A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation

Pedro A F Galante, Devraj Sandhu, Raquel De Sousa Abreu, Michael Gradassi, Natanja Slager, Christine Vogel, Sandro Jose De Souza, Luiz O F Penalva

Research output: Contribution to journalArticle

Abstract

RNA binding proteins (RBPs) are involved in several posttranscriptional stages of gene expression and dictate the quality and quantity of the cellular proteome. When aberrantly expressed, they can lead to disease states as well as cancers. A basic requirement to understand their role in normal tissue development and cancer is the build of comprehensive gene expression maps. In this direction, we generated a list with 383 human RBPs based on the NCBI and EMSEMBL databases. SAGE and MPSS were then used to verify their levels of expression in normal tissues while SAGE and microarray datasets were used to perform comparisons between normal and tumor tissues. As main outcomes of our studies, we identified clusters of co-expressed or co-regulated genes that could act together in the development and maintenance of specific tissues; we also obtained a high confidence list of RBPs aberrantly expressed in several tumor types. This later list contains potential candidates to be explored as diagnostic and prognostic markers as well as putative targets for cancer therapy approaches.

Original languageEnglish (US)
JournalRNA Biology
Volume6
Issue number4
StatePublished - 2009

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RNA-Binding Proteins
Computer Simulation
Neoplasms
Gene Expression
Proteome
Maintenance
Outcome Assessment (Health Care)
Databases
Genes

Keywords

  • Cancer
  • Gene expression analysis
  • MPSS
  • Oncogenomics
  • Post-transcriptional regulation
  • RNA binding proteins
  • SAGE

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

Cite this

Galante, P. A. F., Sandhu, D., De Sousa Abreu, R., Gradassi, M., Slager, N., Vogel, C., ... Penalva, L. O. F. (2009). A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation. RNA Biology, 6(4).

A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue : Identification of potential players in tumor formation. / Galante, Pedro A F; Sandhu, Devraj; De Sousa Abreu, Raquel; Gradassi, Michael; Slager, Natanja; Vogel, Christine; De Souza, Sandro Jose; Penalva, Luiz O F.

In: RNA Biology, Vol. 6, No. 4, 2009.

Research output: Contribution to journalArticle

Galante, PAF, Sandhu, D, De Sousa Abreu, R, Gradassi, M, Slager, N, Vogel, C, De Souza, SJ & Penalva, LOF 2009, 'A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation', RNA Biology, vol. 6, no. 4.
Galante, Pedro A F ; Sandhu, Devraj ; De Sousa Abreu, Raquel ; Gradassi, Michael ; Slager, Natanja ; Vogel, Christine ; De Souza, Sandro Jose ; Penalva, Luiz O F. / A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue : Identification of potential players in tumor formation. In: RNA Biology. 2009 ; Vol. 6, No. 4.
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