Jun 15, 2016

ANFIS-based Fuzzy Systems for Searching DNA-Protein Binding Sites

BioRxiv : the Preprint Server for Biology
Dianhui WangWitold Pedrycz


Transcriptional regulation mainly controls how genes are expressed and how cells behave based on the transcription factor (TF) proteins that bind upstream of the transcription start sites (TSSs) of genes. These TF DNA binding sites (TFBSs) are usually short (5-15 base pairs) and degenerate (some positions can have multiple possible alternatives). Traditionally, computational methods scan DNA sequences using the position weight matrix (PWM) of a given TF, calculate binding scores for each K-mer against the PWM, and finally classify a K-mer as to whether it is a putative TFBS or a background sequence based on a cut-off threshold. The FSCAN system, which is proposed in this paper, employs machine learning techniques to build a learner model that is able to identify TFBSs in a set of bound sequences without the need for a cut-off threshold. Our proposed method utilizes fuzzy inference techniques along with a distribution-based filtering algorithm to predict the binding sites of a TF given its PWM model and phastCons scores for the input DNA sequences. Data imbalance reduction techniques are also used to ease the learning of the adaptive-neuro fuzzy inference system (ANFIS) algorithm. The proposed system is tested on 22 ChIP-chip se...Continue Reading

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Mentioned in this Paper

Positioning Attribute
Transcriptional Regulation
Abnormal Degeneration
Bounded by
Saccharomyces cerevisiae allergenic extract
Transcription Initiation Site
Transcription, Genetic

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