Dataset Information

Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma.

ABSTRACT:

Background

Epigenetics refers to the reversible functional modifications of the genome that do not correlate to changes in the DNA sequence. The aim of this study is to understand DNA methylation patterns across different stages of lung adenocarcinoma (LUAD).

Results

Our study identified 72, 93 and 170 significant DNA methylated genes in Stages I, II and III respectively. A set of common 34 significant DNA methylated genes located in the promoter section of the true CpG islands were found across stages, and these were: HOX genes, FOXG1, GRIK3, HAND2, PRKCB, etc. Of the total significant DNA methylated genes, 65 correlated with transcription function. The epigenetic analysis identified the following novel genes across all stages: PTGDR, TLX3, and POU4F2. The stage-wise analysis observed the appearance of NEUROG1 gene in Stage I and its re-appearance in Stage III. The analysis showed similar epigenetic pattern across Stage I and Stage III. Pathway analysis revealed important signaling and metabolic pathways of LUAD to correlate with epigenetics. Epigenetic subnetwork analysis identified a set of seven conserved genes across all stages: UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF, and RAP1A. A detailed literature analysis elucidated epigenetic genes like FOXG1, HLA-G, and NKX6-2 to be known as prognostic targets.

Conclusion

Integrating epigenetic information for genes with expression data can be useful for comprehending in-depth disease mechanism and for the ultimate goal of better target identification.

SUBMITTER: Pradhan MP

PROVIDER: S-EPMC3882327 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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Publications

Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma.

Pradhan Meeta P MP Desai Akshay A Palakal Mathew J MJ

BMC systems biology 20131226

<h4>Background</h4>Epigenetics refers to the reversible functional modifications of the genome that do not correlate to changes in the DNA sequence. The aim of this study is to understand DNA methylation patterns across different stages of lung adenocarcinoma (LUAD).<h4>Results</h4>Our study identified 72, 93 and 170 significant DNA methylated genes in Stages I, II and III respectively. A set of common 34 significant DNA methylated genes located in the promoter section of the true CpG islands we ...[more]

PMID: 24369052

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Dataset Information

Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma.

Background

Results

Conclusion

Publications

Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma.

Similar Datasets

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