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Acknowledgements:

 

External software resources:

  • EXPANDER uses the FreeHEP Java Library, which is distributed under the LGPL license. FreeHEP copyright holders: CERN, Geneva, Switzerland SLAC, Stanford, California, U.S.A. University of California Santa Cruz, U.S.A.
  • EXPANDER uses the XStream Java Library, which is distributed under the BSD license. Copyright holders: (c) Joe Walnes 2003-2005
  • EXPANDER  uses the Caryoscope java component, which is distributed under the MIT license. Copyright holders: Copyright 2003-2004, Ihab A.B. Awad; Copyright 2006, Anjalee Sujanani; Stanford University. 
  • A portion of the user interface code is due to Sun Microsystems.Inc. Copyright 1994-2004 Sun Microsystems, Inc. (see license for details).
  • Expander interfaces with the R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0 .Installation instructions are given in the R project site.
  • EXPANDER interfaces with Bioconductor packages - affy and gcrma,  which are available under LGPL license. Additional Bioconductor packages may be required for .CEL files pre-processing, depending on the organism and chip type (described in the Input Data section of the user manual). Interested users can install these packages independently under the terms of the Bioconductor license and then use them from inside EXPANDER. Installation instructions are given in the R External Application section of the EXPANDER user manual
  • EXPANDER interfaces with Stanford samr package for R, which is available under LGPL license. Interested users can install samr independently under the terms of the LGPL license and then use it from inside EXPANDER.Installation instructions are given in the R External Application section of the EXPANDER user manual
  • Expander interfaces with the Henrik Bengtsson aroma.affymetrix package for R, which is available under the LGPL license. Interested users can install aroma.affymetrix independently under the terms of the LGPL license and then use it from inside EXPANDER. Installation instructions are given in the R External Application section of the EXPANDER user manual
  • Expander interfaces with the limma package for R, which is available under GPL licnese.
    Citation: Smyth, GK (2005). Limma: linear models for microarray data. In: 'Bioinformatics and Computational Biology Solutions using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, pages 397-420.
  • Expander interfaces with the edgeR package for R, which is available under GPL licnese.
    Citation: Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26,139-140.
  • Expander interfaces with the DESeq2 package for R, which is available under LGPL licnese.
    Citation: Michael I Love, Wolfgang Huber and Simon Anders (2014): Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biology, 15, pp. 550. http://doi.org/10.1186/s13059-014-0550-8.
  • Expander uses a FASTA genome data from Ensembl biomart , which is available under APACHE VERSION 2.0 licnese.
    Data is available at Ensembl site.
  • Expander uses a protein-protein interaction data from intAct , which is available under EBL terms of use. Data is available at intAct site .
    Citation: The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Orchard S et al [PMID: 24234451] Nucl. Acids Res. (2013) doi: 10.1093/nar/gkt1115
  • Expander uses position weight matrices data from TRANSFAC 7.0 public access from 2005.
    Data is available at gene-regulation website.
    Citation: Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nuc Ac Res 34(Database issue):D108-110.
  • Expander uses pathway data from KEGG database, which is available under KEGG academic terms of use.
    Data is available upon registration at kegg ftp site.
  • Expander uses pathway data from WikiPathways database, which is available under Creative Commons Attribution 3.0 Unported license.
    Data is available at WikiPathways site.
    Citation: Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo C, Pico AR. (2011) WikiPathways: building research communities on biological pathways. NAR.
  • Expander uses gene annotation data from UCSC database, which is freely available for any purpose as indicated at UCSC Sequence and Annotation Downloads website.
    Data is available at UCSC Sequence and Annotation Downloads website.
  • Expander uses micro-RNAs data from miRBase . Data is available at miRBase site. Citations:
    miRBase: annotating high confidence microRNAs using deep sequencing data. Kozomara A, Griffiths-Jones S.NAR 2014 42:D68-D73
    miRBase: integrating microRNA annotation and deep-sequencing data. Kozomara A, Griffiths-Jones S. NAR 2011 39:D152-D157
    miRBase: tools for microRNA genomics. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. NAR 2008 36:D154-D158
    miRBase: microRNA sequences, targets and gene nomenclature. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. NAR 2006 34:D140-D144 The microRNA Registry. Griffiths-Jones S. NAR 2004 32:D109-D111
  • Expander uses a Gene-Ontology (GO) data from:
    - Gene Ontology Consortium , which is available under the Creative Commons Attribution 4.0 Unported License.
    Data is available at: geneOntology 
    - Gene to GO association from NCBI which is available via NCBI ftp site
    Copyright holders: National Center for Biotechnology Information, U.S. National Library of Medicine 8600 Rockville Pike, Bethesda MD, 20894 USA
    - GO from EBI, which is available under EBL terms of use.
    Data is available at QuickGO site

Grant support:

Expander is developed with past and present support from the Ministry of Science and and Technology, Israel, the Israel Science Foundation, and the European Commission Seventh Framework Programme

 

Our "Power Users":

We gratefully thank the following members of the EXPANDER users community who provided suggestions for improvement, tested beta versions and/or contributed other valuable ideas.
  • Dr. Alberto de la Fuente, CRS4 Bioinformatica Computational Systems Biology, Sardinia.
  • Mr. Amir Apelbaum, Dept. Biological Chemistry, The Weizmann Institute of Science
  • Dr. Metsada Pasmanik-Chor, Bioinformatics unit, Tel-Aviv University
  • Mr. Haim Belinson,  Dept. Neurobiology, Tel-Aviv University
  • Dr. Haim Sharon, Sackler Medical School,  Tel-Aviv University
  • Dr. Eitan Rubin, Ben Gurion University
  • Ms. Sharon Bruckner, Computational Genomics Group, Tel-Aviv University