaver, 2010, FuncBase: a resource for quantitative gene function annotation, Bioinformatics, 26, 1806, 10.1093/bioinformatics/btq265
Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc., B, 57, 289, 10.1111/j.2517-6161.1995.tb02031.x
Berriz, 2008, The Synergizer service for translating gene, protein and other biological identifiers, Bioinformatics, 24, 2272, 10.1093/bioinformatics/btn424
Bieri, 2007, WormBase: new content and better access, Nucleic Acids Res., 35, 506, 10.1093/nar/gkl818
Bologna, G., A.-L. Veuthey, M. Pagni, L. Lane, and A. Bairoch 2011 A preliminary study on the prediction of human protein functions, in ‘Proceedings of the 4th international conference on Interplay between natural and artificial computation - Volume Part I’, IWINAC’11, Springer-Verlag, Berlin, Heidelberg, pp. 334–343. Available at:http://dl.acm.org/citation.cfm?id=2009405.2009440
Bredel, 2005, Functional network analysis reveals extended gliomagenesis pathway maps and three novel MYC-interacting genes in human gliomas, Cancer Res., 65, 8679, 10.1158/0008-5472.CAN-05-1204
Dai, 2005, Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data, Nucleic Acids Res., 33, e175, 10.1093/nar/gni179
Deng, 2004, An integrated probabilistic model for functional prediction of proteins, J. Comput. Biol., 11, 463, 10.1089/1066527041410346
Eppig, 2007, The mouse genome database (mgd): new features facilitating a model system, Nucleic Acids Res., 35, D630, 10.1093/nar/gkl940
Gunsalus, 2004, RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects, Nucleic Acids Res., 32, D406, 10.1093/nar/gkh110
Gunsalus, 2005, Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis, Nature, 436, 861, 10.1038/nature03876
Hamosh, 2005, Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders, Nucleic Acids Res., 33, 514, 10.1093/nar/gki033
Huttenhower, 2009, Exploring the human genome with functional maps, Genome Res., 19, 1093, 10.1101/gr.082214.108
Huttenhower, 2010, A quick guide to large-scale genomic data mining, PLOS Comput. Biol., 6, e1000779, 10.1371/journal.pcbi.1000779
Joshi, 2004, Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae, OMICS, 8, 322, 10.1089/omi.2004.8.322
Karaoz, 2004, Whole-genome annotation by using evidence integration in functional-linkage networks, Proc. Natl. Acad. Sci. USA, 101, 2888, 10.1073/pnas.0307326101
Keshava Prasad, 2009, Human Protein Reference Database–2009 update, Nucleic Acids Res., 37, D767, 10.1093/nar/gkn892
King, 2003, Predicting phenotype from patterns of annotation, Bioinformatics, 19, 183, 10.1093/bioinformatics/btg1024
Ko, 2009, Integrative approaches to the prediction of protein functions based on the feature selection, BMC Bioinformatics, 10, 455, 10.1186/1471-2105-10-455
Lanckriet, 2004, A statistical framework for genomic data fusion, Bioinformatics, 20, 2626, 10.1093/bioinformatics/bth294
Lee, 2004, A probabilistic functional network of yeast genes, Science, 306, 1555, 10.1126/science.1099511
Lee, 2010, Predicting genetic modifier loci using functional gene networks, Genome Res., 20, 1143, 10.1101/gr.102749.109
Lee, 2011, Prioritizing candidate disease genes by network-based boosting of genome-wide association data, Genome Res., 21, 1109, 10.1101/gr.118992.110
Letovsky, 2003, Predicting protein function from protein/protein interaction data: a probabilistic approach, Bioinformatics, 19, 197, 10.1093/bioinformatics/btg1026
Li, 2005, LRP5/6 in Wnt signaling and tumorigenesis, Future Oncol., 1, 673, 10.2217/14796694.1.5.673
Linghu, 2009, Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network, Genome Biol., 10, R91, 10.1186/gb-2009-10-9-r91
Luu, 2004, Wnt/beta-catenin signaling pathway as a novel cancer drug target, Curr. Cancer Drug Targets, 4, 653, 10.2174/1568009043332709
Mulder, 2005, InterPro, progress and status in 2005, Nucleic Acids Res., 33, 201, 10.1093/nar/gki106
Nash, 2007, Expanded protein information at SGD: new pages and proteome browser, Nucleic Acids Res., 35, 468, 10.1093/nar/gkl931
O’Brien, 2005, Inparanoid: a comprehensive database of eukaryotic orthologs, Nucleic Acids Res., 33, 476, 10.1093/nar/gki107
Pena-Castillo, 2008, A critical assessment of Mus musculus gene function prediction using integrated genomic evidence, Genome Biol., 9, S2, 10.1186/gb-2008-9-s1-s2
Piekutowska-Abramczuk, 2009, The frequency of NBN molecular variants in pediatric astrocytic tumors, J. Neuro-oncol., 96, 161, 10.1007/s11060-009-9958-5
Pujana, 2007, Network modeling links breast cancer susceptibility and centrosome dysfunction, Nat. Genet., 39, 1338, 10.1038/ng.2007.2
Schwikowski, 2000, A network of protein-protein interactions in yeast, Nat. Biotechnol., 18, 1257, 10.1038/82360
Shete, 2009, Genome-wide association study identifies five susceptibility loci for glioma, Nat. Genet., 41, 899, 10.1038/ng.407
Smith, 2005, The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information, Genome Biol., 6, R7, 10.1186/gb-2004-6-1-r7
Sokolov, 2010, Hierarchical classification of gene ontology terms using the GOstruct method, J. Bioinform. Comput. Biol., 8, 357, 10.1142/S0219720010004744
Szklarczyk, 2011, The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored, Nucleic Acids Res., 39, D561, 10.1093/nar/gkq973
Tasan, 2008, An en masse phenotype and function prediction system for Mus musculus, Genome Biol., 9, S8, 10.1186/gb-2008-9-s1-s8
Tian, 2008, Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function, Genome Biol., 9, S7, 10.1186/gb-2008-9-s1-s7
Troyanskaya, 2003, A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae), Proc. Natl. Acad. Sci. USA, 100, 8348, 10.1073/pnas.0832373100
Wang, 2010, ‘It’s the machine that matters: predicting gene function and phenotype from protein networks’, J. Proteomics, 73, 2277, 10.1016/j.jprot.2010.07.005
Wong, 2004, Combining biological networks to predict genetic interactions, Proc. Natl. Acad. Sci. USA, 101, 15682, 10.1073/pnas.0406614101