Grit online (v2.0)

Predict transcription factor binding sites using mixed Student's t-test statistics.

Downloads Project Source Contribute

1. Download Gene-set

Select a Genome using the select boxes in the right, the default listed the first 15 genomes, typing the scientific name of the orgnisms in the search box to filter results.

Homo sapiens is a species of primate in the family Hominidae (great apes).

Taxonomy ID: 9606

Common name: Human

Select a Genome

FLAVER.bed WKS.gmt GSEA.gmt

2. Format Specification

We provide two file formats for transcription factor binding sites.

The gmt file format is specified by one transcirprion factor per line, the first column is the transcirprion factor ID, the second column is the URL, from the third column are the target genes that the transcription can bind with. Each column was seprated by a TAB character.

The bed file format specification is avaiable at UCSC web site, it has six columns seprated by TAB characters, one line per transcription factor binding site. The fourth column is the name of the binding site specified by TRANSCRIPTION_FACTOR_NAME; GENE_PROTEIN_ACCESSION|OFFICIAL_GENE_SYMBOL.


3. Software

We provide four softwares for transcription factor binding sites analysis. Grit is for transcription factor binding site prediction. Flave, WKS and GSEA are for key transctiption factor mining.



Predict transcription factor binding sites for orthologous genes using mixed Student's t-test statistics.

An example run should like: grit-2.0 -m Motiff_Jaspar-2022+HOCO-v11.txt -i mammalian_-1k_+100.txt -b mammalian_rdm2000.txt -x hsapiens -t 0.05 -p 0 -c 256 -u 12345 -o human-tfbs.txt.

This command takes three input files: Motiff_Jaspar-2022+HOCO-v11.txt, mammalian_-1k_+100.txt, and mammalian_rdm2000.txt. It will produce an output file named human-tfbs.txt. Full instruction is avaiavle in Grit's user manual.

Download Readme

Publications

  • Grit paper

    Tinghua Huang, Hong Xiao, Qi Tian, Zhen He, Min Yao. Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics. PloS Computational Biology, 2022.

  • Flaver paper

    Min Yao, Hao He, Binyu Wang, Xinmiao Huang, Sunli Zheng, Jianwu Wang, Xuejun Gao, Tinghua Huang. Testing the significance of ranked gene-sets in genome-wide transcriptome profiling data using weighted rank correlation statistics, Current Genomics, 2024.

    Huang Tinghua, Niu Siqi, Zhang Fanghong, Wang Binyu, Wang Jianwu, Liu Guoping, Yao Min, Correlating gene expression levels with transcription factor binding sites facilitates identification of key transcription factors from transcriptome data, Frontiers in Genetics, 2024.

FAQs

  • Some of the species are not available?

    The species in the list marked as "comming soon..." will be updated when the analysis is finished.

  • Something doesn't work. Can you fix it?

    Yes! Please report all issues to the maintainer: Dr. Tinghua Huang and Dr. Min Yao.

  • What browsers are supported?

    All modern desktop browsers are supported (Firefox, Chrome, Safari and IE9). Legacy support for IE8 is also enabled.

Maintainer

  • Dr. Tinghua Huang, Yangtze University, Email: thua45@yangtzeu.edu.cn
  • Dr. Min Yao, Yangtze University, Email: minyao@yangtzeu.edu.cn