Method for recognizing transcription factor binding site
A technology for binding sites and transcription factors, applied in the field of transcription factor binding site recognition, which can solve the problems of low sensitivity, low test accuracy, and low test specificity.
Inactive Publication Date: 2013-11-13
HARBIN ENG UNIV
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Gene chip is a direct measurement of biological information, and its sensitivity is high, but compared with high-throughput DNA sequencing, its test accuracy is not high, and its test specificity is low; high-throughput DNA sequencing has higher Detection resolution, its test accuracy is high, the test specificity is good, but because it is an indirect measurement of biological information, its sensitivity is low
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[0027] The present invention will be further described below in conjunction with accompanying drawing:
[0028] A transcription factor binding site prediction method based on conditional random field fusion gene chip data and DNA sequencing data, comprising the following steps:
[0029] (1) Using conditional random field identification technology and using ChIP-chip gene chip data to conduct preliminary identification of transcription factor binding sites;
[0030] (2) Preliminary identification of transcription factor binding sites using ChIP-seq DNA sequencing data using conditional random field identification technology;
[0031] (3) Final identification of transcription factor binding sites is carried out by means of decision-level fusion. That is, for the base fragments at the same position, weighted fusion of the preliminary identification results of transcription factor binding sites from ChIP-chip gene chip data and ChIP-seq DNA sequencing data respectively, and the f...
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The invention belongs to the information detection field of molecular biology, and particularly relates to a method for recognizing a transcription factor binding site, wherein the method is based on the conditional random field technology, and ChIP (Chromatin immunoprecipitaion)-chip gene chip data and ChIP-seq DNA (deoxyribonucleic acid) sequencing data are merged according to the method. The method disclosed by the invention comprises the steps: creating a conditional random field model; obtaining ChIP-chip experiment detection values, and recognizing corresponding state values; obtaining ChIP-seq experiment detection values, and recognizing corresponding state values; testing the recognizing accuracy of the conditional random field model; weighting and merging the recognition probability of the nth DNA base fragment of a recognition result; and comparing and recognizing the transcription factor binding site. According to the method, the conditional random field is used for merging ChIP-chip and ChIP-seq experiment detection data to recognize the transcription factor binding site. By experimental verification, compared with recognition methods which adopt a single technology, the method disclosed by the invention is superior in the aspect of recognition accuracy rate.
Description
technical field [0001] The invention belongs to the field of molecular biological information detection, and in particular relates to a transcription factor binding site recognition method based on conditional random field technology and fusion of ChIP-chip gene chip data and ChIP-seq DNA sequencing data. Background technique [0002] Transcription factors are functional proteins that regulate gene transcription, and the identification of their binding sites on the DNA gene promoter region plays a significant role in the study of gene transcription regulation mechanisms. It is an important and difficult point in life science research. With the advancement of information science experiment technology, the experimental methods used to obtain molecular biological information are also changing with each passing day. Among them, the standard experiment for detecting the binding state of specific proteins in DNA regions on a genome-wide scale is chromatin immunoprecipitation (Chro...
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IPC IPC(8): G06F19/12
Inventor 冯伟兴董彦生贺波陈若雷王科俊
Owner HARBIN ENG UNIV