NDLI: Cross-species identification of hydroxylation sites for ARD and FIH interaction

Content Provider	IEEE Xplore Digital Library
Author	Ying-Tsang Lo Tsan-Huang Shih Han-Jia Lin Tun-Wen Pai Chang, M.D.-T.
Copyright Year	2011
Description	Author affiliation: Dept.of Computer Science and Engineering, Nation Taiwan Ocean University, Keelung, Taiwan (Ying-Tsang Lo; Tsan-Huang Shih; Tun-Wen Pai) \|\| Institute of Molecular and Cellular Biology & Department of Medical Science, National Tsing Hua University, Hsinchu 300, Taiwan (Chang, M.D.-T.) \|\| Institute of Bioscience and Biotechnology, Nation Taiwan Ocean University, Keelung, Taiwan (Han-Jia Lin)
Abstract	Ankyrin repeat domain (ARD) proteins contain various numbers of internal repeat units. They are considered as one important factor to influence hypoxia response through hydroxylation interaction with Factor Inhibiting HIF (FIH) enzymes which can repress HIF under normoxia environment. In this study, we adopted sequence based method and applied conserved hydroxylation motif patterns for identifying ASN/ASP/HIS hydroxylation sites on ARDs. First, a set of known ARD proteins was collected, and all corresponding repeat units were manually constructed and verified by removing redundant units. All extracted segments served as fundamental seed units to retrieve all ARDs proteins from 5 different species. Those ARD candidates were automatically segmented and a conserved hydroxylation motif pattern was applied for identifying all hydroxylation sites. As a result, the retrieval performance for ARDs achieved a sensitivity of 82% and a specificity of 98% for human species based on a testing dataset of 1,244 protein sequences. For hydroxylation site prediction, a sensitivity of 72.2% and a positive prediction value of 62% were achieved based on a set of 18 experimentally verified hydroxylation residues.
Starting Page	345
Ending Page	350
File Size	767051
Page Count	6
File Format	PDF
ISBN	9781457716614
e-ISBN	9781457716669
e-ISBN	9781457716652
DOI	10.1109/ISB.2011.6033176
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-09-02
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Iris Databases ARD Hydroxylation HIF FIH Systems biology Humans Internal repeat
Content Type	Text
Resource Type	Article

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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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