MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data
-
* Corresponding author: Bruce R Conklin bconklin@gladstone.ucsf.edu
Genome Biology 2003, 4:R7 doi:10.1186/gb-2003-4-1-r7
Accesses
- Last 30 days: 184 accesses
- Last year: 2392 accesses
- All time: 31165 accesses
Cited by
BioMed Central: 71 citations
|
Research article
Chang Liu, Jianqin Li, Liangjie Wang, Fuqun Wu, Linfang Huang, Yue Xu, Jieyu Ye, Bin Xiao, Fanyi Meng, Shilin Chen, Mo Yang BMC Complementary and Alternative Medicine 2012, 12:5 (16 January 2012) |
|
Research article
Maria de la Paz Celorio-Mancera, Seung-Joon Ahn, Heiko Vogel, David G Heckel BMC Genomics 2011, 12:575 (23 November 2011) |
|
Research article
Differential transcriptomic profiles effected by oil palm phenolics indicate novel health outcomes Soon-Sen Leow, Shamala Sekaran, Kalyana Sundram, YewAi Tan, Ravigadevi Sambanthamurthi BMC Genomics 2011, 12:432 (25 August 2011) |
|
Short Report
Limited redundancy in genes regulated by Cyclin T2 and Cyclin T1 Rajesh Ramakrishnan, Wendong Yu, Andrew P Rice BMC Research Notes 2011, 4:260 (26 July 2011) |
|
Research article
Transcriptomic responses in mouse brain exposed to chronic excess of the neurotransmitter glutamate Xinkun Wang, Xiaodong Bao, Ranu Pal, Abdulbaki Agbas, Elias K Michaelis BMC Genomics 2010, 11:360 (7 June 2010) |
|
Research
Gokhan Yilmaz, J Steven Alexander, Cigdem Erkuran Yilmaz, D Neil Granger Experimental & Translational Stroke Medicine 2010, 2:11 (28 May 2010) |
|
Research
Rachel A Heimeier, Biswajit Das, Daniel R Buchholz, Maria Fiorentino, Yun-Bo Shi Genome Biology 2010, 11:R55 (19 May 2010) The developmental transcriptome of the Xenopus laevis intestine, from embryo to adult, reveals insights into the regulation of gut development in all vertebrates. |
|
Research article
Marjan J van Erk, Suzan Wopereis, Carina Rubingh, Trinette van Vliet, Elwin Verheij, Nicole HP Cnubben, Theresa L Pedersen, John W Newman, Age K Smilde, Jan Greef, Henk FJ Hendriks, Ben van Ommen BMC Medical Genomics 2010, 3:5 (23 February 2010) |
|
Software
Lists2Networks: Integrated analysis of gene/protein lists Alexander Lachmann, Avi Ma'ayan BMC Bioinformatics 2010, 11:87 (12 February 2010) |
|
Research article
Detecting disease associated modules and prioritizing active genes based on high throughput data Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen BMC Bioinformatics 2010, 11:26 (13 January 2010) |
|
Research article
Pavlo L Kovalenko, Zhentao Zhang, Min Cui, Steve K Clinton, James C Fleet BMC Genomics 2010, 11:26 (13 January 2010) |
|
Research
Dennis Prickett, Michael Watson BMC Proceedings 2009, 3(Suppl 4):S7 (16 July 2009) |
|
Research
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) |
|
Research article
Jianzhong Li, Xia Chen, Xuelian Gong, Ying Liu, Hao Feng, Lei Qiu, Zhenlin Hu, Junping Zhang BMC Genomics 2009, 10:241 (22 May 2009) |
|
Research
Satish B Cheepala, Weihong Yin, Zanobia Syed, Jennifer N Gill, Alaina McMillian, Heather E Kleiner, Mark Lynch, Rasiah Loganantharaj, Marjan Trutschl, Urska Cvek, John L Clifford Molecular Cancer 2009, 8:27 (11 May 2009) |
|
Research article
Xinkun Wang, Asma Zaidi, Ranu Pal, Alexander S Garrett, Rogelio Braceras, Xue-wen Chen, Mary L Michaelis, Elias K Michaelis BMC Neuroscience 2009, 10:12 (19 February 2009) |
|
Method
KEGG spider: interpretation of genomics data in the context of the global gene metabolic network Alexey V Antonov, Sabine Dietmann, Hans W Mewes Genome Biology 2008, 9:R179 (18 December 2008) A web-based tool for interpretation of experimentally-derived gene lists that provides global models uniting genes from different metabolic pathways. |
|
Research article
Histone deacetylase inhibitors: A new mode for inhibition of cholesterol metabolism Sridar V Chittur, Niquiche Sangster-Guity, Paulette J McCormick BMC Genomics 2008, 9:507 (29 October 2008) |
|
Research article
Olga Martínez-Augustin, Manel Merlos, Antonio Zarzuelo, María Suárez, Fermín de Medina BMC Genomics 2008, 9:490 (17 October 2008) |
|
Software
Presenting and exploring biological pathways with PathVisio Martijn P van Iersel, Thomas Kelder, Alexander R Pico, Kristina Hanspers, Susan Coort, Bruce R Conklin, Chris Evelo BMC Bioinformatics 2008, 9:399 (25 September 2008) |
|
Methodology article
Testing gene set enrichment for subset of genes: Sub-GSE Xiting Yan, Fengzhu Sun BMC Bioinformatics 2008, 9:362 (2 September 2008) |
|
Research article
Altered gene expression in highly purified enterocytes from patients with active coeliac disease Suzanne Bracken, Greg Byrne, Jacinta Kelly, John Jackson, Conleth Feighery BMC Genomics 2008, 9:377 (8 August 2008) |
|
Research article
Freddy J Troost, Peter van Baarlen, Patrick Lindsey, Andrea Kodde, Willem M de Vos, Michiel Kleerebezem, Robert-Jan M Brummer BMC Genomics 2008, 9:374 (5 August 2008) |
|
Research article
Dawei Liu, Debashis Ghosh, Xihong Lin BMC Bioinformatics 2008, 9:292 (24 June 2008) The effect of genetic pathways on disease outcome can be estimated by combining both parametric and non-parametric modeling using kernel machines, a framework that includes nonlinear effects and interactions between genes within a single pathway.
|
|
Research article
Zhiqiang Pan, Ameeta K Agarwal, Tao Xu, Qin Feng, Scott R Baerson, Stephen O Duke, Agnes M Rimando BMC Medical Genomics 2008, 1:7 (20 March 2008) |
|
Research Article
S Gaudan, A Jimeno Yepes, V Lee, D Rebholz-Schuhmann EURASIP Journal on Bioinformatics and Systems Biology 2008, 2008:342746 (3 March 2008) |
|
Database
MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters Philip J Law, Clotilde Claudel-Renard, Fourie Joubert, Abraham I Louw, Dave K Berger BMC Genomics 2008, 9:105 (28 February 2008) |
|
Research article
Ana Oliveira, Kiran Patil, Jens Nielsen BMC Systems Biology 2008, 2:17 (8 February 2008) |
|
Research article
Gene regulatory networks in lactation: identification of global principles using bioinformatics Danielle G Lemay, Margaret C Neville, Michael C Rudolph, Katherine S Pollard, J German BMC Systems Biology 2007, 1:56 (27 November 2007) |
|
Research article
Analysis of gene expression during neurite outgrowth and regeneration Moriah L Szpara, Karen Vranizan, Yu Tai, Corey S Goodman, Terence P Speed, John Ngai BMC Neuroscience 2007, 8:100 (23 November 2007) |
|
Research
Molecular signatures define two main classes of meningiomas Lucia Carvalho, Ivan Smirnov, Gilson S Baia, Zora Modrusan, Justin S Smith, Peter Jun, Joseph F Costello, Michael W McDermott, Scott R VandenBerg, Anita Lal Molecular Cancer 2007, 6:64 (15 October 2007) |
|
Research article
Fasting induces a biphasic adaptive metabolic response in murine small intestine Milka Sokolović, Diederik Wehkamp, Aleksandar Sokolović, Jacqueline Vermeulen, Lisa A Gilhuijs-Pederson, Rachel IM van Haaften, Yuri Nikolsky, Chris TA Evelo, Antoine HC van Kampen, Theodorus BM Hakvoort, Wouter H Lamers BMC Genomics 2007, 8:361 (9 October 2007) |
|
Methodology article
Linking microarray reporters with protein functions Stan Gaj, Arie van Erk, Rachel IM van Haaften, Chris TA Evelo BMC Bioinformatics 2007, 8:360 (26 September 2007) |
|
Research article
Soma Mandal, James R Davie BMC Cancer 2007, 7:181 (20 September 2007) |
|
Software
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. |
|
Methodology article
Randall Hulshizer, Eric M Blalock BMC Bioinformatics 2007, 8:240 (5 July 2007) |
|
Software
Markus Weniger, Julia C Engelmann, Jörg Schultz BMC Bioinformatics 2007, 8:179 (2 June 2007) |
|
Methodology article
Gunnar Schramm, Marc Zapatka, Roland Eils, Rainer König BMC Bioinformatics 2007, 8:149 (8 May 2007) |
|
Research article
Carsten W Lederer, Antonietta Torrisi, Maria Pantelidou, Niovi Santama, Sebastiano Cavallaro BMC Genomics 2007, 8:26 (23 January 2007) Identification of genes misregulated in the motor cortex of people with amyotrophic lateral sclerosis (ALS) has uncovered novel aspects of ALS pathology and points to using existing medication to rapidly develop new symptomatic therapies.
|
|
Review
Lyn-Marie Birkholtz, Olivier Bastien, Gordon Wells, Delphine Grando, Fourie Joubert, Vinod Kasam, Marc Zimmermann, Philippe Ortet, Nicolas Jacq, Nadia Saïdani, Sylvaine Roy, Martin Hofmann-Apitius, Vincent Breton, Abraham I Louw, Eric Maréchal Malaria Journal 2006, 5:110 (17 November 2006) A review of the different tools and strategies that have recently been developed to process the huge amount of data produced by the X-omic projects. This includes the comparison of protein sequences, high throughput reconstruction of molecular phylogenies, representation of biological processes, methods to integrate X-omic generated data following drug treatments and in silico prediction of protein structure and identification of specific ligand.
|
|
Research
David M Levine, David R Haynor, John C Castle, Sergey B Stepaniants, Matteo Pellegrini, Mao Mao, Jason M Johnson Genome Biology 2006, 7:R93 (17 October 2006) A comparison of five different measures of pathway expression and a public map of pathway expression in human tissues are presented. |
|
Research
Tzu-Ling Sung, Andrew P Rice Retrovirology 2006, 3:66 (2 October 2006) |
|
Methodology article
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
Jamie A Lee, Robert S Sinkovits, Dennis Mock, Eva L Rab, Jennifer Cai, Peng Yang, Brian Saunders, Robert C Hsueh, Sangdun Choi, Shankar Subramaniam, Richard H Scheuermann, BMC Bioinformatics 2006, 7:237 (2 May 2006) |
|
Research article
Biologically relevant effects of mRNA amplification on gene expression profiles Rachel IM van Haaften, Blanche Schroen, Ben JA Janssen, Arie van Erk, Jacques JM Debets, Hubert JM Smeets, Jos FM Smits, Arthur van den Wijngaard, Yigal M Pinto, Chris TA Evelo BMC Bioinformatics 2006, 7:200 (11 April 2006) |
|
Methodology
A flexible representation of omic knowledge for thorough analysis of microarray data Yoshikazu Hasegawa, Motoaki Seki, Yoshiki Mochizuki, Naohiko Heida, Katsura Hirosawa, Naoki Okamoto, Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Kei Iida, Kisik Lee, Shigehiko Kanaya, Taku Demura, Kazuo Shinozaki, Akihiko Konagaya, Tetsuro Toyoda Plant Methods 2006, 2:5 (2 March 2006) |
|
Software
GO-Diff: Mining functional differentiation between EST-based transcriptomes Zuozhou Chen, Weilin Wang, Xuefeng Ling, Jane Liu, Liangbiao Chen BMC Bioinformatics 2006, 7:72 (16 February 2006) |
|
Methodology article
Finding biological process modifications in cancer tissues by mining gene expression correlations Giacomo Gamberoni, Sergio Storari, Stefano Volinia BMC Bioinformatics 2006, 7:6 (9 January 2006) |
|
Research
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. |
|
Methodology article
Pathway level analysis of gene expression using singular value decomposition John Tomfohr, Jun Lu, Thomas B Kepler BMC Bioinformatics 2005, 6:225 (12 September 2005) |
|
Methodology article
Automation of gene assignments to metabolic pathways using high-throughput expression data Liviu Popescu, Golan Yona BMC Bioinformatics 2005, 6:217 (31 August 2005) |
|
Software
L2L: a simple tool for discovering the hidden significance in microarray expression data John C Newman, Alan M Weiner Genome Biology 2005, 6:R81 (31 August 2005) A database with lists of differentially expressed genes from published microarray studies is presented together with an application for mining the database with the user’s own microarray data, allowing the identification of novel biological patterns in microarray data. |
|
Research article
Dynamic covariation between gene expression and proteome characteristics Mansour Sharabiani, Markku Siermala, Tommi O Lehtinen, Mauno Vihinen BMC Bioinformatics 2005, 6:215 (30 August 2005) |
|
Software
DynGO: a tool for visualizing and mining of Gene Ontology and its associations Hongfang Liu, Zhang-Zhi Hu, Cathy H Wu BMC Bioinformatics 2005, 6:201 (9 August 2005) |
|
Methodology article
PAGE: Parametric Analysis of Gene Set Enrichment Seon-Young Kim, David J Volsky BMC Bioinformatics 2005, 6:144 (8 June 2005) |
|
Research article
Pascale Anderle, Thierry Sengstag, David M Mutch, Martin Rumbo, Viviane Praz, Robert Mansourian, Mauro Delorenzi, Gary Williamson, Matthew-Alan Roberts BMC Genomics 2005, 6:69 (10 May 2005) |
|
Methodology article
Dmitry N Grigoryev, Shwu-Fan Ma, Brett A Simon, Rafael A Irizarry, Shui Q Ye, Joe GN Garcia BMC Genomics 2005, 6:62 (4 May 2005) |
|
Research
Identifying genetic networks underlying myometrial transition to labor Nathan Salomonis, Nathalie Cotte, Alexander C Zambon, Katherine S Pollard, Karen Vranizan, Scott W Doniger, Gregory Dolganov, Bruce R Conklin Genome Biology 2005, 6:R12 (28 January 2005) A time course of gene expression at the onset of labor reveals transcriptional networks associated with activation of the uterine muscle and identifies targets for drugs to prevent premature labor. |
|
Research article
Gene expression in the brain and kidney of rainbow trout in response to handling stress Aleksei Krasnov, Heikki Koskinen, Petri Pehkonen, Caird E Rexroad, Sergey Afanasyev, Hannu Mölsä BMC Genomics 2005, 6:3 (6 January 2005) |
|
Methodology article
Comparing functional annotation analyses with Catmap Thomas Breslin, Patrik Edén, Morten Krogh BMC Bioinformatics 2004, 5:193 (9 December 2004) |
|
Research article
Handling multiple testing while interpreting microarrays with the Gene Ontology Database Michael V Osier, Hongyu Zhao, Kei-Hoi Cheung BMC Bioinformatics 2004, 5:124 (6 September 2004) |
|
Methodology article
Graph-based iterative Group Analysis enhances microarray interpretation Rainer Breitling, Anna Amtmann, Pawel Herzyk BMC Bioinformatics 2004, 5:100 (23 July 2004) Graph-based iterative Group Analysis (GiGA), a graph-based approach to identify biologically relevant changes in expression data, visually enhances microarray interpretation.
|
|
Research article
Expression profile of genes regulated by activity of the Na-H exchanger NHE1 Luanna K Putney, Diane L Barber BMC Genomics 2004, 5:46 (16 July 2004) |
|
Review
Science review: Searching for gene candidates in acute lung injury Dmitry N Grigoryev, James H Finigan, Paul Hassoun, Joe GN Garcia Critical Care 2004, 8:440-447 (30 June 2004) |
|
Software
Visualization and analysis of microarray and gene ontology data with treemaps Eric H Baehrecke, Niem Dang, Ketan Babaria, Ben Shneiderman BMC Bioinformatics 2004, 5:84 (28 June 2004) |
|
Software
Guohui Zhou, Xinyu Wen, Hang Liu, Michael J Schlicht, Martin J Hessner, Peter J Tonellato, Milton W Datta BMC Bioinformatics 2004, 5:46 (29 April 2004) |
|
Method
Orthologous gene-expression profiling in multi-species models: search for candidate genes Dmitry N Grigoryev, Shwu-Fan Ma, Rafael A Irizarry, Shui Ye, John Quackenbush, Joe GN Garcia Genome Biology 2004, 5:R34 (27 April 2004) An analytical approach that simultaneously evaluates multi-species experimental models is presented. This approach may be a useful tool in the selection of process-related candidate genes. |
|
Methodology article
Rainer Breitling, Anna Amtmann, Pawel Herzyk BMC Bioinformatics 2004, 5:34 (29 March 2004) |
|
Software
Bing Zhang, Denise Schmoyer, Stefan Kirov, Jay Snoddy BMC Bioinformatics 2004, 5:16 (18 February 2004) |
|
Research
Time- and exercise-dependent gene regulation in human skeletal muscle Alexander C Zambon, Erin L McDearmon, Nathan Salomonis, Karen M Vranizan, Kirsten L Johansen, Deborah Adey, Joseph S Takahashi, Morris Schambelan, Bruce R Conklin Genome Biology 2003, 4:R61 (25 September 2003) Skeletal muscle remodeling is a critical component of an organism's response to environmental changes. Exercise causes structural changes in muscle and can induce phase shifts in circadian rhythms, fluctuations in physiology and behavior with a period of around 24 hours that are maintained by a core clock mechanism. Both exercise-induced remodeling and circadian rhythms rely on the transcriptional regulation of key genes. |
|
Software
Identifying biological themes within lists of genes with EASE Douglas A Hosack, Glynn Dennis, Brad T Sherman, H Lane, Richard A Lempicki Genome Biology 2003, 4:R70 (11 September 2003) EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE and other high-throughput genomic data. |