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The functional landscape of mouse gene expression

Wen Zhang, Quaid D Morris, Richard Chang, Ofer Shai, Malina A Bakowski, Nicholas Mitsakakis, Naveed Mohammad, Mark D Robinson, Ralph Zirngibl, Eszter Somogyi, Nancy Laurin, Eftekhar Eftekharpour, Eric Sat, Jörg Grigull, Qun Pan, Wen-Tao Peng, Nevan Krogan, Jack Greenblatt, Michael Fehlings, Derek van der Kooy, Jane Aubin, Benoit G Bruneau, Janet Rossant, Benjamin J Blencowe, Brendan J Frey and Timothy R Hughes*

Journal of Biology 2004, 3:21 doi:10.1186/jbiol16

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Selection for the compactness of highly expressed genes in Gallus gallus

You S Rao, Zhang F Wang, Xue W Chai, Guo Z Wu, Ming Zhou, Qing H Nie, Xi Q Zhang Biology Direct 2010, 5:35 (14 May 2010)

Methodology article   Open Access Highly Accessed

Integrative approaches to the prediction of protein functions based on the feature selection

Seokha Ko, Hyunju Lee BMC Bioinformatics 2009, 10:455 (31 December 2009)

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Identification and characterization of endonuclein binding proteins: evidence of modulatory effects on signal transduction and chaperone activity

Maja Ludvigsen, Morten Østergaard, Henrik Vorum, Christian Jacobsen, Bent Honoré BMC Biochemistry 2009, 10:34 (22 December 2009)

Methodology article   Open Access

Generation of Gene Ontology benchmark datasets with various types of positive signal

Petri Törönen, Petri Pehkonen, Liisa Holm BMC Bioinformatics 2009, 10:319 (7 October 2009)

Research   Open Access

Gene set analysis methods applied to chicken microarray expression data

Axel Skarman, Li Jiang, Henrik Hornshøj, Bart Buitenhuis, Jakob Hedegaard, Lene N Conley, Peter Sørensen BMC Proceedings 2009, 3(Suppl 4):S8 (16 July 2009)

Research article   Open Access

Functional annotations of diabetes nephropathy susceptibility loci through analysis of genome-wide renal gene expression in rat models of diabetes mellitus

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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Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues

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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Articulation of three core metabolic processes in Arabidopsis: Fatty acid biosynthesis, leucine catabolism and starch metabolism

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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Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy

Wan Kim, Chase Krumpelman, Edward M Marcotte Genome Biology 2008, 9(Suppl 1):S5 (27 June 2008)

Method   Open Access

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

Sara Mostafavi, Debajyoti Ray, David Warde-Farley, Chris Grouios, Quaid Morris Genome Biology 2008, 9(Suppl 1):S4 (27 June 2008)

Research   Open Access

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)

Methodology article   Open Access

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)

Research article   Open Access

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)

Method   Open Access

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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Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm, Bombyx mori

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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Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation

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)

Research article   Open Access

Simultaneous host and parasite expression profiling identifies tissue-specific transcriptional programs associated with susceptibility or resistance to experimental cerebral malaria

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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Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways

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.

Methodology article   Open Access

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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Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks

Cecily J Wolfe, Isaac S Kohane, Atul J Butte BMC Bioinformatics 2005, 6:227 (14 September 2005)

Method   Open Access

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 in-situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes is presented. Exogenous RNA controls derived from yeast allow quantitative estimation of absolute endogenous transcript abundance

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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)

Research news   Free

Co-regulation of mouse genes predicts function

Jonathan B Weitzman Journal of Biology 2004, 3:19 (6 December 2004)