NDLI: Modeling Associated Protein-DNA Pattern Discovery with Unified Scores

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Modeling Associated Protein-DNA Pattern Discovery with Unified Scores

Content Provider	IEEE Xplore Digital Library
Author	Tak-Ming Chan Leung-Yau Lo Ho-Yin Sze-To Kwong-Sak Leung Xinshu Xiao Man-Hon Wong
Copyright Year	2004
Abstract	Understanding protein-DNA interactions, specifically transcription factor (TF) and transcription factor binding site (TFBS) bindings, is crucial in deciphering gene regulation. The recent associated TF-TFBS pattern discovery combines one-sided motif discovery on both the TF and the TFBS sides. Using sequences only, it identifies the short protein-DNA binding cores available only in high-resolution 3D structures. The discovered patterns lead to promising subtype and disease analysis applications. While the related studies use either association rule mining or existing TFBS annotations, none has proposed any formal unified (both-sided) model to prioritize the top verifiable associated patterns. We propose the unified scores and develop an effective pipeline for associated TF-TFBS pattern discovery. Our stringent instance-level evaluations show that the patterns with the top unified scores match with the binding cores in 3D structures considerably better than the previous works, where up to 90 percent of the top 20 scored patterns are verified. We also introduce extended verification from literature surveys, where the high unified scores correspond to even higher verification percentage. The top scored patterns are confirmed to match the known WRKY binding cores with no available 3D structures and agree well with the top binding affinities of in vivo experiments.
Sponsorship	IEEE Computer Society
Page Count	12
File Size	1052442
Starting Page	696
Ending Page	707
File Format	PDF
ISSN	15455963
Volume Number	10
Issue Number	3
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2013-01-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Three-dimensional displays Association rules Pattern matching DNA Diseases TF-TFBS associated pattern discovery proteins bioinformatics bonds (chemical) data mining genetics molecular biophysics molecular configurations in vivo experiment associated protein-DNA pattern discovery modeling protein-DNA interaction transcription factor binding site gene regulation one-sided motif discovery sequence usage short protein-DNA binding core identification high resolution 3D structure subtype analysis application disease analysis application association rule mining existing TFBS annotation formal unified model both-sided model associated TF-TFBS pattern discovery instance-level evaluation top unified score pattern 3D structure binding core scored pattern verification literature survey extended verification high unified score high verification percentage top scored pattern WRKY binding core top binding affinity binding rules Bioinformatics protein-DNA interactions motif discovery
Content Type	Text
Resource Type	Article
Subject	Applied Mathematics Genetics Biotechnology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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Modeling Associated Protein-DNA Pattern Discovery with Unified Scores

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