Introduction

Accurately identifying the binding sites of transcription factors (TFs) is crucial to understanding the mechanisms of transcriptional regulation and human disease. We present incorporating Find Occurrence of Regulatory Motifs (iFORM), an easy-to-use and efficient tool for scanning DNA sequences with TF motifs described as position weight matrices (PWMs). Both performance assessment with a receiver operating characteristic (ROC) curve and a correlation-based approach demonstrated that iFORM achieves higher accuracy and sensitivity by integrating five classical motif discovery programs using Fisher's combined probability test. We have used iFORM to provide accurate results on a variety of data in the ENCODE Project and the NIH Roadmap Epigenomics Project, and the tool has demonstrated its utility in further elucidating individual roles of functional elements. Both the source and binary codes for iFORM can be freely accessed at https://github.com/wenjiegroup/iFORM. The identified TF binding sites across human cell and tissue types using iFORM have been deposited in the Gene Expression Omnibus under the accession ID GSE53962.

Publications

  1. iFORM: Incorporating Find Occurrence of Regulatory Motifs.
    Cite this
    Ren C, Chen H, Yang B, Liu F, Ouyang Z, Bo X, Shu W, 2016-01-01 - PLoS ONE

Credits

  1. Chao Ren
    Developer

    Department of Biotechnology, Beijing Institute of Radiation Medicine, China

  2. Hebing Chen
    Developer

    Department of Biotechnology, Beijing Institute of Radiation Medicine, China

  3. Bite Yang
    Developer

    Department of Biotechnology, Beijing Institute of Radiation Medicine, China

  4. Feng Liu
    Developer

    Department of Biotechnology, Beijing Institute of Radiation Medicine, China

  5. Zhangyi Ouyang
    Developer

    Department of Biotechnology, Beijing Institute of Radiation Medicine, China

  6. Xiaochen Bo
    Developer

    Department of Biotechnology, Beijing Institute of Radiation Medicine, China

  7. Wenjie Shu
    Investigator

    Department of Biotechnology, Beijing Institute of Radiation Medicine, China

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Summary
AccessionBT006441
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Country/RegionChina
Submitted ByWenjie Shu