Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
暂无分享,去创建一个
Carsten O. Daub | Piero Carninci | Yoshihide Hayashizaki | Hideya Kawaji | Alistair R. R. Forrest | Erik van Nimwegen | Marina Lizio | Harukazu Suzuki | Jessica Severin | Michael Rehli | Kate Schroder | Katharine M. Irvine | Piero Carninci | Y. Hayashizaki | K. Schroder | Harukazu Suzuki | D. Hume | A. Forrest | S. Katayama | H. Kawaji | J. Severin | C. Daub | M. Rehli | E. Nimwegen | M. Lizio | K. Irvine | A. Waterhouse | D. Hume | Jessica Severin
[1] Huajun Chen,et al. The Semantic Web , 2011, Lecture Notes in Computer Science.
[2] Piero Carninci,et al. Additional data file 5 , 2003 .
[3] Yoshihide Hayashizaki,et al. Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation , 2009, Genome Biology.
[4] E. Birney,et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002, Nature.
[5] Andrew M. Waterhouse,et al. The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation , 2009, Genome Biology.
[6] J. Kawai,et al. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. , 2010, Genome research.
[7] C. Kai,et al. CAGE: cap analysis of gene expression , 2006, Nature Methods.
[8] Mihaela Zavolan,et al. Inference of miRNA targets using evolutionary conservation and pathway analysis , 2007, BMC Bioinformatics.
[9] Toshio Kojima,et al. High-resolution analysis of aberrant regions in autosomal chromosomes in human leukemia THP-1 cell line , 2009, BMC Research Notes.
[10] J. Kawai,et al. The regulated retrotransposon transcriptome of mammalian cells , 2009, Nature Genetics.
[11] Nigel W. Hardy,et al. The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". , 2008, Omics : a journal of integrative biology.
[12] Jun Kawai,et al. CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis , 2005, Nucleic Acids Res..
[13] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[14] Christoph Rodak,et al. MirZ: an integrated microRNA expression atlas and target prediction resource , 2009, Nucleic Acids Res..
[15] Ibrahim Emam,et al. ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression , 2008, Nucleic Acids Res..
[16] Martin S. Taylor,et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line , 2009, Nature Genetics.
[17] Kenta Nakai,et al. DBTSS: database of transcription start sites, progress report 2008 , 2007, Nucleic Acids Res..
[18] S. Batalov,et al. Antisense Transcription in the Mammalian Transcriptome , 2005, Science.
[19] Satoshi Takahashi,et al. The RIKEN integrated database of mammals , 2010, Nucleic Acids Res..
[20] Paul T. Spellman,et al. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB , 2006, BMC Bioinformatics.
[21] S. Lewis,et al. The generic genome browser: a building block for a model organism system database. , 2002, Genome research.
[22] J. Kawai,et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[23] James R. Knight,et al. Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.
[24] C. Bult,et al. Functional annotation of a full-length mouse cDNA collection , 2001, Nature.
[25] R. Maki,et al. The proto-oncogene PU.1 regulates expression of the myeloid-specific CD11b promoter. , 1993, The Journal of biological chemistry.
[26] J. Kawai,et al. Tiny RNAs associated with transcription start sites in animals , 2009, Nature Genetics.
[27] Carsten O. Daub,et al. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan , 2010, Nature Methods.
[28] Ariel S. Schwartz,et al. An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man , 2010, Cell.
[29] S. Salzberg,et al. The Transcriptional Landscape of the Mammalian Genome , 2005, Science.
[30] Jun Kawai,et al. The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells. , 2010, Molecular immunology.
[31] M Suzuki,et al. Explorer Induction of microRNAs , mir-155 , mir-222 , mir-424 and mir-503 , promotes monocytic differentiation through combinatorial regulation , 2010 .
[32] Erik van Nimwegen,et al. SwissRegulon: a database of genome-wide annotations of regulatory sites , 2006, Nucleic Acids Res..
[33] Martin S. Taylor,et al. Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.
[34] Jun Kawai,et al. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. , 2009, Genome research.
[35] Carsten O. Daub,et al. SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes , 2009, BMC Bioinformatics.
[36] Piero Carninci,et al. Tag-based approaches for transcriptome research and genome annotation , 2005, Nature Methods.
[37] Shigeru Tsuchiya,et al. Establishment and characterization of a human acute monocytic leukemia cell line (THP‐1) , 1980, International journal of cancer.
[38] Ting Wang,et al. ENCODE whole-genome data in the UCSC Genome Browser , 2009, Nucleic Acids Res..
[39] John Quackenbush,et al. Data-driven normalization strategies for high-throughput quantitative RT-PCR , 2009, BMC Bioinformatics.
[40] Terrence S. Furey,et al. The UCSC Genome Browser Database , 2003, Nucleic Acids Res..
[41] D. Tenen,et al. The Sp1 transcription factor binds the CD11b promoter specifically in myeloid cells in vivo and is essential for myeloid-specific promoter activity. , 1993, The Journal of biological chemistry.
[42] Masaru Tomita,et al. Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns , 2010, BMC Genomics.
[43] Sean R. Eddy,et al. The Distributed Annotation System , 2001, BMC Bioinformatics.
[44] Piotr J. Balwierz,et al. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data , 2009, Genome Biology.
[45] K. Nakai,et al. Massive transcriptional start site analysis of human genes in hypoxia cells , 2009, Nucleic acids research.
[46] James A. Hendler,et al. The Semantic Web" in Scientific American , 2001 .
[47] Geoffrey J Faulkner,et al. A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. , 2008, Genomics.