publication . Article . 2012

GeneWeaver: a web-based system for integrative functional genomics

Erich J. Baker; Jeremy J. Jay; Jason A. Bubier; Michael A. Langston; Elissa J. Chesler;
Open Access English
  • Published: 01 Jan 2012 Journal: Nucleic Acids Research, volume 40, issue Database issue, pages D1067-D1076 (issn: 0305-1048, eissn: 1362-4962, Copyright policy)
  • Publisher: Oxford University Press
Abstract
High-throughput genome technologies have produced a wealth of data on the association of genes and gene products to biological functions. Investigators have discovered value in combining their experimental results with published genome-wide association studies, quantitative trait locus, microarray, RNA-sequencing and mutant phenotyping studies to identify gene-function associations across diverse experiments, species, conditions, behaviors or biological processes. These experimental results are typically derived from disparate data repositories, publication supplements or reconstructions from primary data stores. This leaves bench biologists with the complex and...
Persistent Identifiers
Subjects
ACM Computing Classification System: ComputingMethodologies_PATTERNRECOGNITION
free text keywords: Articles, Conceptual framework, Data science, Identifier, Genomics, Web application, business.industry, business, Data set, Functional genomics, Genetics, Ontology, Biology, Disparate system
Funded by
NIH| INIA:Complex Trait Analysis--Alcohol /Stress Interaction
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01AA013499-02
  • Funding stream: NATIONAL INSTITUTE ON ALCOHOL ABUSE AND ALCOHOLISM
34 references, page 1 of 3

Guo, AY, Webb, BT, Miles, MF, Zimmerman, MP, Kendler, KS, Zhao, Z. ERGR: an ethanol-related gene resource. Nucleic Acids Res.. 2009; 37: D840-D845 [OpenAIRE] [PubMed]

Le-Niculescu, H, Patel, SD, Niculescu, AB. Convergent integration of animal model and human studies of bipolar disorder (manic-depressive illness). Curr. Opin. Pharmacol.. 2010; 10: 594-600 [PubMed]

Li, CY, Mao, X, Wei, L. Genes and (common) pathways underlying drug addiction. PLoS Comput. Biol.. 2008; 4: e2 [OpenAIRE] [PubMed]

Mulligan, MK, Ponomarev, I, Hitzemann, RJ, Belknap, JK, Tabakoff, B, Harris, RA, Crabbe, JC, Blednov, YA, Grahame, NJ, Phillips, TJ. Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis. Proc. Natl Acad. Sci. USA. 2006; 103: 6368-6373 [OpenAIRE] [PubMed]

Nissenbaum, J, Devor, M, Seltzer, Z, Gebauer, M, Michaelis, M, Tal, M, Dorfman, R, Abitbul-Yarkoni, M, Lu, Y, Elahipanah, T. Susceptibility to chronic pain following nerve injury is genetically affected by CACNG2. Genome Res.. 2010; 20: 1180-1190 [OpenAIRE] [PubMed]

Austin, CP, Battey, JF, Bradley, A, Bucan, M, Capecchi, M, Collins, FS, Dove, WF, Duyk, G, Dymecki, S, Eppig, JT. The knockout mouse project. Nat. Genet.. 2004; 36: 921-924 [OpenAIRE] [PubMed]

Li, Z, Vizeacoumar, FJ, Bahr, S, Li, J, Warringer, J, Vizeacoumar, FS, Min, R, Vandersluis, B, Bellay, J, Devit, M. Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat. Biotechnol.. 2011; 29: 361-367 [OpenAIRE] [PubMed]

Mnaimneh, S, Davierwala, AP, Haynes, J, Moffat, J, Peng, WT, Zhang, W, Yang, X, Pootoolal, J, Chua, G, Lopez, A. Exploration of essential gene functions via titratable promoter alleles. Cell. 2004; 118: 31-44 [OpenAIRE] [PubMed]

Blake, JA, Bult, CJ, Kadin, JA, Richardson, JE, Eppig, JT. The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res.. 2011; 39: D842-D848 [OpenAIRE] [PubMed]

Smith, CL, Eppig, JT. The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Interdiscip. Rev. Syst. Biol. Med.. 2009; 1: 390-399

The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res.. 2010; 38: D331-D335 [OpenAIRE] [PubMed]

Guan, Y, Ackert-Bicknell, CL, Kell, B, Troyanskaya, OG, Hibbs, MA. Functional genomics complements quantitative genetics in identifying disease-gene associations. PLoS Comput. Biol.. 2010; 6: e1000991 [OpenAIRE] [PubMed]

Neely, GG, Hess, A, Costigan, M, Keene, AC, Goulas, S, Langeslag, M, Griffin, RS, Belfer, I, Dai, F, Smith, SB. A genome-wide Drosophila screen for heat nociception identifies alpha2delta3 as an evolutionarily conserved pain gene. Cell. 2010; 143: 628-638 [OpenAIRE] [PubMed]

McGary, KL, Park, TJ, Woods, JO, Cha, HJ, Wallingford, JB, Marcotte, EM. Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc. Natl Acad. Sci. USA. 2010; 107: 6544-6549 [OpenAIRE] [PubMed]

Baker, EJ, Jay, JJ, Philip, VM, Zhang, Y, Li, Z, Kirova, R, Langston, MA, Chesler, EJ. Ontological Discovery Environment: a system for integrating gene-phenotype associations. Genomics. 2009; 94: 377-387 [OpenAIRE] [PubMed]

34 references, page 1 of 3
Abstract
High-throughput genome technologies have produced a wealth of data on the association of genes and gene products to biological functions. Investigators have discovered value in combining their experimental results with published genome-wide association studies, quantitative trait locus, microarray, RNA-sequencing and mutant phenotyping studies to identify gene-function associations across diverse experiments, species, conditions, behaviors or biological processes. These experimental results are typically derived from disparate data repositories, publication supplements or reconstructions from primary data stores. This leaves bench biologists with the complex and...
Persistent Identifiers
Subjects
ACM Computing Classification System: ComputingMethodologies_PATTERNRECOGNITION
free text keywords: Articles, Conceptual framework, Data science, Identifier, Genomics, Web application, business.industry, business, Data set, Functional genomics, Genetics, Ontology, Biology, Disparate system
Funded by
NIH| INIA:Complex Trait Analysis--Alcohol /Stress Interaction
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01AA013499-02
  • Funding stream: NATIONAL INSTITUTE ON ALCOHOL ABUSE AND ALCOHOLISM
34 references, page 1 of 3

Guo, AY, Webb, BT, Miles, MF, Zimmerman, MP, Kendler, KS, Zhao, Z. ERGR: an ethanol-related gene resource. Nucleic Acids Res.. 2009; 37: D840-D845 [OpenAIRE] [PubMed]

Le-Niculescu, H, Patel, SD, Niculescu, AB. Convergent integration of animal model and human studies of bipolar disorder (manic-depressive illness). Curr. Opin. Pharmacol.. 2010; 10: 594-600 [PubMed]

Li, CY, Mao, X, Wei, L. Genes and (common) pathways underlying drug addiction. PLoS Comput. Biol.. 2008; 4: e2 [OpenAIRE] [PubMed]

Mulligan, MK, Ponomarev, I, Hitzemann, RJ, Belknap, JK, Tabakoff, B, Harris, RA, Crabbe, JC, Blednov, YA, Grahame, NJ, Phillips, TJ. Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis. Proc. Natl Acad. Sci. USA. 2006; 103: 6368-6373 [OpenAIRE] [PubMed]

Nissenbaum, J, Devor, M, Seltzer, Z, Gebauer, M, Michaelis, M, Tal, M, Dorfman, R, Abitbul-Yarkoni, M, Lu, Y, Elahipanah, T. Susceptibility to chronic pain following nerve injury is genetically affected by CACNG2. Genome Res.. 2010; 20: 1180-1190 [OpenAIRE] [PubMed]

Austin, CP, Battey, JF, Bradley, A, Bucan, M, Capecchi, M, Collins, FS, Dove, WF, Duyk, G, Dymecki, S, Eppig, JT. The knockout mouse project. Nat. Genet.. 2004; 36: 921-924 [OpenAIRE] [PubMed]

Li, Z, Vizeacoumar, FJ, Bahr, S, Li, J, Warringer, J, Vizeacoumar, FS, Min, R, Vandersluis, B, Bellay, J, Devit, M. Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat. Biotechnol.. 2011; 29: 361-367 [OpenAIRE] [PubMed]

Mnaimneh, S, Davierwala, AP, Haynes, J, Moffat, J, Peng, WT, Zhang, W, Yang, X, Pootoolal, J, Chua, G, Lopez, A. Exploration of essential gene functions via titratable promoter alleles. Cell. 2004; 118: 31-44 [OpenAIRE] [PubMed]

Blake, JA, Bult, CJ, Kadin, JA, Richardson, JE, Eppig, JT. The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res.. 2011; 39: D842-D848 [OpenAIRE] [PubMed]

Smith, CL, Eppig, JT. The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Interdiscip. Rev. Syst. Biol. Med.. 2009; 1: 390-399

The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res.. 2010; 38: D331-D335 [OpenAIRE] [PubMed]

Guan, Y, Ackert-Bicknell, CL, Kell, B, Troyanskaya, OG, Hibbs, MA. Functional genomics complements quantitative genetics in identifying disease-gene associations. PLoS Comput. Biol.. 2010; 6: e1000991 [OpenAIRE] [PubMed]

Neely, GG, Hess, A, Costigan, M, Keene, AC, Goulas, S, Langeslag, M, Griffin, RS, Belfer, I, Dai, F, Smith, SB. A genome-wide Drosophila screen for heat nociception identifies alpha2delta3 as an evolutionarily conserved pain gene. Cell. 2010; 143: 628-638 [OpenAIRE] [PubMed]

McGary, KL, Park, TJ, Woods, JO, Cha, HJ, Wallingford, JB, Marcotte, EM. Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc. Natl Acad. Sci. USA. 2010; 107: 6544-6549 [OpenAIRE] [PubMed]

Baker, EJ, Jay, JJ, Philip, VM, Zhang, Y, Li, Z, Kirova, R, Langston, MA, Chesler, EJ. Ontological Discovery Environment: a system for integrating gene-phenotype associations. Genomics. 2009; 94: 377-387 [OpenAIRE] [PubMed]

34 references, page 1 of 3
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