GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies
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* Corresponding author: Jay Snoddy snoddyj@ornl.gov
BMC Bioinformatics 2004, 5:16 doi:10.1186/1471-2105-5-16
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Da Huang, Brad T Sherman, Qina Tan, Jack R Collins, W Gregory Alvord, Jean Roayaei, Robert Stephens, Michael W Baseler, H Clifford Lane, Richard A Lempicki Genome Biology 2007, 8:R183 (4 September 2007) The DAVID gene functional classification tool uses a novel fuzzy clustering algorithm to condense a list of genes or associated biological terms into organized classes of related genes or biology, called biological modules. |
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Shane W Oram, Xing Liu, Tin-Lap Lee, Wai-Yee Chan, Yun-Fai Lau BMC Cancer 2006, 6:154 (9 June 2006) |
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Quality control for terms and definitions in ontologies and taxonomies Jacob Köhler, Katherine Munn, Alexander Rüegg, Andre Skusa, Barry Smith BMC Bioinformatics 2006, 7:212 (19 April 2006) |
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Jason M Doherty, Lynn K Carmichael, Jason C Mills BMC Bioinformatics 2006, 7:151 (17 March 2006) |
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Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart Rong Mao, Xiaowen Wang, Edward L Spitznagel, Laurence P Frelin, Jason C Ting, Huashi Ding, Jung-whan Kim, Ingo Ruczinski, Thomas J Downey, Jonathan Pevsner Genome Biology 2005, 6:R107 (16 December 2005) Microarray analysis of transcript levels in fetal cerebellum and heart tissues of Down syndrome patients showed a disruption only of chromosome 21 gene expression. |
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Giacomo Finocchiaro, Francesco Mancuso, Heiko Muller BMC Bioinformatics 2005, 6(Suppl 4):S14 (1 December 2005) |
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Mechanisms of aging in senescence-accelerated mice Todd A Carter, Jennifer A Greenhall, Shigeo Yoshida, Sebastian Fuchs, Robert Helton, Anand Swaroop, David J Lockhart, Carrolee Barlow Genome Biology 2005, 6:R48 (1 June 2005) Gene-expression analysis and polymorphism screening to study molecular senescence of the retina and hippocampus in two rare inbred mouse models of accelerated neurological senescence as well as a related and an unrelated normal strain showed that most age-related gene expression changes were strain-specific. |
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GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments SA Kirov, X Peng, E Baker, D Schmoyer, B Zhang, J Snoddy BMC Bioinformatics 2005, 6:72 (24 March 2005) |
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GOToolBox: functional analysis of gene datasets based on Gene Ontology David Martin, Christine Brun, Elisabeth Remy, Pierre Mouren, Denis Thieffry, Bernard Jacq Genome Biology 2004, 5:R101 (26 November 2004) Tools are presented to identify Gene Ontology terms that are over- or under-represented in a dataset, to cluster genes by function and to find genes with similar annotations. |