GREAT improves functional interpretation of cis-regulatory regions
暂无分享,去创建一个
Cory Y. McLean | G. Bejerano | M. Hiller | A. Wenger | C. McLean | B. Schaar | Dave Bristor | S. L. Clarke | C. B. Lowe | S. Clarke
[1] M. Gilman,et al. YY1 facilitates the association of serum response factor with the c-fos serum response element , 1995, Molecular and cellular biology.
[2] J. Massagué,et al. SMADs: mediators and regulators of TGF-β signaling , 1998 .
[3] J. Massagué,et al. SMADs: mediators and regulators of TGF-beta signaling. , 1998, Current opinion in genetics & development.
[4] C. Bertolotto,et al. Cleavage of the Serum Response Factor during Death Receptor-induced Apoptosis Results in an Inhibition of the c-FOS Promoter Transcriptional Activity* , 2000, The Journal of Biological Chemistry.
[5] D. Storm,et al. SRF‐dependent gene expression is required for PI3‐kinase‐regulated cell proliferation , 2000, The EMBO journal.
[6] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[7] Wolfgang Wurst,et al. Neural plate patterning: Upstream and downstream of the isthmic organizer , 2001, Nature Reviews Neuroscience.
[8] A. Wilkie,et al. Genetics of craniofacial development and malformation , 2001, Nature Reviews Genetics.
[9] Juan Carlos Izpisúa Belmonte,et al. Patterning mechanisms controlling vertebrate limb development. , 2001, Annual review of cell and developmental biology.
[10] P. Levings,et al. The human β‐globin locus control region , 2002 .
[11] Tom H. Pringle,et al. The human genome browser at UCSC. , 2002, Genome research.
[12] P. Levings,et al. The human beta-globin locus control region. , 2002, European journal of biochemistry.
[13] A. Tarnawski,et al. Serum response factor: discovery, biochemistry, biological roles and implications for tissue injury healing. , 2002, Journal of physiology and pharmacology : an official journal of the Polish Physiological Society.
[14] J. Massagué,et al. E2F4/5 and p107 as Smad Cofactors Linking the TGFβ Receptor to c-myc Repression , 2002, Cell.
[15] L. Niswander. Pattern formation: old models out on a limb , 2003, Nature Reviews Genetics.
[16] Denis Duboule,et al. A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster , 2003, Cell.
[17] B. Oostra,et al. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. , 2003, Human molecular genetics.
[18] D. Haussler,et al. Ultraconserved Elements in the Human Genome , 2004, Science.
[19] Purvesh Khatri,et al. Ontological analysis of gene expression data: current tools, limitations, and open problems , 2005, Bioinform..
[20] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[21] J. Dopazo. Functional interpretation of microarray experiments. , 2006, Omics : a journal of integrative biology.
[22] Gary D. Bader,et al. cPath: open source software for collecting, storing, and querying biological pathways , 2006, BMC Bioinformatics.
[23] C. Nusbaum,et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. , 2006, Genome research.
[24] Michael R. Green,et al. Transcriptional regulatory elements in the human genome. , 2006, Annual review of genomics and human genetics.
[25] David Haussler,et al. The UCSC Known Genes , 2006, Bioinform..
[26] D. Allison,et al. Microarray data analysis: from disarray to consolidation and consensus , 2006, Nature Reviews Genetics.
[27] J. Rubenstein,et al. Neuronal production and precursor proliferation defects in the neocortex of mice with loss of function in the canonical Wnt signaling pathway , 2006, Neuroscience.
[28] D. Haussler,et al. A distal enhancer and an ultraconserved exon are derived from a novel retroposon , 2006, Nature.
[29] David Bryant,et al. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists , 2007, Nucleic Acids Res..
[30] W-H Kim,et al. SRF is a nuclear repressor of Smad3-mediated TGF-beta signaling. , 2007, Oncogene.
[31] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[32] E. Mardis. ChIP-seq: welcome to the new frontier , 2007, Nature Methods.
[33] K. Fujiwara,et al. Serum response factor: master regulator of the actin cytoskeleton and contractile apparatus. , 2007, American journal of physiology. Cell physiology.
[34] A. Mortazavi,et al. Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.
[35] David Haussler,et al. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes , 2007, Proceedings of the National Academy of Sciences.
[36] W-H Kim,et al. SRF is a nuclear repressor of Smad3-mediated TGF-β signaling , 2007, Oncogene.
[37] N. D. Clarke,et al. Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells , 2008, Cell.
[38] Tao Liu,et al. TreeFam: 2008 Update , 2007, Nucleic Acids Res..
[39] R. Myers,et al. An Integrated Software System for Analyzing Chip-chip and Chip-seq Data (supplementary Information) , 2008 .
[40] Judith A. Blake,et al. The Mouse Genome Database (MGD): mouse biology and model systems , 2007, Nucleic Acids Res..
[41] D. Duboule,et al. Global control regions and regulatory landscapes in vertebrate development and evolution. , 2008, Advances in genetics.
[42] R. Shamir,et al. Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. , 2008, Genome research.
[43] K. Lange,et al. Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids , 2008, Nature Genetics.
[44] S. Batzoglou,et al. Genome-Wide Analysis of Transcription Factor Binding Sites Based on ChIP-Seq Data , 2008, Nature Methods.
[45] P. Park,et al. Design and analysis of ChIP-seq experiments for DNA-binding proteins , 2008, Nature Biotechnology.
[46] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[47] Judith A. Blake,et al. The Mouse Genome Database genotypes::phenotypes , 2008, Nucleic Acids Res..
[48] Ivan Ovcharenko,et al. Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements , 2009, Bioinform..
[49] G. Tuteja,et al. Extracting transcription factor targets from ChIP-Seq data , 2009, Nucleic acids research.
[50] Raymond K. Auerbach,et al. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls , 2009, Nature Biotechnology.
[51] A. Visel,et al. ChIP-seq accurately predicts tissue-specific activity of enhancers , 2009, Nature.
[52] P. Park. ChIP–seq: advantages and challenges of a maturing technology , 2009, Nature Reviews Genetics.
[53] Jennifer A. Mitchell,et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells , 2010, Nature Genetics.