Association of variations in I kappa B-epsilon with Graves’ disease using classical and myGrid methodologies

Bioinformatics experiments can be modelled as workflows whereby the order of each computational resource used has been pre-defined. Workflows in the Grid project are composed and enacted using the Taverna workflow system. We have compared the use of Taverna with classical approaches for performing bioinformatics experiments in the genetic analysis of Graves’ disease. Both classical and myGrid methodologies identified I kappa B-epsilon as a candidate gene involved in Graves’ disease, demonstrating that Grid is capable of producing the same results as the classical bioinformatics approach.

[1]  Evelyn Camon,et al.  The EMBL Nucleotide Sequence Database , 2000, Nucleic Acids Res..

[2]  Carole A. Goble,et al.  myGrid: personalised bioinformatics on the information grid , 2003, ISMB.

[3]  S. Pearce,et al.  Evidence for a Graves' disease susceptibility locus at chromosome Xp11 in a United Kingdom population. , 2001, The Journal of clinical endocrinology and metabolism.

[4]  L. Stein.  Creating a bioinformatics nation , 2002, Nature.

[5]  Carole A. Goble,et al.  A Suite of Daml+Oil Ontologies to Describe Bioinformatics Web Services and Data , 2003, Int. J. Cooperative Inf. Syst..

[6]  Bruno W. S. Sobral,et al.  A Life Scientist's Gateway to Distributed Data Management and Computing: The PathPort/ToolBus Framework , 2003, OMICS.

[7]  A. Israël,et al.  I kappa B epsilon, a novel member of the I kappa B family, controls RelA and cRel NF-kappa B activity. , 1997, The EMBO journal.

[8]  Matthew R. Pocock,et al.  Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..

[9]  T. Oinn,et al.  Soaplab - a unified Sesame door to analysis tools , 2003 .

[10]  Anil Wipat,et al.  Experiences with e-Science workflow specification and enactment in bioinformatics , 2003 .

[11]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[12]  Hideaki Sugawara,et al.  Development of DDBJ-XML and Its Application to a Database of cDNA , 2000 .

[13]  Chris Greenhalgh,et al.  Performing \emph{In Silico} Experiments on the Grid: A Users' Perspective , 2003 .

[14]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[15]  Sergio Contrino,et al.  ArrayExpress—a public repository for microarray gene expression data at the EBI , 2004, Nucleic Acids Res..

[16]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[17]  Robert Stevens,et al.  Performing in silico Experiments on the Grid : A Users Perspective , 2003 .

[18]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[19]  Benjamin M. Bolstad,et al.  affy - analysis of Affymetrix GeneChip data at the probe level , 2004, Bioinform..

[20]  David M. Booth,et al.  Web Services Architecture , 2004 .

[21]  A. Israël,et al.  I kappa B epsilon, a novel member of the IκB family, controls RelA and cRel NF‐κB activity , 1997 .

[22]  Alan J. Robinson,et al.  XEMBL: distributing EMBL data in XML format , 2002, Bioinform..