Cited By
View all- Mou XJamil H(2019)Visual Life Sciences Workflow Design using Distributed and Heterogeneous ResourcesIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2018.2886185(1-1)Online publication date: 2019
A workflow for the computational identification of candidate regulatory elements in noncoding DNA
Authors: 
Jeffrey A. Thompson, Craig R. Lessard, Samuel McFarland, Robert L. Morris, Clare Bates CongdonAuthors Info & Claims
Jeffrey A. Thompson, Craig R. Lessard, Samuel McFarland, Robert L. Morris, Clare Bates CongdonAuthors Info & ClaimsPages 643 - 644
Abstract
Computational methods of inferring regions of noncoding DNA that regulate gene activity are important to efficient biological validation of gene regulatory control. In many cases the available resources may allow for relatively few biological assays to be performed, and computational results allow these assays to be tightly focused on the highest confidence candidate regulatory regions. Here, we present a workflow for the computational identification of candidate regulatory regions that incorporates multiple lines of evidence and illustrate its use to select high-confidence targets for experimental verification using the ciliary gene Tektin3 as an example. The Tektin3 protein is vital for ciliogenesis, a process in which cilia are formed. Cilia are important organelles of cells that are involved in numerous activities, and are related to many human diseases. The study of ciliogenesis genes may lead to advances in treatment for related diseases in humans, including diseases caused by malformation of the cilia.
References
[1]
T. L. Bailey, N. Williams, C. Misleh, and W. W. Li. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res., 34:W369--373, Jul 2006.
[2]
C. B. Congdon, J. C. Aman, G. M. Nava, H. R. Gaskins, and C. J. Mattingly. An evaluation of information content as a metric for the inference of putative conserved noncoding regions in DNA sequences using a genetic algorithms approach. IEEE/ACM Trans Comput Biol Bioinform, 5:1--14, 2008.
[3]
I. Dunham, A. Kundaje, S. F. Aldred, P. J. Collins, C. A. Davis, F. Doyle, C. B. Epstein, S. Frietze, J. Harrow, R. Kaul, J. Khatun, B. R. Lajoie, S. G. Landt, B.-K. Lee, F. Pauli, K. R. Rosenbloom, et al. An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414):57--74, 2012.
[4]
K. Inaba. Sperm flagella: comparative and phylogenetic perspectives of protein components. Molecular human reproduction, 17(8):524--538, 2011.
[5]
V. Matys, O. V. Kel-Margoulis, E. Fricke, I. Liebich, S. Land, A. Barre-Dirrie, I. Reuter, D. Chekmenev, M. Krull, K. Hornischer, N. Voss, P. Stegmaier, B. Lewicki-Potapov, H. Saxel, A. E. Kel, and E. Wingender. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34:D108--110, Jan 2006.
[6]
A. Roy, W. Yan, K. H. Burns, and M. M. Matzuk. Tektin3 encodes an evolutionarily conserved putative testicular microtubules-related protein expressed preferentially in male germ cells. Molecular reproduction and development, 67(3):295--302, 2004.
Index Terms
- A workflow for the computational identification of candidate regulatory elements in noncoding DNA
Recommendations
Identification and characterization of promoters and cis-regulatory elements of genes involved in secondary metabolites production in hop (Humulus lupulus. L)
Display Omitted Single or combination of different cis-acting regulatory elements involved in the transcriptional regulation metabolic genes involved in biosynthesis of prenylflavanoid (PF) and bitter acid (BA) production in Humulus lupulus.The presence ...
microRNA: human disease and development
microRNAs or miRNAs are an abundant class of highly conversed, small non-coding RNAs that present an entirely new theme of post-transcriptional gene regulation. miRNAs play a key role in diverse biological systems, such as virology, embryogenesis, ...
Towards Using Probabilities and Logic to Model Regulatory Networks
CBMS '14: Proceedings of the 2014 IEEE 27th International Symposium on Computer-Based Medical SystemsTranscriptional regulation plays an important role in every cellular decision. Unfortunately, understanding the dynamics that govern how a cell will respond to diverse environmental cues is difficult using intuition alone. We introduce logic based ...
Comments
Information & Contributors
Information
Published In
Copyright © 2014 Owner/Author.
Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author.
Sponsors
Publisher
Association for Computing Machinery
New York, NY, United States
Publication History
Published: 20 September 2014
Check for updates
Author Tags
Qualifiers
- Poster
Conference
BCB '14
Sponsor:
Acceptance Rates
Overall Acceptance Rate 254 of 885 submissions, 29%
Contributors
Other Metrics
Bibliometrics & Citations
Bibliometrics
Article Metrics
- View Citations1Total Citations
- 69Total Downloads
- Downloads (Last 12 months)2
- Downloads (Last 6 weeks)0
Reflects downloads up to 05 Mar 2025
Other Metrics
Citations
Cited By
View all- Mou XJamil H(2019)Visual Life Sciences Workflow Design using Distributed and Heterogeneous ResourcesIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2018.2886185(1-1)Online publication date: 2019
View Options
Login options
Check if you have access through your login credentials or your institution to get full access on this article.
Sign in