Journal of Computer Applications ›› 2018, Vol. 38 ›› Issue (6): 1826-1830.DOI: 10.11772/j.issn.1001-9081.2017112749
FENG Yanxia, ZHANG Zhihong, ZHANG Shaoqiang
Received:
2017-11-22
Revised:
2018-01-16
Online:
2018-06-10
Published:
2018-06-13
Supported by:
通讯作者:
张少强
作者简介:
冯艳霞(1991-),女,山西吕梁人,硕士研究生,CCF会员,主要研究方向:生物信息计算;张志红(1991-),女,河南周口人,硕士研究生,主要研究方向:生物信息计算;张少强(1976-),男,天津人,教授,博士,CCF会员,主要研究方向:生物信息计算。
基金资助:
CLC Number:
FENG Yanxia, ZHANG Zhihong, ZHANG Shaoqiang. Cis-regulatory motif finding algorithm in chromatin immunoprecipitation sequencing datasets[J]. Journal of Computer Applications, 2018, 38(6): 1826-1830.
冯艳霞, 张志红, 张少强. 基于染色质免疫共沉淀的高通量测序数据集的 顺式调控模体发现算法[J]. 计算机应用, 2018, 38(6): 1826-1830.
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URL: http://www.joca.cn/EN/10.11772/j.issn.1001-9081.2017112749
[1] LIU X S, BRUTLAG D L, LIU J S. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments[J]. Nature Biotechnology, 2002, 20(8):835-839. [2] ZAMBELLI F, PESOLE G, PAVESI G. Motif discovery and transcription factor binding sites before and after the next-generation sequencing era[J]. Briefings in Bioinformatics, 2013, 14(2):225-237. [3] BAILEY T L, WILLIAMS N, MISLEH C, et al. MEME:discovering and analyzing DNA and protein sequence motifs[J]. Nucleic Acids Research, 2006, 34(Web Server issue):W369-W373. [4] THOMAS-CHOLLIER M, DARBO E, HERRMANN C, et al. A complete workflow for the analysis of full-size ChIP-Seq (and similar) data sets using peak-motifs[J]. Nature Protocols, 2012, 7(8):1551-1568. [5] PAVESI G, MEREGHETTI P, MAURI G, et al. Weeder Web:discovery of transcription factor binding sites in a set of sequences from co-regulated genes[J]. Nucleic Acids Research, 2004, 32(Web Server issue):W199-W203. [6] QU H Z, FANG X D. A brief review on the human encyclopedia of DNA elements (ENCODE) project[J]. Genomics, Proteomics & Bioinformatics, 2013, 11(3):135-141. [7] WILBANKS E G, FACCIOTTI M T. Evaluation of algorithm performance in ChIP-seq peak detection[J]. PLoS One, 2010, 5(7):e11471. [8] YAO Z, MACQUARRIE K L, FONG A P, et al. Discriminative motif analysis of high-throughput dataset[J]. Bioinformatics, 2014, 30(6):775-783. [9] DOWN T A, HUBBARD TJ. NestedMICA:sensitive inference of over-represented motifs in nucleic acid sequence[J]. Nucleic Acids Research, 2005, 33(5):1445-1453. [10] BAILEY T L. DREME:motif discovery in transcription factor ChIP-Seq data[J]. Bioinformatics, 2011, 27(12):1653-1659. [11] LINHART C, HALPERIN Y, SHAMIR R. Transcription factor and microRNA motif discovery:the Amadeus platform and a compendium of metazoan target sets[J]. Genome Research, 2008, 18(7):1180-1189. [12] ETTWILLER L, PATEN B, RAMIALISON M, et al. Trawler:de novo regulatory motif discovery pipeline for chromatin immuneprecipitation[J]. Nature Methods, 2007, 4(7):563-565. [13] CHEN X, XU H, YUAN P, et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells[J]. Cell, 2008, 133(6):1106-1117. [14] PEVNY L, SIMON M C, ROBERTSON E, et al. Erythroid differentiation in chimaeric mice blocked by a targeted mutation in the gene for transcription factor GATA-1[J]. Nature, 1991, 349(6306):257-260. [15] TALLACK M R, WHITINGTON T, YUEN W S, et al. A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells[J]. Genome Research, 2010, 20(8):1052-1063. [16] DUNHAM I, KUNDAJE A, ALDRED S F, et al. An integrated encyclopedia of DNA elements in the human genome[J]. Nature, 2012, 89(7414):57-74. [17] HSU D, KAKADE S M, ZHANG T. A spectral algorithm for learning hidden Markov models[J]. Journal of Computer and System Sciences, 2012, 78(5):1460-1480. [18] GHANDI M, MOHAMMAD-NOORI M, BEER M A. Robust k-mer frequency estimation using gapped k-mers[J]. Journal of Mathematical Biology, 2014, 69(2):469-500. [19] MCLEAY R C, BAILEY T L. Motif enrichment analysis:a unified framework and an evaluation on ChIP data[EB/OL].[2017-10-16]. https://core.ac.uk/download/pdf/81051776.pdf. [20] TOUZET H, VARRE J S. Efficient and accurate P-value computation for position weight matrices[EB/OL].[2017-10-16]. https://almob.biomedcentral.com/track/pdf/10.1186/1748-7188-2-15. [21] SCHONES D E, SUMAZIN P, ZHANG M Q. Similarity of position frequency matrices for transcription factor binding sites[J], Bioinformatics, 2005, 21(3):307-313. [22] KORHONEN J, MARTINMAKI P, PIZZI C, et al. MOODS:fast search for position weight matrix matches in DNA sequences[J]. Bioinformatics, 2009, 25(23):3181-3182. [23] GUPTA S, STAMATOYANNOPOULOS J A, BAILEY T L, et al. Quantifying similarity between motifs[J]. Genome Biology, 2007, 8(2):Article R24. |
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