Coexpression analysis of potential prostate cancer biomarkers

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About Coexpression analysis of potential prostate cancer biomarkers


Description

Prostate cancer is one of the most common cancers in men, mostly occurring above the age of 50 with its incidence rate increasing with age. Despite its wide spread in males, PCa tumors often remain unnoticed and until metastasis occur. Therefore, testing for the presence of prostate specific antigen (PSA test) is often performed. However, since PSA is not prostate cancer specific and does not offer prognostic value, many patients with benign tumors undergo unnecessary treatment, as they cannot be distinguished from aggressive forms. At the same time, modern medicine is unable to predict the occurrence of metastasis and resistant disease.

Hence, our goal is to investigate novel genes and transcripts in prostate cancer that can address the need for highly specific biomarkers and help in prognosis of tumor development.

The project

As mentioned above, we have found novel prostate cancer specific transcripts using Affymetrix Exon Array and RNA-Seq data. To continue this research, we intend to perform an extensive coexpression analysis to reveal corregulated transcription factors that might be responsible for the gene regulation of the novel transcripts. The student will optimize the new algorithm for coexpression and develop a pipeline for coexpression analysis of transcripts, resulting in a coexpression network for our novel gene candidates. This pipeline should be organized in modules to easily boost the pipelines capabilities, enabling us to perform further research towards coregulation and potential binding partners on DNA level (ChIP-Seq).


The Department of Urology of the Erasmus MC Rotterdam is offering student projects in the field of bioinformatics for Bachelor and Master students. Our research questions focus on discovery of novel genes for prostate cancer (PCa) by integration of several established high throughput technologies.

The research group

The group headed by Prof. Dr. Guido Jenster consists of about 20 scientists including postdocs, PhD students, technicians, bioinformaticians and BSc and MSc students.

The research is focused on genes and pathways responsible for prostate cancer initiation and progression. In addition, model systems and biomarkers for this disease are being developed. The latest technologies including in RNA-Seq and DNA-Seq are implemented to optimally identify and validate genes and markers of interest.

Contact details:

  • phone: +31-10-704 3672
  • fax: +31-10-704 4661
  • e-mail: g.jenster@erasmusmc.nl

Further information