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From Differentiated Genes to Affected Pathways

Shailesh Patil, Bharath Venkatesh, Randeep Singh
doi: https://doi.org/10.1101/038901
Shailesh Patil
1SAP Labs India, 138, EPIP Zone, Whitefield, Bengaluru, Karnataka 560066
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Bharath Venkatesh
1SAP Labs India, 138, EPIP Zone, Whitefield, Bengaluru, Karnataka 560066
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Randeep Singh
1SAP Labs India, 138, EPIP Zone, Whitefield, Bengaluru, Karnataka 560066
2Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai, Maharashtra 410210
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Abstract

Expression analysis and variant calling workflows are employed to identify genes that either exhibit a differential behaviour or have a significant functional impact of mutations. This is always followed by pathway analysis which provides greater insights and simplifies explanation of observed phenotype. The current techniques used towards this purpose have some serious limitations. In this paper, we propose a theoretical framework to overcome many limitations of current techniques. Our framework takes into account the networked nature of the data and provides facility to weigh each gene differently and in the process we do away with the need of arbitrary cut-offs. This framework is designed to be modular and provides the researchers with flexibility to plug analytical tools of their choice for every component. We also demonstrate effectiveness of our approach for personalized and cohort analysis of cancer gene expression samples with PageRank as one of the modules in the framework.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 07, 2016.
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From Differentiated Genes to Affected Pathways
Shailesh Patil, Bharath Venkatesh, Randeep Singh
bioRxiv 038901; doi: https://doi.org/10.1101/038901
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From Differentiated Genes to Affected Pathways
Shailesh Patil, Bharath Venkatesh, Randeep Singh
bioRxiv 038901; doi: https://doi.org/10.1101/038901

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