Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. Nat Genet. 2000, 25: 25-29. 10.1038/75556.
Article
PubMed Central
CAS
PubMed
Google Scholar
Resnik P: Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language. J Art Intel Res. 1999, 11: 95-130.
Google Scholar
Schlicker A, Domingues FS, Rahnenfuhrer J, Lengauer T: A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics. 2006, 7: 302-10.1186/1471-2105-7-302.
Article
PubMed Central
PubMed
Google Scholar
Yu H, Gao L, Tu K, Guo Z: Broadly predicting specific gene functions with expression similarity and taxonomy similarity. Gene. 2005, 352: 75-81.
Article
CAS
PubMed
Google Scholar
Wang JZ, Du ZD, Payattakool R, Yu PS, Chen CF: A new method to measure the semantic similarity of GO terms. Bioinformatics. 2007, 23 (10): 1274-1281. 10.1093/bioinformatics/btm087.
Article
CAS
PubMed
Google Scholar
Kumar A, Smith B, Borgelt C: Dependence relationships between Gene Ontology terms based on TIGR gene product annotations. Proceedings of the 3rd International Workshop on Computational Terminology (CompuTerm 2004). 2004, 31-38.
Google Scholar
Myhre S, Tveit H, Mollestad T, Lægreid A: Additional gene ontology structure for improved biological reasoning. Bioinformatics. 2006, 22 (16): 2020-2027. 10.1093/bioinformatics/btl334.
Article
CAS
PubMed
Google Scholar
Bodenreider O, Aubry M, Burgun A: Non-lexical approaches to identifying associative relations in the gene ontology. Proceedings of the Pacific Symposium on Biocomputing. 2005, 91-102.
Google Scholar
Sevilla JL, Segura V, Podhorski A, Guruceaga E, Mato JM, Martinez-Cruz LA, Corrales FJ, Rubio A: Correlation between gene expression and GO semantic similarity. IEEE ACM T Comput Bi. 2005, 2 (4): 330-338.
CAS
Google Scholar
Mistry M, Pavlidis P: Gene ontology term overlap as a measure of gene functional similarity. BMC bioinformatics. 2008, 9: 327-10.1186/1471-2105-9-327.
Article
PubMed Central
PubMed
Google Scholar
Baeza-Yates R, Ribeiro-Neto B: Modern Information Retrieval. 1999, Addison-Wesley New York
Google Scholar
Rhee SY, Wood V, Dolinski K, Draghici S: Use and misuse of the gene ontology annotations. Nat Rev Genet. 2008, 9 (7): 509-515. 10.1038/nrg2363.
Article
CAS
PubMed
Google Scholar
Bebek G, Koyutürk M, Price N, Chance M: Network biology methods integrating biological data for translational science. Brief Bioinform. 2012, 13 (3): 446-459.
Article
PubMed Central
PubMed
Google Scholar
Savage R, Ghahramani Z, Griffin J, Bernard J, Wild D: Discovering transcriptional modules by Bayesian data integration. Bioinformatics. 2010, 26 (12): i158-i167. 10.1093/bioinformatics/btq210.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lee I, Li ZH, Marcotte EM: An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae. PLoS ONE. 2007, 2 (10): e988-10.1371/journal.pone.0000988.
Article
PubMed Central
PubMed
Google Scholar
Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY: Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol. 2010, 28 (2): 149-156. 10.1038/nbt.1603.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lee I, Blom U, Wang P, Shim J, Marcotte E: Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res. 2011, 21 (7): 1109-1121. 10.1101/gr.118992.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ogren P, Cohen K, Acquaah-Mensah G, Eberlein J, Hunter L: The compositional structure of Gene Ontology terms. Proceedings of the Pacific Symposium on Biocomputing. 2004, 214-225.
Google Scholar
O'Madadhain J, Fisher D, Smyth P, White S, Boey Y: Analysis and visualization of network data using JUNG. J Stat Software. 2005, 10 (2): 1-25.
Google Scholar
Hill DP, Davis AP, Richardson JE, Corradi JP, Ringwald M, Eppig JT, Blake JA: Program description: Strategies for biological annotation of mammalian systems: implementing gene ontologies in mouse genome informatics. Genomics. 2001, 74: 121-8. 10.1006/geno.2001.6513.
Article
CAS
PubMed
Google Scholar
Camon E, Barrell D, Dimmer E, Lee V, Magrane M, Maslen J, Binns D, Apweiler R: An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics. 2005, 6 (Suppl 1): S17-10.1186/1471-2105-6-S1-S17.
Article
PubMed Central
PubMed
Google Scholar
Caspi R, Foerster H, Fulcher C, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee S, Christophe T, Zhang P, Karp PD: MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2006, 34 (suppl 1): D511-D516.
Article
PubMed Central
CAS
PubMed
Google Scholar
Heagerty P, Zheng Y: Survival model predictive accuracy and ROC curves. Biometrics. 2005, 61: 92-105. 10.1111/j.0006-341X.2005.030814.x.
Article
PubMed
Google Scholar
Yukawa M, Sakon M, Kambayashi J, Shiba E, Kawasaki T, Ariyoshi H, Mori T: Proteasome and its novel endogeneous activator in human platelets. Biochem Biophys Res Commun. 1991, 178: 256-262. 10.1016/0006-291X(91)91807-O.
Article
CAS
PubMed
Google Scholar
Hill DP, Davis AP, Richardson JE, Corradi JP, Ringwald M, Eppig JT, Blake JA: Gene Ontology: tool for the unification of biology. Nat Genet. 2000, 25: 25-29. 10.1038/75556.
Article
PubMed Central
PubMed
Google Scholar
Zetka M, Kawasaki I, Strome S, Müller F: Synapsis and chiasma formation in Caenorhabditis elegans require HIM-3, a meiotic chromosome core component that functions in chromosome segregation. Genes & Dev. 1999, 13 (17): 2258-2270. 10.1101/gad.13.17.2258.
Article
CAS
Google Scholar
Jia Z, Moulson C, Pei Z, Miner J, Watkins P: Fatty acid transport protein 4 is the principal very long chain fatty acyl-CoA synthetase in skin fibroblasts. J Biol Chem. 2007, 282 (28): 20573-20583. 10.1074/jbc.M700568200.
Article
CAS
PubMed
Google Scholar
Nikolov D, Burley S: RNA polymerase II transcription initiation: a structural view. P Natl Acad Sci USA. 1997, 94: 15-22. 10.1073/pnas.94.1.15.
Article
CAS
Google Scholar
Grandin N, Charbonneau M: Hsp90 levels affect telomere length in yeast. Mol Genet Genomics. 2001, 265: 126-134. 10.1007/s004380000398.
Article
CAS
PubMed
Google Scholar
Taipale M, Jarosz D, Lindquist S: HSP90 at the hub of protein homeostasis: emerging mechanistic insights. Nat Rev Mol Cell Bio. 2010, 11 (7): 515-528. 10.1038/nrm2918.
Article
CAS
Google Scholar
Zetka M, Kawasaki I, Strome S, Müller F: Synapsis and chiasma formation in Caenorhabditis elegans require HIM-3, a meiotic chromosome core component that functions in chromosome segregation. Genetics. 2003, 163 (1): 69-77.
Google Scholar
Caspi R, Foerster H, Fulcher C, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee S, Shearer A, Tissier C, Walk TC, Zhang P, Karp PD: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2008, 36 (suppl 1): D623-D631.
PubMed Central
CAS
PubMed
Google Scholar
Liekens A, De Knijf J, Daelemans W, Goethals B, De Rijk P, Del-Favero J: BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation. Genome Biology. 2011, 12 (6): R57-10.1186/gb-2011-12-6-r57.
Article
PubMed Central
PubMed
Google Scholar
Hoffmann E, Borts R: Meiotic recombination intermediates and mismatch repair proteins. Cytogenet Genome Res. 2004, 107 (3-4): 232-248. 10.1159/000080601.
Article
CAS
PubMed
Google Scholar
Bandipalliam P: Syndrome of early onset colon cancers, hematologic malignancies & features of neurofibromatosis in HNPCC families with homozygous mismatch repair gene mutations. Familial Cancer. 2005, 4 (4): 323-333. 10.1007/s10689-005-8351-6.
Article
CAS
PubMed
Google Scholar
Subramanian D, Griffith J: Interactions between p53, hMSH2-hMSH6 and HMG I (Y) on Holliday junctions and bulged bases. Nucleic Acids Res. 2002, 30 (11): 2427-2434. 10.1093/nar/30.11.2427.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bardwell A, Bardwell L, Iyer N, Svejstrup J, Feaver W, Kornberg R, Friedberg E: Yeast nucleotide excision repair proteins Rad2 and Rad4 interact with RNA polymerase II basal transcription factor b (TFIIH). Mol Cell Biol. 1994, 14 (6): 3569-3576.
Article
PubMed Central
CAS
PubMed
Google Scholar
Comai L, Tanese N, Tjian R: The TATA-binding protein and associated factors are integral components of the RNA polymerase I transcription factor, SL1. Cell. 1992, 68 (5): 965-976. 10.1016/0092-8674(92)90039-F.
Article
CAS
PubMed
Google Scholar
Wang Z, Buratowski S, Svejstrup J, Feaver W, Wu X, Kornberg R, Donahue T, Friedberg E: The yeast TFB1 and SSL1 genes, which encode subunits of transcription factor IIH, are required for nucleotide excision repair and RNA polymerase II transcription. Mol Cell Biol. 1995, 15 (4): 2288-2293.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pavri R, Zhu B, Li G, Trojer P, Mandal S, Shilatifard A, Reinberg D: Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell. 2006, 125 (4): 703-717. 10.1016/j.cell.2006.04.029.
Article
CAS
PubMed
Google Scholar
Exinger F, Lacroute F: 6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae. Curr Genet. 1992, 22: 9-11. 10.1007/BF00351735.
Article
CAS
PubMed
Google Scholar
Jiang Y, Rossi G, Ferro-Novick S: Bet2p and Mad2p are components of a prenyltransferase that adds geranylgeranyl onto Ypt1p and Sec4p. Nature. 1993, 366: 84-86. 10.1038/366084a0.
Article
CAS
PubMed
Google Scholar
Arnesen T: Protein N-terminal acetylation: NAT 2007-2008 Symposia. BMC Proceedings. 2009, 3 (Suppl 6): S1-10.1186/1753-6561-3-s6-s1.
Article
PubMed Central
PubMed
Google Scholar