My NCBISign In
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, Timothy R Hughes
J Biol. 2004; 3(5): 21. Published online 2004 December 6. doi: 10.1186/jbiol16
PMCID:
PMC549719
Abstract Full Text PDF–678K Supplementary Material

Is Cited by the Following 101 Articles in this Archive:

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks
Jesse Gillis, Paul Pavlidis
PLoS Comput Biol. 2012 March; 8(3): e1002444. Published online 2012 March 29. doi: 10.1371/journal.pcbi.1002444
PMCID:
PMC3315453
Abstract Full Text PDF–414K Supplementary Material
Gene-Based Analysis of Regionally Enriched Cortical Genes in GWAS Data Sets of Cognitive Traits and Psychiatric Disorders
Kari M. Ersland, Andrea Christoforou, Christine Stansberg, Thomas Espeseth, Manuel Mattheisen, Morten Mattingsdal, Gudmundur A. Hardarson, Thomas Hansen, Carla P. D. Fernandes, Sudheer Giddaluru, René Breuer, Jana Strohmaier, Srdjan Djurovic, Markus M. Nöthen, Marcella Rietschel, Astri J. Lundervold, Thomas Werge, Sven Cichon, Ole A. Andreassen, Ivar Reinvang, Vidar M. Steen, Stephanie Le Hellard
PLoS One. 2012; 7(2): e31687. Published online 2012 February 22. doi: 10.1371/journal.pone.0031687
PMCID:
PMC3285182
Abstract Full Text PDF–400K Supplementary Material
Molecular Mechanisms of Fiber Differential Development between G. barbadense and G. hirsutum Revealed by Genetical Genomics
Xiangdong Chen, Wangzhen Guo, Bingliang Liu, Yuanming Zhang, Xianliang Song, Yu Cheng, Lili Zhang, Tianzhen Zhang
PLoS One. 2012; 7(1): e30056. Published online 2012 January 11. doi: 10.1371/journal.pone.0030056
PMCID:
PMC3256209
Abstract Full Text PDF–1017K Supplementary Material
No Excess Gene Movement Is Detected off the Avian or Lepidopteran Z Chromosome
Melissa A. Toups, James B. Pease, Matthew W. Hahn
Genome Biol Evol. 2011; 3: 1381–1390. Published online 2011 October 24. doi: 10.1093/gbe/evr109
PMCID:
PMC3242482
Abstract Full Text PDF–143K
Global Gene Expression during the Human Organogenesis: From Transcription Profiles to Function Predictions
Lu Xue, Hong Yi, Zan Huang, Yun-Bo Shi, Wen-Xin Li
Int J Biol Sci. 2011; 7(7): 1068–1076. Published online 2011 September 7.
PMCID:
PMC3174391
Abstract Full Text PDF–869K
A General Model for Binary Cell Fate Decision Gene Circuits with Degeneracy: Indeterminacy and Switch Behavior in the Absence of Cooperativity
Mircea Andrecut, Julianne D. Halley, David A. Winkler, Sui Huang
PLoS One. 2011; 6(5): e19358. Published online 2011 May 19. doi: 10.1371/journal.pone.0019358
PMCID:
PMC3098230
Abstract Full Text PDF–261K Supplementary Material
A Gene-Phenotype Network for the Laboratory Mouse and Its Implications for Systematic Phenotyping
Octavio Espinosa, John M. Hancock
PLoS One. 2011; 6(5): e19693. Published online 2011 May 19. doi: 10.1371/journal.pone.0019693
PMCID:
PMC3098258
Abstract Full Text PDF–926K Supplementary Material
Networking in a global world: Establishing functional connections between neural splicing regulators and their target transcripts
John A. Calarco, Mei Zhen, Benjamin J. Blencowe
RNA. 2011 May; 17(5): 775–791. doi: 10.1261/rna.2603911
PMCID:
PMC3078728
Abstract Full Text PDF–439K
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data
Sami K Kilpinen, Kalle A Ojala, Olli P Kallioniemi
BioData Min. 2011; 4: 5. Published online 2011 March 31. doi: 10.1186/1756-0381-4-5
PMCID:
PMC3080808
Abstract Full Text PDF–3.5M Supplementary Material
Gene expression in the rat brain: High similarity but unique differences between frontomedial-, temporal- and occipital cortex
Christine Stansberg, Kari M Ersland, Paul van der Valk, Vidar M Steen
BMC Neurosci. 2011; 12: 15. Published online 2011 January 26. doi: 10.1186/1471-2202-12-15
PMCID:
PMC3040714
Abstract Full Text PDF–2.3M Supplementary Material
Analysis of Kinase Gene Expression Patterns across 5681 Human Tissue Samples Reveals Functional Genomic Taxonomy of the Kinome
Sami Kilpinen, Kalle Ojala, Olli Kallioniemi
PLoS One. 2010; 5(12): e15068. Published online 2010 December 3. doi: 10.1371/journal.pone.0015068
PMCID:
PMC2997066
Abstract Full Text PDF–1.5M Supplementary Material
Pathology tissue–chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples
Mirco Fanelli, Stefano Amatori, Iros Barozzi, Matias Soncini, Roberto Dal Zuffo, Gabriele Bucci, Maria Capra, Micaela Quarto, Gaetano Ivan Dellino, Ciro Mercurio, Myriam Alcalay, Giuseppe Viale, Pier Giuseppe Pelicci, Saverio Minucci
Proc Natl Acad Sci U S A. 2010 December 14; 107(50): 21535–21540. Published online 2010 November 24. doi: 10.1073/pnas.1007647107
PMCID:
PMC3003125
Abstract Full Text PDF–1.2M Supplementary Material
Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations
Yuanfang Guan, Cheryl L. Ackert-Bicknell, Braden Kell, Olga G. Troyanskaya, Matthew A. Hibbs
PLoS Comput Biol. 2010 November; 6(11): e1000991. Published online 2010 November 11. doi: 10.1371/journal.pcbi.1000991
PMCID:
PMC2978695
Abstract Full Text PDF–1.0M Supplementary Material
Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq
Hao Sun, Jiejun Wu, Priyankara Wickramasinghe, Sharmistha Pal, Ravi Gupta, Anirban Bhattacharyya, Francisco J. Agosto-Perez, Louise C. Showe, Tim H.-M. Huang, Ramana V. Davuluri
Nucleic Acids Res. 2011 January; 39(1): 190–201. Published online 2010 September 14. doi: 10.1093/nar/gkq775
PMCID:
PMC3017616
Abstract Full Text PDF–4.5M Supplementary Material
Gene expression atlas for human embryogenesis
Hong Yi, Lu Xue, Ming-Xiong Guo, Jian Ma, Yan Zeng, Wei Wang, Jin-Yang Cai, Hai-Ming Hu, Hong-Bing Shu, Yun-Bo Shi, Wen-Xin Li
FASEB J. 2010 September; 24(9): 3341–3350. doi: 10.1096/fj.10-158782
PMCID:
PMC2923361
Abstract Full Text Supplementary Material
Gene Expression in Chicken Reveals Correlation with Structural Genomic Features and Conserved Patterns of Transcription in the Terrestrial Vertebrates
Haisheng Nie, Richard P. M. A. Crooijmans, Aart Lammers, Evert M. van Schothorst, Jaap Keijer, Pieter B. T. Neerincx, Jack A. M. Leunissen, Hendrik-Jan Megens, Martien A. M. Groenen
PLoS One. 2010; 5(8): e11990. Published online 2010 August 5. doi: 10.1371/journal.pone.0011990
PMCID:
PMC2916831
Abstract Full Text PDF–501K Supplementary Material
Computational analysis of tissue-specific gene networks: application to murine retinal functional studies
Jianfei Hu, Jun Wan, Laszlo Hackler, Jr., Donald J. Zack, Jiang Qian
Bioinformatics. 2010 September 15; 26(18): 2289–2297. Published online 2010 July 8. doi: 10.1093/bioinformatics/btq408
PMCID:
PMC2935398
Abstract Full Text PDF–483K Supplementary Material
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
Biol Direct. 2010; 5: 35. Published online 2010 May 14. doi: 10.1186/1745-6150-5-35
PMCID:
PMC2883972
Abstract Full Text PDF–831K Supplementary Material
An atlas of combinatorial transcriptional regulation in mouse and man
The FANTOM consortium and RIKEN Omics Science Center
Cell. Author manuscript; available in PMC 2011 March 5.
Published in final edited form as: Cell. 2010 March 5; 140(5): 744–752. doi: 10.1016/j.cell.2010.01.044
PMCID:
PMC2836267
Abstract Full Text PDF–2.2M Supplementary Material
Conservation and Regulatory Associations of a Wide Affinity Range of Mouse Transcription Factor Binding Sites
Savina A. Jaeger, Esther T. Chan, Michael F. Berger, Rolf Stottmann, Timothy R. Hughes, Martha L. Bulyk
Genomics. Author manuscript; available in PMC 2011 April 1.
Published in final edited form as: Genomics. 2010 April; 95(4): 185–195. Published online 2010 January 15. doi: 10.1016/j.ygeno.2010.01.002
PMCID:
PMC2848887
Abstract Full Text PDF–2.1M Supplementary Material
Integrative approaches to the prediction of protein functions based on the feature selection
Seokha Ko, Hyunju Lee
BMC Bioinformatics. 2009; 10: 455. Published online 2009 December 31. doi: 10.1186/1471-2105-10-455
PMCID:
PMC2813249
Abstract Full Text PDF–2.9M Supplementary Material
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 Biochem. 2009; 10: 34. Published online 2009 December 22. doi: 10.1186/1471-2091-10-34
PMCID:
PMC2810291
Abstract Full Text PDF–2.2M
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
Daniel Ramsköld, Eric T. Wang, Christopher B. Burge, Rickard Sandberg
PLoS Comput Biol. 2009 December; 5(12): e1000598. Published online 2009 December 11. doi: 10.1371/journal.pcbi.1000598
PMCID:
PMC2781110
Abstract Full Text PDF–927K Supplementary Material
Generation of Gene Ontology benchmark datasets with various types of positive signal
Petri Törönen, Petri Pehkonen, Liisa Holm
BMC Bioinformatics. 2009; 10: 319. Published online 2009 October 7. doi: 10.1186/1471-2105-10-319
PMCID:
PMC2762998
Abstract Full Text PDF–301K Supplementary Material
Gene set analysis methods applied to chicken microarray expression data
Axel Skarman, Li Jiang, Hornshøj Henrik, Bart Buitenhuis, Jakob Hedegaard, Lene N Conley, Peter Sørensen
BMC Proc. 2009; 3(Suppl 4): S8. Published online 2009 July 16. doi: 10.1186/1753-6561-3-S4-S8
PMCID:
PMC2712751
Abstract Full Text PDF–509K Supplementary Material
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 Med Genomics. 2009; 2: 41. Published online 2009 July 9. doi: 10.1186/1755-8794-2-41
PMCID:
PMC2717999
Abstract Full Text PDF–478K Supplementary Material
An Integrated Strategy to Study Muscle Development and Myofilament Structure in Caenorhabditis elegans
Barbara Meissner, Adam Warner, Kim Wong, Nicholas Dube, Adam Lorch, Sheldon J. McKay, Jaswinder Khattra, Teresa Rogalski, Aruna Somasiri, Iasha Chaudhry, Rebecca M. Fox, David M. Miller, III, David L. Baillie, Robert A. Holt, Steven J. M. Jones, Marco A. Marra, Donald G. Moerman
PLoS Genet. 2009 June; 5(6): e1000537. Published online 2009 June 26. doi: 10.1371/journal.pgen.1000537
PMCID:
PMC2694363
Abstract Full Text PDF–1.3M Supplementary Material
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. Published online 2009 June 17. doi: 10.1186/1471-2164-10-269
PMCID:
PMC2706266
Abstract Full Text PDF–741K Supplementary Material
Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology
Brian Cox, Max Kotlyar, Andreas I Evangelou, Vladimir Ignatchenko, Alex Ignatchenko, Kathie Whiteley, Igor Jurisica, S Lee Adamson, Janet Rossant, Thomas Kislinger
Mol Syst Biol. 2009; 5: 279. Published online 2009 June 16. doi: 10.1038/msb.2009.37
PMCID:
PMC2710868
Abstract Full Text PDF–1.2M Supplementary Material
Increasing MicroRNA Target Prediction Confidence by the Relative R-squared Method
Hsiuying Wang, Wen-Hsiung Li
J Theor Biol. Author manuscript; available in PMC 2010 August 21.
Published in final edited form as: J Theor Biol. 2009 August 21; 259(4): 793–798. Published online 2009 May 20. doi: 10.1016/j.jtbi.2009.05.007
PMCID:
PMC2744435
Abstract Full Text PDF–1.1M
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