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Manolis Kellis. Kumar, Nischay Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science. Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science 2014-03-06T15:41:44Z 2014-03-06T15:41:44Z 2013 2013 http://hdl.handle.net/1721.1/85434 870678983 Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2013. Title as it appears in MIT Commencement Exercises program, June 7, 2013: Classification of existing genes and de novo discovery of new genes using chromatin state segmentations in human epigenomes. Cataloged from PDF version of thesis. Includes bibliographical references (pages 49-50). Combinatorial patterns of chromatin marks have been shown to play a significant role in gene regulation activities by changing the landscape of the DNA through chemical means. Recent work has expanded on this observation using ChIP-seq signals of chromatin marks and supervised algorithms to build gene expression prediction models based on correlation analysis. However, no approach to date has attempted to use chromatin states to identify various classes of genes outside of the high-low expression classes. This research aims to fill this void by utilizing chromatin state segmentation and RNA-seq expression datasets from the NIH Roadmap Epigenomes project. A gene classification model was built using a k-fuzzy clustering approach of chromatin state features from a subset of training genes and then applied to a larger test set of genes. The models were found to be robust and show striking correspondence between training and test sets. 8 classes of genes that represent silent, repressed, and subsets of actively transcribed genes were identified and several metrics to validate the classes were computed. The systematic analysis outlined in this research is shown to a be promising approach for gene classification and future de novo discovery of gene like regions. by Nischay Kumar. M.Eng. 50 pages eng Massachusetts Institute of Technology M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 Electrical Engineering and Computer Science. Classification of genes using clustering of chromatin state segmentations in human epigenomes Classification of existing genes and de novo discovery of new genes using chromatin state segmentations in human epigenomes Thesis application/pdf Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="dc6b28de-c4f4-4202-bbd6-ca9f1ff8af39"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>Classification of genes using clustering of chromatin state segmentations in human epigenomes</Title> <Subtitle>Classification of existing genes and de novo discovery of new genes using chromatin state segmentations in human epigenomes</Subtitle> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2013</PublicationDate> <Authors> <Author> <DisplayName>Kumar, Nischay</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://dspace.mit.edu/handle/1721.1/7582</License> <Keyword>Electrical Engineering and Computer Science.</Keyword> <Abstract>Combinatorial patterns of chromatin marks have been shown to play a significant role in gene regulation activities by changing the landscape of the DNA through chemical means. Recent work has expanded on this observation using ChIP-seq signals of chromatin marks and supervised algorithms to build gene expression prediction models based on correlation analysis. However, no approach to date has attempted to use chromatin states to identify various classes of genes outside of the high-low expression classes. This research aims to fill this void by utilizing chromatin state segmentation and RNA-seq expression datasets from the NIH Roadmap Epigenomes project. A gene classification model was built using a k-fuzzy clustering approach of chromatin state features from a subset of training genes and then applied to a larger test set of genes. The models were found to be robust and show striking correspondence between training and test sets. 8 classes of genes that represent silent, repressed, and subsets of actively transcribed genes were identified and several metrics to validate the classes were computed. The systematic analysis outlined in this research is shown to a be promising approach for gene classification and future de novo discovery of gene like regions.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>