Additional data file 5

EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets that requires minimal development for new data types and search patterns. The FANTOM4 EdgeExpress database http://fantom.gsc.riken.jp/4/edgeexpress summarizes gene expression patterns in the context of alternative promoter structures and regulatory transcription factors and microRNAs using intuitive gene-centric and sub-network views. This is an important resource for gene regulation in acute myeloid leukemia, monocyte/macrophage differentiation and human transcriptional networks.

[1]  Shigeru Tsuchiya,et al.  Establishment and characterization of a human acute monocytic leukemia cell line (THP‐1) , 1980, International journal of cancer.

[2]  William A. Giovinazzo Object-Oriented Data Warehouse Design: Building A Star Schema , 2000 .

[3]  Zhiping Weng,et al.  Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. , 2007, Genome research.

[4]  Ioannis Xenarios,et al.  DIP: the Database of Interacting Proteins , 2000, Nucleic Acids Res..

[5]  T. Speed,et al.  Statistical issues in cDNA microarray data analysis. , 2003, Methods in molecular biology.

[6]  J. Rowley,et al.  Cytogenetic and molecular analysis of the acute monocytic leukemia cell line THP‐1 with an MLL‐AF9 translocation , 2000, Genes, chromosomes & cancer.

[7]  W. L. Ruzzo,et al.  MicroRNA Discovery and Profiling in Human Embryonic Stem Cells by Deep Sequencing of Small RNA Libraries , 2008, Stem cells.

[8]  Hideaki Sugawara,et al.  DNA Data Bank of Japan (DDBJ) for genome scale research in life science , 2002, Nucleic Acids Res..

[9]  Kenta Nakai,et al.  DBTSS: database of transcription start sites, progress report 2008 , 2007, Nucleic Acids Res..

[10]  Christian von Mering,et al.  STRING 7—recent developments in the integration and prediction of protein interactions , 2006, Nucleic Acids Res..

[11]  E. Birney,et al.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002, Nature.

[12]  Geoffrey J Faulkner,et al.  Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases , 2006, Genome Biology.

[13]  Zhiping Weng,et al.  Global mapping of c-Myc binding sites and target gene networks in human B cells , 2006, Proceedings of the National Academy of Sciences.

[14]  C. Bult,et al.  Functional annotation of a full-length mouse cDNA collection , 2001, Nature.

[15]  Jennifer M. Rust,et al.  The BioGRID Interaction Database , 2011 .

[16]  Stijn van Dongen,et al.  Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data , 2007, PLoS Comput. Biol..

[17]  Robert D. Finn,et al.  ProServer: a simple, extensible Perl DAS server , 2007, Bioinform..

[18]  Alistair G. Rust,et al.  Ensembl 2002: accommodating comparative genomics , 2003, Nucleic Acids Res..

[19]  Victor X Jin,et al.  A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. , 2007, Genome research.

[20]  Peter C. Hollenhorst,et al.  Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. , 2007, Genes & development.

[21]  D. Lancet,et al.  GeneCards: integrating information about genes, proteins and diseases. , 1997, Trends in genetics : TIG.

[22]  D. Bartel,et al.  Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome , 2008, Current Biology.

[23]  W. Huber,et al.  Model-based variance-stabilizing transformation for Illumina microarray data , 2008, Nucleic acids research.

[24]  Obi L. Griffith,et al.  ORegAnno: an open-access community-driven resource for regulatory annotation , 2007, Nucleic Acids Res..

[25]  angesichts der Corona-Pandemie,et al.  UPDATE , 1973, The Lancet.

[26]  Steven M. Johnson,et al.  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. , 2008, Genome research.

[27]  Kazuho Ikeo,et al.  CIBEX: center for information biology gene expression database. , 2003, Comptes rendus biologies.

[28]  Allen D. Delaney,et al.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.

[29]  T. Graf,et al.  MafB is an inducer of monocytic differentiation , 2000, The EMBO journal.

[30]  Ian M. Donaldson,et al.  BIND: the Biomolecular Interaction Network Database , 2001, Nucleic Acids Res..

[31]  Gordon K Smyth,et al.  Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2004, Statistical applications in genetics and molecular biology.

[32]  S. Ranade,et al.  Stem cell transcriptome profiling via massive-scale mRNA sequencing , 2008, Nature Methods.

[33]  S. Swerdlow,et al.  A functional c-myb gene is required for normal murine fetal hepatic hematopoiesis , 1991, Cell.

[34]  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.

[35]  Emden R. Gansner,et al.  Graphviz - Open Source Graph Drawing Tools , 2001, GD.

[36]  E. Birney,et al.  EnsMart: a generic system for fast and flexible access to biological data. , 2003, Genome research.

[37]  Martin S. Taylor,et al.  The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line , 2009, Nature Genetics.

[38]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[39]  Jun Kawai,et al.  CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis , 2005, Nucleic Acids Res..

[40]  R. Myers,et al.  Serum response factor binding sites differ in three human cell types. , 2007, Genome research.

[41]  Dipanwita Roy Chowdhury,et al.  Human protein reference database as a discovery resource for proteomics , 2004, Nucleic Acids Res..

[42]  Stijn van Dongen,et al.  miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..

[43]  C. Buske,et al.  Overexpression of HOXA10 perturbs human lymphomyelopoiesis in vitro and in vivo. , 2001, Blood.

[44]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[45]  Mihaela Zavolan,et al.  Inference of miRNA targets using evolutionary conservation and pathway analysis , 2007, BMC Bioinformatics.

[46]  Martin S. Taylor,et al.  Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.

[47]  Tim Hui-Ming Huang,et al.  MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data , 2005, Nucleic Acids Res..

[48]  Geoffrey J Faulkner,et al.  A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. , 2008, Genomics.

[49]  T. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2006, Nucleic Acids Res..