ArticlePloS one2014
Integrated exon level expression analysis of driver genes explain their role in colorectal cancer.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 26 citations in OpenAlex.
- Molecular classification of colorectal cancer using the gene expression profile of tumor samples.Experimental biology and medicine (Maywood, N.J.) · 2019Trial
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- Type IV P-Type ATPases: Recent Updates in Cancer Development, Progression, and Treatment.Cancers · 2023Review
- Alternatively Spliced Isoforms ofJournal of personalized medicine · 2023Article
- Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data.Frontiers in bioinformatics · 2021Review
- Free fatty acids receptors 2 and 3 control cell proliferation by regulating cellular glucose uptake.World journal of gastrointestinal oncology · 2020Article
- Colorectal cancer in Saudi Arabia as the proof-of-principle model for implementing strategies of predictive, preventive, and personalized medicine in healthcare.The EPMA journal · 2020Review
- Genome-wide prediction and prioritization of human aging genes by data fusion: a machine learning approach.BMC genomics · 2019Article
- Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2019Article
- Elucidating the Reprograming of Colorectal Cancer Metabolism Using Genome-Scale Metabolic Modeling.Frontiers in oncology · 2019Article
- iGEMS: an integrated model for identification of alternative exon usage events.Nucleic acids research · 2016Article
- Filtered selection coupled with support vector machines generate a functionally relevant prediction model for colorectal cancer.OncoTargets and therapy · 2016Article
- Long non-coding RNA LINC01296 is a potential prognostic biomarker in patients with colorectal cancer.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2015Article
- Correction: Integrated exon level expression analysis of driver genes explain their role in colorectal cancer.PloS one · 2015Article
- Gene expression profile analysis of colorectal cancer to investigate potential mechanisms using bioinformatics.OncoTargets and therapy · 2015Article
- Effect of sampling procedure on the quality control metrics of cytoscan HD array for studying cytogenetic aspects of colorectal cancer.International journal of health sciencesArticle
Corrections and comments
- Erratum issued
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Integrated analysis of genomic and transcriptomic level changes holds promise for a better understanding of colorectal cancer (CRC) biology. There is a pertinent need to explain the functional effect of genome level changes by integrating the information at the transcript level. Using high resolution cytogenetics array, we had earlier identified driver genes by 'Genomic Identification of Significant Targets In Cancer (GISTIC)' analysis of paired tumour-normal samples from colorectal cancer patients. In this study, we analyze these driver genes at three levels using exon array data--gene, exon and network. Gene level analysis revealed a small subset to experience differential expression. These results were reinforced by carrying out separate differential expression analyses (SAM and LIMMA). ATP8B1 was found to be the novel gene associated with CRC that shows changes at cytogenetic, gene and exon levels. Splice index of 29 exons corresponding to 13 genes was found to be significantly altered in tumour samples. Driver genes were used to construct regulatory networks for tumour and normal groups. There were rearrangements in transcription factor genes suggesting the presence of regulatory switching. The regulatory pattern of AHR gene was found to have the most significant alteration. Our results integrate data with focus on driver genes resulting in highly enriched novel molecules that need further studies to establish their role in CRC.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.