GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments

GeneProf Data (http://www.geneprof.org) is an open web resource for analysed functional genomics experiments. We have built up a large collection of completely processed RNA-seq and ChIP-seq studies by carefully and transparently reanalysing and annotating high-profile public data sets. GeneProf makes these data instantly accessible in an easily interpretable, searchable and reusable manner and thus opens up the path to the advantages and insights gained from genome-scale experiments to a broader scientific audience. Moreover, GeneProf supports programmatic access to these data via web services to further facilitate the reuse of experimental data across tools and laboratories.

[1]  Paul T. Spellman,et al.  GenomeGraphs: integrated genomic data visualization with R , 2009, BMC Bioinformatics.

[2]  Toshihisa Takagi,et al.  DDBJ new system and service refactoring , 2012, Nucleic Acids Res..

[3]  Florian Halbritter,et al.  GeneProf: analysis of high-throughput sequencing experiments , 2011, Nature Methods.

[4]  Xiu Lin,et al.  Facing growth in the European Nucleotide Archive , 2012, Nucleic Acids Res..

[5]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[6]  David S. Goodsell,et al.  The RCSB Protein Data Bank: new resources for research and education , 2012, Nucleic Acids Res..

[7]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[8]  J. Nichols,et al.  Functional Expression Cloning of Nanog, a Pluripotency Sustaining Factor in Embryonic Stem Cells , 2003, Cell.

[9]  Sean R. Davis,et al.  NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..

[10]  Carole A. Goble,et al.  The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud , 2013, Nucleic Acids Res..

[11]  Mary Goldman,et al.  The UCSC Genome Browser database: extensions and updates 2013 , 2012, Nucleic Acids Res..

[12]  Laurent Gil,et al.  Ensembl 2013 , 2012, Nucleic Acids Res..

[13]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[14]  Ting Wang,et al.  ENCODE whole-genome data in the UCSC Genome Browser , 2009, Nucleic Acids Res..

[15]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[16]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[17]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[18]  Heather A. Piwowar,et al.  Sharing Detailed Research Data Is Associated with Increased Citation Rate , 2007, PloS one.

[19]  Bernd Wiswedel,et al.  Extending KNIME for next-generation sequencing data analysis , 2011, Bioinform..

[20]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[21]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[22]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[23]  T. Mikkelsen,et al.  The NIH Roadmap Epigenomics Mapping Consortium , 2010, Nature Biotechnology.

[24]  David Haussler,et al.  ENCODE whole-genome data in the UCSC genome browser (2011 update) , 2010, Nucleic Acids Res..

[25]  Christie S. Chang,et al.  The BioGRID interaction database: 2013 update , 2012, Nucleic Acids Res..

[26]  Philip Cayting,et al.  An encyclopedia of mouse DNA elements (Mouse ENCODE) , 2012, Genome Biology.

[27]  Maria Keays,et al.  ArrayExpress update—trends in database growth and links to data analysis tools , 2012, Nucleic Acids Res..

[28]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[29]  C. Ball,et al.  Repeatability of published microarray gene expression analyses , 2009, Nature Genetics.

[30]  Nicola Festuccia,et al.  Esrrb Is a Direct Nanog Target Gene that Can Substitute for Nanog Function in Pluripotent Cells , 2012, Cell stem cell.