BTECH: A platform to integrate genomic, transcriptomic and epigenomic alterations in brain tumors

Min Wang, Hehuang Xie, Wendy Stellpflug, Veena Rajaram, Maria De Fatima Bonaldo, Stewart Goldman, Tadanori Tomita, Marcelo Bento Soares

Research output: Contribution to journalArticle

5 Scopus citations

Abstract

The identification of molecular signatures predictive of clinical behavior and outcome in brain tumors has been the focus of many studies in the recent years. Despite the wealth of data that are available in the public domain on alterations in the genome, epigenome and transcriptome of brain tumors, the underlying molecular mechanisms leading to tumor initiation and progression remain largely unknown. Unfortunately, most of these data are scattered in multiple databases and supplementary materials of publications, thus making their retrieval, evaluation, comparison and visualization a rather arduous task. Here we report the development and implementation of an open access database (BTECH), a community resource for the deposition of a wide range of molecular data derived from brain tumor studies. This comprehensive database integrates multiple datasets, including transcript profiles, epigenomic CpG methylation data, DNA copy number alterations and structural chromosomal rearrangements, tumor-associated gene lists, SNPs, genomic features concerning Alu repeats and general genomic annotations. A genome browser has also been developed that allows for the simultaneous visualization of the different datasets and the various annotated features. Besides enabling an integrative view of diverse datasets through the genome browser, we also provide links to the original references for users to have a more accurate understanding of each specific dataset. This integrated platform will facilitate uncovering interactions among genetic and epigenetic factors associated with brain tumor development. BTECH is freely available at http://cmbteg.childrensmemorial.org/.

Original languageEnglish (US)
Pages (from-to)59-67
Number of pages9
JournalNeuroinformatics
Volume9
Issue number1
DOIs
StatePublished - Mar 1 2011

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Keywords

  • Brain tumor
  • DNA methylation
  • Database
  • Epigenomics
  • Gene expression
  • Genome browser
  • Genomics

ASJC Scopus subject areas

  • Software
  • Neuroscience(all)
  • Information Systems

Cite this

Wang, M., Xie, H., Stellpflug, W., Rajaram, V., De Fatima Bonaldo, M., Goldman, S., Tomita, T., & Soares, M. B. (2011). BTECH: A platform to integrate genomic, transcriptomic and epigenomic alterations in brain tumors. Neuroinformatics, 9(1), 59-67. https://doi.org/10.1007/s12021-010-9091-9