Identification of transcription factor binding sites based on the chi-square (χ2) distance of a probabilistic vector model

Lun Huang; Mohammad Al Bataineh; G. E. Atkin; Ismaeel Mohammed; Wei Zhang; Maria Parra; Maria Del Mar Perez

doi:10.1109/FBIE.2009.5405793

Identification of transcription factor binding sites based on the chi-square (χ²) distance of a probabilistic vector model

Lun Huang, Mohammad Al Bataineh, G. E. Atkin, Ismaeel Mohammed, Wei Zhang, Maria Parra, Maria Del Mar Perez

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

4 Citations (Scopus)

Abstract

This paper describes a new approach for locating signals, such as promoter sequences, in nucleic acid sequences. Transcription Factor (TF) binding to its DNA target site is a fundamental regulatory interaction. The most common model used to represent TF binding specificities is a position weight matrix (PWM) [1], which assumes independence between binding positions. However, in many cases, this simplifying assumption does not hold. In this paper, we present a Chi-Square (χ²) distance model [2], which is based on the distance between the profiles of component vectors. It is a novel probabilistic method for modeling TF-DNA interactions. Our approach uses χ² distances to represent TF binding specificities. Simulation results show that the proposed approach identifies TF binding sites significantly better than the PWM model method.

Original language	English
Title of host publication	FBIE 2009 - 2009 International Conference on Future BioMedical Information Engineering
Pages	73-76
Number of pages	4
DOIs	https://doi.org/10.1109/FBIE.2009.5405793
Publication status	Published - 2009
Externally published	Yes
Event	2009 International Conference on Future BioMedical Information Engineering, FBIE 2009 - Sanya, China Duration: Dec 13 2009 → Dec 14 2009

Publication series

Name	FBIE 2009 - 2009 International Conference on Future BioMedical Information Engineering

Conference

Conference	2009 International Conference on Future BioMedical Information Engineering, FBIE 2009
Country/Territory	China
City	Sanya
Period	12/13/09 → 12/14/09

Keywords

Chi-square distance
Promoter
Transcription factor

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics
Health Information Management

Access to Document

10.1109/FBIE.2009.5405793

Cite this

Huang, L., Al Bataineh, M., Atkin, G. E., Mohammed, I., Zhang, W., Parra, M., & Perez, M. D. M. (2009). Identification of transcription factor binding sites based on the chi-square (χ²) distance of a probabilistic vector model. In FBIE 2009 - 2009 International Conference on Future BioMedical Information Engineering (pp. 73-76). Article 5405793 (FBIE 2009 - 2009 International Conference on Future BioMedical Information Engineering). https://doi.org/10.1109/FBIE.2009.5405793

Identification of transcription factor binding sites based on the chi-square (χ²) distance of a probabilistic vector model. / Huang, Lun; Al Bataineh, Mohammad; Atkin, G. E. et al.
FBIE 2009 - 2009 International Conference on Future BioMedical Information Engineering. 2009. p. 73-76 5405793 (FBIE 2009 - 2009 International Conference on Future BioMedical Information Engineering).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Huang, L, Al Bataineh, M, Atkin, GE, Mohammed, I, Zhang, W, Parra, M & Perez, MDM 2009, Identification of transcription factor binding sites based on the chi-square (χ²) distance of a probabilistic vector model. in FBIE 2009 - 2009 International Conference on Future BioMedical Information Engineering., 5405793, FBIE 2009 - 2009 International Conference on Future BioMedical Information Engineering, pp. 73-76, 2009 International Conference on Future BioMedical Information Engineering, FBIE 2009, Sanya, China, 12/13/09. https://doi.org/10.1109/FBIE.2009.5405793

Huang L, Al Bataineh M, Atkin GE, Mohammed I, Zhang W, Parra M et al. Identification of transcription factor binding sites based on the chi-square (χ²) distance of a probabilistic vector model. In FBIE 2009 - 2009 International Conference on Future BioMedical Information Engineering. 2009. p. 73-76. 5405793. (FBIE 2009 - 2009 International Conference on Future BioMedical Information Engineering). doi: 10.1109/FBIE.2009.5405793

Huang, Lun ; Al Bataineh, Mohammad ; Atkin, G. E. et al. / Identification of transcription factor binding sites based on the chi-square (χ²) distance of a probabilistic vector model. FBIE 2009 - 2009 International Conference on Future BioMedical Information Engineering. 2009. pp. 73-76 (FBIE 2009 - 2009 International Conference on Future BioMedical Information Engineering).

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