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Chung FH, Jin ZH, Hsu TT, Hsu CL, Liu HC, Lee HC. Gene-Set Local Hierarchical Clustering (GSLHC)--A Gene Set-Based Approach for Characterizing Bioactive Compounds in Terms of Biological Functional Groups. PLoS One 2015; 10:e0139889. [PMID: 26473729 PMCID: PMC4652590 DOI: 10.1371/journal.pone.0139889] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/19/2015] [Indexed: 01/05/2023] Open
Abstract
Gene-set-based analysis (GSA), which uses the relative importance of functional gene-sets, or molecular signatures, as units for analysis of genome-wide gene expression data, has exhibited major advantages with respect to greater accuracy, robustness, and biological relevance, over individual gene analysis (IGA), which uses log-ratios of individual genes for analysis. Yet IGA remains the dominant mode of analysis of gene expression data. The Connectivity Map (CMap), an extensive database on genomic profiles of effects of drugs and small molecules and widely used for studies related to repurposed drug discovery, has been mostly employed in IGA mode. Here, we constructed a GSA-based version of CMap, Gene-Set Connectivity Map (GSCMap), in which all the genomic profiles in CMap are converted, using gene-sets from the Molecular Signatures Database, to functional profiles. We showed that GSCMap essentially eliminated cell-type dependence, a weakness of CMap in IGA mode, and yielded significantly better performance on sample clustering and drug-target association. As a first application of GSCMap we constructed the platform Gene-Set Local Hierarchical Clustering (GSLHC) for discovering insights on coordinated actions of biological functions and facilitating classification of heterogeneous subtypes on drug-driven responses. GSLHC was shown to tightly clustered drugs of known similar properties. We used GSLHC to identify the therapeutic properties and putative targets of 18 compounds of previously unknown characteristics listed in CMap, eight of which suggest anti-cancer activities. The GSLHC website http://cloudr.ncu.edu.tw/gslhc/ contains 1,857 local hierarchical clusters accessible by querying 555 of the 1,309 drugs and small molecules listed in CMap. We expect GSCMap and GSLHC to be widely useful in providing new insights in the biological effect of bioactive compounds, in drug repurposing, and in function-based classification of complex diseases.
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Affiliation(s)
- Feng-Hsiang Chung
- Institute of Systems Biology and Bioinformatics, National Central University, Zhongli, 32001, Taiwan
- Center for Dynamical Biomarkers and Translational Medicine, National Central University, Zhongli, 32001, Taiwan
| | - Zhen-Hua Jin
- Institute of Systems Biology and Bioinformatics, National Central University, Zhongli, 32001, Taiwan
| | - Tzu-Ting Hsu
- Institute of Systems Biology and Bioinformatics, National Central University, Zhongli, 32001, Taiwan
| | - Chueh-Lin Hsu
- Institute of Systems Biology and Bioinformatics, National Central University, Zhongli, 32001, Taiwan
| | - Hsueh-Chuan Liu
- Institute of Systems Biology and Bioinformatics, National Central University, Zhongli, 32001, Taiwan
| | - Hoong-Chien Lee
- Institute of Systems Biology and Bioinformatics, National Central University, Zhongli, 32001, Taiwan
- Center for Dynamical Biomarkers and Translational Medicine, National Central University, Zhongli, 32001, Taiwan
- Department of Physics, Chung Yuan Christian University, Zhongli, 32023, Taiwan
- Physics Division, National Center for Theoretical Sciences, Hsinchu, 30043, Taiwan
- * E-mail:
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Banno K, Kisu I, Yanokura M, Tsuji K, Masuda K, Ueki A, Kobayashi Y, Yamagami W, Nomura H, Tominaga E, Susumu N, Aoki D. Epimutation and cancer: a new carcinogenic mechanism of Lynch syndrome (Review). Int J Oncol 2012; 41:793-7. [PMID: 22735547 PMCID: PMC3582986 DOI: 10.3892/ijo.2012.1528] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/28/2012] [Indexed: 12/18/2022] Open
Abstract
Epimutation is defined as abnormal transcriptional repression of active genes and/or abnormal activation of usually repressed genes caused by errors in epigenetic gene repression. Epimutation arises in somatic cells and the germline, and constitutional epimutation may also occur. Epimutation is the first step of tumorigenesis and can be a direct cause of carcinogenesis. Cancers associated with epimutation include Lynch syndrome (hereditary non-polyposis colorectal cancer, HNPCC), chronic lymphocytic leukemia, breast cancer and ovarian cancer. Epimutation has been shown for many tumor suppressor genes, including RB, VHL, hMLH1, APC and BRCA1, in sporadic cancers. Methylation has recently been shown in DNA from normal tissues and peripheral blood in cases of sporadic colorectal cancer and many studies show constitutive epimutation in cancers. Epimutation of DNA mismatch repair (MMR) genes (BRCA1, hMLH1 and hMSH2) involved in development familial cancers has also been found. These results have led to a focus on epimutation as a novel oncogenic mechanism.
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Affiliation(s)
- Kouji Banno
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan.
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Hesson LB, Hitchins MP, Ward RL. Epimutations and cancer predisposition: importance and mechanisms. Curr Opin Genet Dev 2010; 20:290-8. [PMID: 20359882 DOI: 10.1016/j.gde.2010.02.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2009] [Revised: 01/31/2010] [Accepted: 02/20/2010] [Indexed: 01/24/2023]
Abstract
Germline sequence mutations in tumour suppressor genes can cause cancer predisposition syndromes. More recently, epimutations have also been proposed to cause at least one such syndrome, hereditary non-polyposis colorectal cancer (HNPCC). 'Epigenetic predisposition', is defined as an inherited propensity to an altered epigenetic state in normal tissues that confers a predisposition to disease. Genetic sequence variations acting in cis or trans may contribute to epigenetic variations. Understanding the origin of epimutations will inform cancer risk assessment and will also aid the design and application of new therapies that target the epigenome.
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Affiliation(s)
- Luke B Hesson
- Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Kensington, New South Wales, Australia
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