Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database

DOI PDF 被引用文献3件
  • Joshua D Fortriede
    Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
  • Troy J Pells
    Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
  • Stanley Chu
    Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
  • Praneet Chaturvedi
    Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
  • DongZhuo Wang
    Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
  • Malcom E Fisher
    Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
  • Christina James-Zorn
    Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
  • Ying Wang
    Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
  • Mardi J Nenni
    Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
  • Kevin A Burns
    Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
  • Vaneet S Lotay
    Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
  • Virgilio G Ponferrada
    Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
  • Kamran Karimi
    Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
  • Aaron M Zorn
    Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
  • Peter D Vize
    Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada

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<jats:title>Abstract</jats:title> <jats:p>Xenbase (www.xenbase.org) is a knowledge base for researchers and biomedical scientists that employ the amphibian Xenopus as a model organism in biomedical research to gain a deeper understanding of developmental and disease processes. Through expert curation and automated data provisioning from various sources Xenbase strives to integrate the body of knowledge on Xenopus genomics and biology together with the visualization of biologically significant interactions. Most current studies utilize next generation sequencing (NGS) but until now the results of different experiments were difficult to compare and not integrated with other Xenbase content. Xenbase has developed a suite of tools, interfaces and data processing pipelines that transforms NCBI Gene Expression Omnibus (GEO) NGS content into deeply integrated gene expression and chromatin data, mapping all aligned reads to the most recent genome builds. This content can be queried and visualized via multiple tools and also provides the basis for future automated ‘gene expression as a phenotype’ and gene regulatory network analyses.</jats:p>

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