Meta-analysis of cancer transcriptomes: A new approach to uncover molecular pathological events in different cancer tissues

Sundus Iqbal, Hira Ejaz, Muhammad Sulaman Nawaz, Juan J. Loor, Aisha Naeem

Research output: Contribution to journalArticlepeer-review

Abstract

To explore secrets of metastatic cancers, individual expression of true sets of respective genes must spread across the tissue. In this study, meta-analysis for transcriptional profiles of oncogenes was carried out to hunt critical genes or networks helping in metastasizing cancers. For this, transcriptomic analysis of different cancerous tissues causing leukemia, lung, liver, spleen, colorectal, colon, breast, bladder, and kidney cancers was performed by extracting microarray expression data from online resource; Gene Expression Omnibus. A newly developed bioinformatics technique; Dynamic Impact Approach (DIA) was applied for enrichment analysis of transcriptional profiles using Database for Annotation Visualization and Integrated Discovery (DAVID). Furthermore, oPOSSUM (v. 2.0) and Cytoscape (v. 2.8.2) were used for in-depth analysis of transcription factors and regulatory gene networks respectively. DAVID analysis uncovered the most significantly enriched pathways in molecular functions that were 'Ubiquitin thiolesterase activity' up regulated in blood, breast, bladder, colorectal, lung, spleen, prostrate cancer. 'Transforming growth factor beta receptor activity' was inhibited in all cancers except leukemia, colon and liver cancer. oPOSSUM further revealed highly over-represented Transcription Factors (TFs); Broad-complex_3, Broad-complex_4, and Foxd3 except for leukemia and bladder cancer. From these findings, it is possible to target genes and networks, play a crucial role in the development of cancer. In the future, these transcription factors can serve as potential candidates for the therapeutic drug targets which can impede the deadly spread.

Original languageEnglish (US)
Pages (from-to)1-20
Number of pages20
JournalNetwork Biology
Volume4
Issue number1
DOIs
StatePublished - Mar 1 2014

Keywords

  • DAVID
  • Metastatic cancer
  • Transcription factor
  • Transcriptional analysis
  • oPOSSUM

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Applied Mathematics

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