EDITOR’S CHOICE – Integration of DNA Methylation Data and Gene Expression Data for Prostate Adenocarcinoma: A Proof of Concept – Current Bioinformatics

Journal: Current Bioinformatics

Author(s): Arpit Singh, Razia Rahman, Yasha Hasija

Graphical Abstract:

 

Abstract:

Background: Epigenetics is gaining rapid recognition as it accounts for heritable changes that do not involve changes in the coding sequence, but influences change in gene expressions. DNA methylation is the most extensively studied epigenetic mechanism and has been observed to play a significant role in gene regulation and silencing process.

Objective: In our present work, we focused on understanding the relationship between DNA methylation and gene expression. As a proof of concept, Prostate Adenocarcinoma (PRAD), the second leading cause of death in men, was extensively studied to unravel the epigenetic abnormalities associated with disease pathogenesis which may contribute to better diagnosis and prevention of prostate cancer.

Method: DNA methylation data (level 1) and Gene expression data (level 3) was taken from The Cancer Genome Atlas (TCGA). A total of 36 samples comprising of 18 normal samples and 18 tumor samples were collected from a batch of 184 and matched with tumor samples and normal samples, respectively. The differentially methylated regions were identified and statistical analysis was carried out for the gene expression data amongst the normal and tumor samples. Further, functional enrichment analysis and pathway analysis were carried out for the filtered genes.

Results: Our analysis indicated 453 differentially methylated regions with p-value < 0.05, FDR (false discovery rate) value < 0.05 and beta value (methylation) > 0.2. The integration of gene expression data with methylation data resulted in 180 significant correlations from which 112 genes were filtered under stringent conditions. Out of these 112 genes, 74 genes were filtered through visual inspection of results and their functional enrichment analysis resulted in total 27 clusters with a maximum enrichment score of ~1.86.

Conclusion: The genes “GSTP1” and “FGFR2” were present in our prioritized filtered significant correlations, and it was discovered that these genes were known to play a primary role in prostate cancer pathway and progression. Therefore, this approach may help to prioritize other novel genes and suggest their involvement in the prostate cancer pathway

 

Read more here: http://www.eurekaselect.com/151165

Podcast: Multiscale Products in B spline Wavelet Domain

Author(s): Xiaolei Zhang, Guishan Zhang, Yangjiang Yu, Guocheng Pan, Haitao Deng, Xinbao Shi, Yue Jiao, Renhua Wu, Yaowen Chen.

For article details, visit: http://www.eurekaselect.com/154448/article

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Highlighted Article – Adaptive Genetic Algorithm with Exploration-Exploitation Tradeoff for Preprocessing Microarray Datasets – Current Bioinformatics

CB-Articles_12-6-Sivaraj Rajappan

To access this article, please visit: http://www.eurekaselect.com/147499/article

Upcoming Thematic Issue – Entropy Measures for Medical Image Analysis – Current Bioinformatics

CM- THEMATIC FLYER -Dr. K. Kamalanand

http://benthamscience.com/journals/current-bioinformatics/special-issues/#top

Upcoming Thematic Issue – Entropy Measure for Medical Image Analysis– Current Bioinformatics

CM- THEMATIC FLYER -Dr. K. Kamalanand

http://benthamscience.com/journals/current-bioinformatics/

New Issue :: Current Bioinformatics 12, Issue 2

Current Bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Each issue contains a series of timely, in-depth reviews, drug clinical trial studies and guest edited thematic issues written by leaders in the field, covering a wide range of the integration of biology with computer and information science.

The journal focuses on reviews on advances in computational molecular/structural biology, encompassing areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Developments in these fields have direct implications on key issues related to health care, medicine, genetic disorders, development of agricultural products, renewable energy, environmental protection, etc.

Current Bioinformatics is an essential journal for all academic and industrial researchers who want expert knowledge on all major advances in bioinformatics.

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Articles from the journal Current Bioinformatics 12, Issue 2:

For details on the articles, please visit this link :: http://bit.ly/2plPUKB

 

Upcoming Thematic Issue – Latest machine learning Techniques for Biomedicine and Bioinformatics

CB-THEMATIC FLYER -Quan Zou

http://www.eurekaselect.com/642/journal/current-bioinformatics

Upcoming Thematic Issue – Optimization in design of Natural Structures, Biomaterials, Bioinformatics and Biometric techniques for solving Physiological needs and ultimate performance of Bio-Devices

CB-THEMATIC FLYER -Dr Kelvin KL Wong

http://www.eurekaselect.com/642/journal/current-bioinformatics

Upcoming Thematic Issue – Bioinformatics in Biological Big Data Era

CB- THEMATIC FLYER- Shuigeng Zhou-1

http://benthamscience.com/journals/current-bioinformatics/

 

Upcoming Thematic Issue – Plant Bioinformatics: From Genome to Phenome

cb-thematic-flyer-ming-chen

http://www.eurekaselect.com/642/journal/current-bioinformatics