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Zhao Y, Schaafsma E, Cheng C. Applications of ENCODE data to Systematic Analyses via Data Integration. ACTA ACUST UNITED AC 2019; 11:57-64. [PMID: 31011690 DOI: 10.1016/j.coisb.2018.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Large-scale genomic data have been utilized to generate unprecedented biological findings and new hypotheses. To delineate functional elements in the human genome, the Encyclopedia of DNA Elements (ENCODE) project has generated an enormous amount of genomic data, yielding around 7,000 data profiles in different cell and tissue types. In this article, we reviewed the systematic analyses that have integrated ENCODE data with other data sources to reveal new biological insights, ranging from human genome annotation to the identification of new candidate drugs. These analyses demonstrate the critical impact of ENCODE data on basic biology and translational research.
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Affiliation(s)
- Yanding Zhao
- Department of Biomedical Data Science, The Geisel School of Medicine at Dartmouth College, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States, 03756.,Department of Molecular and Systems Biology, The Geisel School of Medicine at Dartmouth College, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States, 03756
| | - Evelien Schaafsma
- Department of Biomedical Data Science, The Geisel School of Medicine at Dartmouth College, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States, 03756.,Department of Molecular and Systems Biology, The Geisel School of Medicine at Dartmouth College, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States, 03756
| | - Chao Cheng
- Department of Biomedical Data Science, The Geisel School of Medicine at Dartmouth College, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States, 03756.,Department of Molecular and Systems Biology, The Geisel School of Medicine at Dartmouth College, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States, 03756.,Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth College, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States, 03756
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Yang Y, Junjie P, Sanjun C, Ma Y. Long non-coding RNAs in Colorectal Cancer: Progression and Future Directions. J Cancer 2017; 8:3212-3225. [PMID: 29158793 PMCID: PMC5665037 DOI: 10.7150/jca.19794] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 08/29/2017] [Indexed: 12/25/2022] Open
Abstract
Identification of the colorectal adenoma-carcinoma sequence with its corresponding genetic and epigenetic alterations has significantly increased our knowledge of the etiopathogenesis of colorectal cancer (CRC). However, the molecular mechanisms of colorectal carcinogenesis and metastasis haven't been clearly elucidated. Long non-coding ribonucleic acids (lncRNAs) are key participants of gene regulations rather than “noises”. Accumulative studies have implicated that the aberrant expressions of lncRNAs are tightly corelated to CRC screening, diagnosis, prognosis and therapeutic outcomes. Our review focuses on recent findings on the involvement of lncRNAs in CRC oncogenesis and the lncRNA-based clinical implications in patients with CRC.
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Affiliation(s)
- Yongzhi Yang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Peng Junjie
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Cai Sanjun
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
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Theophilou G, Paraskevaidi M, Lima KMG, Kyrgiou M, Martin-Hirsch PL, Martin FL. Extracting biomarkers of commitment to cancer development: potential role of vibrational spectroscopy in systems biology. Expert Rev Mol Diagn 2015; 15:693-713. [DOI: 10.1586/14737159.2015.1028372] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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