ArticleBioMed research international2015
Novel candidate key drivers in the integrative network of genes, microRNAs, methylations, and copy number variations in squamous cell lung carcinoma.
Article in BioMed research international, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 29 citations in OpenAlex.
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- Identification of Novel Lung Cancer Driver Genes Connecting Different Omics Levels With a Heat Diffusion Algorithm.Frontiers in cell and developmental biology · 2022Article
- A methylation-driven gene panel predicts survival in patients with colon cancer.FEBS open bio · 2021Article
- Investigation of miRNA and mRNA Co-expression Network in Ependymoma.Frontiers in bioengineering and biotechnology · 2020Article
- Integrative Analysis of Methylation and Gene Expression in Lung Adenocarcinoma and Squamous Cell Lung Carcinoma.Frontiers in bioengineering and biotechnology · 2020Article
- New Analysis Framework Incorporating Mixed Mutual Information and Scalable Bayesian Networks for Multimodal High Dimensional Genomic and Epigenomic Cancer Data.Frontiers in genetics · 2020Article
- Identification of 5 Gene Signatures in Survival Prediction for Patients with Lung Squamous Cell Carcinoma Based on Integrated Multiomics Data Analysis.BioMed research international · 2020Article
- Smoking alters the evolutionary trajectory of non-small cell lung cancer.Experimental and therapeutic medicine · 2019Article
- A six-gene prognostic model predicts overall survival in bladder cancer patients.Cancer cell international · 2019Article
- Identification and Characterization of MicroRNAs Associated with Somatic Copy Number Alterations in Cancer.Cancers · 2018Article
- Joint Detection of Associations between DNA Methylation and Gene Expression from Multiple Cancers.IEEE journal of biomedical and health informatics · 2018Article
- Identification of the predictive genes for the response of colorectal cancer patients to FOLFOX therapy.OncoTargets and therapy · 2018Article
- Small RNAome sequencing delineates the small RNA landscape of pluripotent adult stem cells in the planarianGenomics data · 2017Article
- Identification of a RNA-Seq based prognostic signature with five lncRNAs for lung squamous cell carcinoma.Oncotarget · 2017Article
- Article
- The impact of the Cancer Genome Atlas on lung cancer.Translational research : the journal of laboratory and clinical medicine · 2015Review
- Genome-wide analysis of microRNA and mRNA expression signatures in cancer.Acta pharmacologica Sinica · 2015Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The mechanisms of lung cancer are highly complex. Not only mRNA gene expression but also microRNAs, DNA methylation, and copy number variation (CNV) play roles in tumorigenesis. It is difficult to incorporate so much information into a single model that can comprehensively reflect all these lung cancer mechanisms. In this study, we analyzed the 129 TCGA (The Cancer Genome Atlas) squamous cell lung carcinoma samples with gene expression, microRNA expression, DNA methylation, and CNV data. First, we used variance inflation factor (VIF) regression to build the whole genome integrative network. Then, we isolated the lung cancer subnetwork by identifying the known lung cancer genes and their direct regulators. This subnetwork was refined by the Bayesian method, and the directed regulations among mRNA genes, microRNAs, methylations, and CNVs were obtained. The novel candidate key drivers in this refined subnetwork, such as the methylation of ARHGDIB and HOXD3, microRNA let-7a and miR-31, and the CNV of AGAP2, were identified and analyzed. On three large public available lung cancer datasets, the key drivers ARHGDIB and HOXD3 demonstrated significant associations with the overall survival of lung cancer patients. Our results provide new insights into lung cancer mechanisms.
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