BMC Bioinformatics

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GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

Bing Zhang, Denise Schmoyer, Stefan Kirov and Jay Snoddy*

BMC Bioinformatics 2004, 5:16 doi:10.1186/1471-2105-5-16

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BioMed Central: 43 citations

Research article   Open Access

Germline DNA copy number variation in familial and early-onset breast cancer

Ana CV Krepischi, Maria Isabel W Achatz, Erika MM Santos, Silvia S Costa, Bianca CG Lisboa, Helena Brentani, Tiago M Santos, Amanda Gonçalves, Amanda F Nóbrega, Peter L Pearson, Angela M Vianna-Morgante, Dirce M Carraro, Ricardo R Brentani, Carla Rosenberg Breast Cancer Research 2012, 14:R24 (7 February 2012)

Research   Open Access

Elucidating the identity of resistance mechanisms to prednisolone exposure in acute lymphoblastic leukemia cells through transcriptomic analysis: A computational approach

Emmanouil G Sifakis, George I Lambrou, Andriana Prentza, Spiros Vlahopoulos, Dimitris Koutsouris, Fotini Tzortzatou-Stathopoulou, Aristotelis A Chatziioannou Journal of Clinical Bioinformatics 2011, 1:36 (20 December 2011)

Research   Open Access

GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution

Toralf Kirsten, Anika Gross, Michael Hartung, Erhard Rahm Journal of Biomedical Semantics 2011, 2:6 (13 September 2011)

Proceedings   Open Access

Generation, analysis and functional annotation of expressed sequence tags from the sheepshead minnow (Cyprinodon variegatus)

Mehdi Pirooznia, Alexander Pozhitkov, Edward J Perkins, Youping Deng, Marius Brouwer BMC Genomics 2010, 11(Suppl 2):S4 (2 November 2010)

Research article   Open Access

Systems genetics analyses predict a transcription role for P2P-R: Molecular confirmation that P2P-R is a transcriptional co-repressor

Philippos Peidis, Thomas Giannakouros, Matthew E Burow, Robert W Williams, Robert E Scott BMC Systems Biology 2010, 4:14 (25 February 2010)

Research   Open Access

Robust TLR4-induced gene expression patterns are not an accurate indicator of human immunity

Kelly L Brown, Reza Falsafi, Winnie Kum, Pamela Hamill, Jennifer L Gardy, Donald J Davidson, Stuart Turvey, Brett B Finlay, David P Speert, Robert EW Hancock Journal of Translational Medicine 2010, 8:6 (27 January 2010)

Proceedings   Open Access

Graph ranking for exploratory gene data analysis

Cuilan Gao, Xin Dang, Yixin Chen, Dawn Wilkins BMC Bioinformatics 2009, 10(Suppl 11):S19 (8 October 2009)

Research article   Open Access

Electric pulses used in electrochemotherapy and electrogene therapy do not significantly change the expression profile of genes involved in the development of cancer in malignant melanoma cells

Vid Mlakar, Vesna Todorovic, Maja Cemazar, Damjan Glavac, Gregor Sersa BMC Cancer 2009, 9:299 (26 August 2009)

Research   Open Access

Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares

Agnès Bonnet, Sandrine Lagarrigue, Laurence Liaubet, Christèle Robert-Granié, Magali SanCristobal, Gwenola Tosser-Klopp BMC Proceedings 2009, 3(Suppl 4):S11 (16 July 2009)

Research   Open Access

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

Jakob Hedegaard, Cristina Arce, Silvio Bicciato, Agnès Bonnet, Bart Buitenhuis, Melania Collado-Romero, Lene N Conley, Magali SanCristobal, Francesco Ferrari, Juan J Garrido, Martien AM Groenen, Henrik Hornshøj, Ina Hulsegge, Li Jiang, Ángeles Jiménez-Marín, Arun Kommadath, Sandrine Lagarrigue, Jack AM Leunissen, Laurence Liaubet, Pieter BT Neerincx et al. BMC Proceedings 2009, 3(Suppl 4):S5 (16 July 2009)

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Novel transcriptional profile in wrist muscles from cerebral palsy patients

Lucas R Smith, Eva Pontén, Yvette Hedström, Samuel R Ward, Henry G Chambers, Shankar Subramaniam, Richard L Lieber BMC Medical Genomics 2009, 2:44 (14 July 2009)

Research   Open Access

Use of serial analysis of gene expression to reveal the specific regulation of gene expression profile in asthmatic rats treated by acupuncture

Lei-Miao Yin, Gong-Hao Jiang, Yu Wang, Yan Wang, Yan-Yan Liu, Wei-Rong Jin, Yu-Dong Xu, Qing-Hua Zhang, Yong-Qing Yang Journal of Biomedical Science 2009, 16:46 (6 May 2009)

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Revisiting the missing protein-coding gene catalog of the domestic dog

Thomas Derrien, Julien Thézé, Amaury Vaysse, Catherine André, Elaine A Ostrander, Francis Galibert, Christophe Hitte BMC Genomics 2009, 10:62 (4 February 2009)

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GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson, Zohar Yakhini BMC Bioinformatics 2009, 10:48 (3 February 2009)

Methodology article   Open Access Highly Accessed

A general modular framework for gene set enrichment analysis

Marit Ackermann, Korbinian Strimmer BMC Bioinformatics 2009, 10:47 (3 February 2009)

Research article   Open Access

Transcriptome profiling of the feeding-to-fasting transition in chicken liver

Colette Désert, Michel J Duclos, Pierre Blavy, Frédéric Lecerf, François Moreews, Christophe Klopp, Marc Aubry, Frédéric Herault, Pascale Le Roy, Cécile Berri, Madeleine Douaire, Christian Diot, Sandrine Lagarrigue BMC Genomics 2008, 9:611 (17 December 2008)

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mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft

Darren Magda, Philip Lecane, Julia Prescott, Patricia Thiemann, Xuan Ma, Patricia K Dranchak, Donna M Toleno, Krishna Ramaswamy, Kimberly D Siegmund, Joseph G Hacia BMC Genomics 2008, 9:521 (3 November 2008)

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Multiple actions of lysophosphatidic acid on fibroblasts revealed by transcriptional profiling

Catelijne Stortelers, Ron Kerkhoven, Wouter H Moolenaar BMC Genomics 2008, 9:387 (14 August 2008)

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Unravelling the molecular control of calvarial suture fusion in children with craniosynostosis

Anna K Coussens, Christopher R Wilkinson, Ian P Hughes, C Phillip Morris, Angela van Daal, Peter J Anderson, Barry C Powell BMC Genomics 2007, 8:458 (12 December 2007)

Research article   Open Access

Differentially expressed genes in embryonic cardiac tissues of mice lacking Folr1 gene activity

Huiping Zhu, Robert M Cabrera, Bogdan J Wlodarczyk, Daniel Bozinov, Deli Wang, Robert J Schwartz, Richard H Finnell BMC Developmental Biology 2007, 7:128 (20 November 2007)

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Regulatory module network of basic/helix-loop-helix transcription factors in mouse brain

Jing Li, Zijing J Liu, Yuchun C Pan, Qi Liu, Xing Fu, Nigel GF Cooper, Yixue Li, Mengsheng Qiu, Tieliu Shi Genome Biology 2007, 8:R244 (19 November 2007)

A comprehensive regulatory module network of 15 bHLH transcription factors over 150 target genes in mouse brain has been constructed.

Software   Open Access

BMDExpress: a software tool for the benchmark dose analyses of genomic data

Longlong Yang, Bruce C Allen, Russell S Thomas BMC Genomics 2007, 8:387 (25 October 2007)

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Five distinct biological processes and 14 differentially expressed genes characterize TEL/AML1-positive leukemia

Virginie Gandemer, Anne-Gaëlle Rio, Marie de Tayrac, Vonnick Sibut, Stéphanie Mottier, Béatrice Ly Sunnaram, Catherine Henry, Annabelle Monnier, Christian Berthou, Edouard Le Gall, André Le Treut, Claudine Schmitt, Jean-Yves Le Gall, Jean Mosser, Marie-Dominique Galibert BMC Genomics 2007, 8:385 (23 October 2007)

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Identification of genes that regulate multiple cellular processes/responses in the context of lipotoxicity to hepatoma cells

Shireesh Srivastava, Zheng Li, Xuerui Yang, Matthew Yedwabnick, Stephen Shaw, Christina Chan BMC Genomics 2007, 8:364 (9 October 2007)

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High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer

Suet F Chin, Andrew E Teschendorff, John C Marioni, Yanzhong Wang, Nuno L Barbosa-Morais, Natalie P Thorne, Jose L Costa, Sarah E Pinder, Mark A van de Wiel, Andrew R Green, Ian O Ellis, Peggy L Porter, Simon Tavaré, James D Brenton, Bauke Ylstra, Carlos Caldas Genome Biology 2007, 8:R215 (7 October 2007)

High resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer, and provides a genome-wide list of common copy number alterations associated with aberrant expression and poor prognosis.

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The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists

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.

Research article   Open Access

Altered expression of mitochondrial and extracellular matrix genes in the heart of human fetuses with chromosome 21 trisomy

Anna Conti, Floriana Fabbrini, Paola D'Agostino, Rosa Negri, Dario Greco, Rita Genesio, Maria D'Armiento, Carlo Olla, Dario Paladini, Mariastella Zannini, Lucio Nitsch BMC Genomics 2007, 8:268 (7 August 2007)

Research article   Open Access

Transcriptome profiling of the small intestinal epithelium in germfree versus conventional piglets

Shankar R Chowdhury, Dale E King, Benjamin P Willing, Mark R Band, Jonathan E Beever, Adrienne B Lane, Juan J Loor, Juan C Marini, Laurie A Rund, Lawrence B Schook, Andrew G Van Kessel, H Rex Gaskins BMC Genomics 2007, 8:215 (5 July 2007)

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FUNC: a package for detecting significant associations between gene sets and ontological annotations

Kay Prüfer, Bjoern Muetzel, Hong-Hai Do, Gunter Weiss, Philipp Khaitovich, Erhard Rahm, Svante Pääbo, Michael Lachmann, Wolfgang Enard BMC Bioinformatics 2007, 8:41 (6 February 2007)

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GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists

Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, Jose M Carazo, Alberto Pascual-Montano Genome Biology 2007, 8:R3 (4 January 2007)

GENECODIS, a web-based tool for finding annotations that frequently co-occur in a set of genes and ranking them by their statistical significance, is presented.

Research   Open Access Highly Accessed

A consensus prognostic gene expression classifier for ER positive breast cancer

Andrew E Teschendorff, Ali Naderi, Nuno L Barbosa-Morais, Sarah E Pinder, Ian O Ellis, Sam Aparicio, James D Brenton, Carlos Caldas Genome Biology 2006, 7:R101 (31 October 2006)

A consensus prognostic classifier for estrogen receptor positive breast tumors has been developed and shown to be valid in nearly 900 samples across different microarray platforms.

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Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression

Jie Wu, Xiaohui Xie Genome Biology 2006, 7:R85 (26 September 2006)

Using comparative sequence analysis, a network among REST, CREB and brain-related miRNAs is propsed to mediate neuronal gene expression.

Proceedings   Open Access

GOFFA: Gene Ontology For Functional Analysis – A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data

Hongmei Sun, Hong Fang, Tao Chen, Roger Perkins, Weida Tong BMC Bioinformatics 2006, 7(Suppl 2):S23 (26 September 2006)

Research article   Open Access

TSPY potentiates cell proliferation and tumorigenesis by promoting cell cycle progression in HeLa and NIH3T3 cells

Shane W Oram, Xing Liu, Tin-Lap Lee, Wai-Yee Chan, Yun-Fai Lau BMC Cancer 2006, 6:154 (9 June 2006)

Methodology article   Open Access Highly Accessed

Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets

Marc Aubry, Annabelle Monnier, Celine Chicault, Marie de Tayrac, Marie-Dominique Galibert, Anita Burgun, Jean Mosser BMC Bioinformatics 2006, 7:241 (4 May 2006)

Research article   Open Access

Transcriptional profiling of mesenchymal stromal cells from young and old rats in response to Dexamethasone

Uri Akavia, Irena Shur, Gideon Rechavi, Dafna Benayahu BMC Genomics 2006, 7:95 (27 April 2006)

Methodology article   Open Access Highly Accessed

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)

Software   Open Access

GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions

Jason M Doherty, Lynn K Carmichael, Jason C Mills BMC Bioinformatics 2006, 7:151 (17 March 2006)

Research   Open Access Highly Accessed

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.

Research article   Open Access

Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control

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.

Database   Open Access

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.