ArticleBMC systems biology2013
Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- Stage-specific coexpression network analysis of Myc in cohorts of renal cancer.Scientific reports · 2023Article
- GRIK3 deficiency promotes non-small cell lung cancer progression by the regulation of the UBE2C/CDK1/Wnt signaling pathway.American journal of cancer research · 2023Article
- Identification of a Novel Renal Metastasis Associated CpG-Based DNA Methylation Signature (RMAMS).International journal of molecular sciences · 2022Article
- Evaluating the tumor immune profile based on a three-gene prognostic risk model in HER2 positive breast cancer.Scientific reports · 2022Article
- Pregnancy exposure to synthetic phenols and placental DNA methylation - An epigenome-wide association study in male infants from the EDEN cohort.Environmental pollution (Barking, Essex : 1987) · 2021Article
- Residential PMEnvironment international · 2021Article
- Integrated bioinformatics identifies the dysregulation induced by aberrant gene methylation in colorectal carcinoma.Genes & diseases · 2021Article
- Whole-Genome Methylation Study of Congenital Lung Malformations in Children.Frontiers in oncology · 2021Article
- Hsa_circ_0038646 promotes cell proliferation and migration in colorectal cancer via miR-331-3p/GRIK3.Oncology letters · 2020Article
- Identification of Differentially Methylated CpG Sites in Fibroblasts from Keloid Scars.Biomedicines · 2020Article
- A comprehensive analysis of metabolomics and transcriptomics in non-small cell lung cancer.PloS one · 2020Article
- Distinguishing Glioblastoma Subtypes by Methylation Signatures.Frontiers in genetics · 2020Article
- Glutamate Ionotropic Receptor Kainate Type Subunit 3 (GRIK3) promotes epithelial-mesenchymal transition in breast cancer cells by regulating SPDEF/CDH1 signaling.Molecular carcinogenesis · 2019Article
- A comprehensive methylation signature identifies lymph node metastasis in esophageal squamous cell carcinoma.International journal of cancer · 2019Article
- Protective Effect ofInternational journal of molecular sciences · 2018Article
- CRLF1 promotes malignant phenotypes of papillary thyroid carcinoma by activating the MAPK/ERK and PI3K/AKT pathways.Cell death & disease · 2018Article
- Proteomics analysis to reveal biological pathways and predictive proteins in the survival of high-grade serous ovarian cancer.Scientific reports · 2017Article
- In silico identification of potential key regulatory factors in smoking-induced lung cancer.BMC medical genomics · 2017Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEpigenetics 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).
resultsOur 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.
conclusionIntegrating 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.
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