The functional landscape of mouse gene expression
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* Corresponding author: Timothy R Hughes t.hughes@utoronto.ca
- Equal contributors
Journal of Biology 2004, 3:21 doi:10.1186/jbiol16
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Yaomin Hu, Pamela J Kaisaki, Karène Argoud, Steven P Wilder, Karin J Wallace, Peng Y Woon, Christine Blancher, Lise Tarnow, Per-Henrik Groop, Samy Hadjadj, Michel Marre, Hans-Henrik Parving, Martin Farrall, Roger D Cox, Mark Lathrop, Nathalie Vionnet, Marie-Thérèse Bihoreau, Dominique Gauguier BMC Medical Genomics 2009, 2:41 (9 July 2009) |
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Definition, conservation and epigenetics of housekeeping and tissue-enriched genes Xinwei She, Carol A Rohl, John C Castle, Amit V Kulkarni, Jason M Johnson, Ronghua Chen BMC Genomics 2009, 10:269 (17 June 2009) |
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Conservation of core gene expression in vertebrate tissues Esther T Chan, Gerald T Quon, Gordon Chua, Tomas Babak, Miles Trochesset, Ralph A Zirngibl, Jane Aubin, Michael JH Ratcliffe, Andrew Wilde, Michael Brudno, Quaid D Morris, Timothy R Hughes Journal of Biology 2009, 8:33 (16 April 2009) High conservation of tissue-specific expression is found across vertebrates yet there is a lack of conservation in common regulatory sequences/signatures.
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Impact of breed and sex on porcine endocrine transcriptome: a bayesian biometrical analysis Miguel Pérez-Enciso, André LJ Ferraz, Ana Ojeda, Manel López-Béjar BMC Genomics 2009, 10:89 (24 February 2009) |
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'Validation' in genome-scale research Timothy R Hughes Journal of Biology 2009, 8:3 (26 January 2009) |
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Promoter-sharing by different genes in human genome – CPNE1 and RBM12 gene pair as an example Wanling Yang, Ping Ng, Minghui Zhao, Thomas KF Wong, Siu-Ming Yiu, Yu Lau BMC Genomics 2008, 9:456 (3 October 2008) |
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Regulon organization of Arabidopsis Wieslawa I Mentzen, Eve Wurtele BMC Plant Biology 2008, 8:99 (30 September 2008) In response to environmental and other experimental perturbations, the Arabidopsis transcriptome shows 998 regulons of co-expressed genes, corresponding to many known biological processes but also including many unannotated genes.
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Sami Kilpinen, Reija Autio, Kalle Ojala, Kristiina Iljin, Elmar Bucher, Henri Sara, Tommi Pisto, Matti Saarela, Rolf I Skotheim, Mari Björkman, John-Patrick Mpindi, Saija Haapa-Paananen, Paula Vainio, Henrik Edgren, Maija Wolf, Jaakko Astola, Matthias Nees, Sampsa Hautaniemi, Olli Kallioniemi Genome Biology 2008, 9:R139 (19 September 2008) A method for the comparison of mRNA expression levels of most human genes across gene expression array experiments, and a database of the results, are presented. |
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Wieslawa I Mentzen, Jianling Peng, Nick Ransom, Basil J Nikolau, Eve Wurtele BMC Plant Biology 2008, 8:76 (11 July 2008) |
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An en masse phenotype and function prediction system for Mus musculus Murat Taşan, Weidong Tian, David P Hill, Francis D Gibbons, Judith A Blake, Frederick P Roth Genome Biology 2008, 9(Suppl 1):S8 (27 June 2008) |
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Consistent probabilistic outputs for protein function prediction Guillaume Obozinski, Gert Lanckriet, Charles Grant, Michael I Jordan, William Noble Genome Biology 2008, 9(Suppl 1):S6 (27 June 2008) |
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Wan Kim, Chase Krumpelman, Edward M Marcotte Genome Biology 2008, 9(Suppl 1):S5 (27 June 2008) |
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Sara Mostafavi, Debajyoti Ray, David Warde-Farley, Chris Grouios, Quaid Morris Genome Biology 2008, 9(Suppl 1):S4 (27 June 2008) |
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Predicting gene function in a hierarchical context with an ensemble of classifiers Yuanfang Guan, Chad L Myers, David C Hess, Zafer Barutcuoglu, Amy A Caudy, Olga G Troyanskaya Genome Biology 2008, 9(Suppl 1):S3 (27 June 2008) |
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A critical assessment of Mus musculus gene function prediction using integrated genomic evidence Lourdes Peña-Castillo, Murat Tasan, Chad L Myers, Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Lin, Gabriel F Berriz, Francis D Gibbons, Gert Lanckriet, Jian Qiu, Charles Grant, Zafer Barutcuoglu, David P Hill, David Warde-Farley, Chris Grouios, Debajyoti Ray, Judith A Blake, Minghua Deng, Michael I Jordan, William S Noble, Quaid Morris, Judith Klein-Seetharaman, Ziv Bar-Joseph, Ting Chen, Fengzhu Sun, Olga G Troyanskaya, Edward M Marcotte, Dong Xu, Timothy R Hughes, Frederick P Roth et al. Genome Biology 2008, 9(Suppl 1):S2 (27 June 2008) |
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Conserved co-expression for candidate disease gene prioritization Martin Oti, Jeroen van Reeuwijk, Martijn A Huynen, Han G Brunner BMC Bioinformatics 2008, 9:208 (23 April 2008) |
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Transcriptome architecture across tissues in the pig André LJ Ferraz, Ana Ojeda, Manel López-Béjar, Lana T Fernandes, Anna Castelló, Josep M Folch, Miguel Pérez-Enciso BMC Genomics 2008, 9:173 (16 April 2008) |
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Extracting expression modules from perturbational gene expression compendia Steven Maere, Patrick Van Dijck, Martin Kuiper BMC Systems Biology 2008, 2:33 (10 April 2008) |
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Switch-like genes populate cell communication pathways and are enriched for extracellular proteins Adam Ertel, Aydin Tozeren BMC Genomics 2008, 9:3 (4 January 2008) |
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Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters Nicolás Bellora, Domènec Farré, M Mar Albà BMC Genomics 2007, 8:459 (13 December 2007) |
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Identification of novel stem cell markers using gap analysis of gene expression data Paul M Krzyzanowski, Miguel A Andrade-Navarro Genome Biology 2007, 8:R193 (17 September 2007) A method for the detection of marker genes in large heterogeneous collections of gene expression data is described and applied to DNA microarray data generated from 83 mouse stem cell-related samples. |
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Qingyou Xia, Daojun Cheng, Jun Duan, Genhong Wang, Tingcai Cheng, Xingfu Zha, Chun Liu, Ping Zhao, Fangyin Dai, Ze Zhang, Ningjia He, Liang Zhang, Zhonghuai Xiang Genome Biology 2007, 8:R162 (4 August 2007) Using a genome-wide oligonucleotide microarray, gene expression was surveyed in multiple silkworm tissues on day 3 of the fifth instar, providing a new resource for annotating the silkworm genome. |
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Housekeeping genes tend to show reduced upstream sequence conservation Domènec Farré, Nicolás Bellora, Loris Mularoni, Xavier Messeguer, M Mar Albà Genome Biology 2007, 8:R140 (13 July 2007) Mammalian housekeeping genes show significantly lower promoter sequence conservation, especially upstream of position -500 with respect to the transcription start site, than genes expressed in a subset of tissues. |
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An analysis of expression patterns of genes encoding proteins with catalytic activities Murat Cankaya, Ana Hernandez, Mehmet Ciftci, Sukru Beydemir, Hasan Ozdemir, Harun Budak, Ilhami Gulcin, Veysel Comakli, Tufan Emircupani, Deniz Ekinci, Muslum Kuzu, Qiuhong Jiang, Gregor Eichele, Omer Kufrevioglu BMC Genomics 2007, 8:232 (12 July 2007) |
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Functional coordination of alternative splicing in the mammalian central nervous system Matthew Fagnani, Yoseph Barash, Joanna Y Ip, Christine Misquitta, Qun Pan, Arneet L Saltzman, Ofer Shai, Leo Lee, Aviad Rozenhek, Naveed Mohammad, Sandrine Willaime-Morawek, Tomas Babak, Wen Zhang, Timothy R Hughes, Derek van der Kooy, Brendan J Frey, Benjamin J Blencowe Genome Biology 2007, 8:R108 (12 June 2007) A microarray analysis provides new evidence suggesting that specific cellular processes in the mammalian CNS are coordinated at the level of alternative splicing, and that a complex splicing code underlies CNS-specific alternative splicing regulation. |
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Christine Stansberg, Audun Vik-Mo, Rita Holdhus, Harald Breilid, Boleslaw Srebro, Kjell Petersen, Hugo A Jørgensen, Inge Jonassen, Vidar M Steen BMC Genomics 2007, 8:94 (4 April 2007) |
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FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data Limin Fu, Enzo Medico BMC Bioinformatics 2007, 8:3 (4 January 2007) |
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Fiona E Lovegrove, Lourdes Peña-Castillo, Naveed Mohammad, W Conrad Liles, Timothy R Hughes, Kevin C Kain BMC Genomics 2006, 7:295 (22 November 2006) |
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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. |
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Global similarity and local divergence in human and mouse gene co-expression networks Panayiotis Tsaparas, Leonardo Mariño-Ramírez, Olivier Bodenreider, Eugene V Koonin, I King Jordan BMC Evolutionary Biology 2006, 6:70 (12 September 2006) Human and mouse co-expression gene networks are frequently highly divergent at the local level but essentially identical at the global level.
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A factor analysis model for functional genomics Rafal Kustra, Romy Shioda, Mu Zhu BMC Bioinformatics 2006, 7:216 (21 April 2006) |
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Cecily J Wolfe, Isaac S Kohane, Atul J Butte BMC Bioinformatics 2005, 6:227 (14 September 2005) |
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Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray Mark G Carter, Alexei A Sharov, Vincent VanBuren, Dawood B Dudekula, Condie E Carmack, Charlie Nelson, Minoru SH Ko Genome Biology 2005, 6:R61 (30 June 2005) An |
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All systems GO for understanding mouse gene function Chris Holmes, Steve DM Brown Journal of Biology 2004, 3:20 (17 December 2004) |
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Co-regulation of mouse genes predicts function Jonathan B Weitzman Journal of Biology 2004, 3:19 (6 December 2004) |