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Network Biology, 2014, 4(1): 1-20
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Article

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

Sundus Iqbal1, Hira Ejaz1, Muhammad Sulaman Nawaz1, Juan J Loor2, Aisha Naeem1
1COMSATS Institute of Information Technology, ChakShahzad, Park Road, Islamabad, 44000, Pakistan
2Mammalian NutriPhysioGenomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA

Received 23 October 2013;Accepted 28 November 2013;Published online 1 March 2014
IAEES

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.

Keywords metastatic cancer;transcriptional analysis;oPOSSUM;transcription factor;DAVID.


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