1. What information is provided in NMATFBS?
The NMATFBS database contains transcription factor binding sites for 10 non-model animals, including pigs, cattle, sheep, and dogs. The database contains information on transcription factor binding sites, transcription factors, and corresponding target genes of 10 species. You can query by entering the species name, gene name, and transcription factor id.
2. What data does NMATFBS contain?
The NMATFBS labeled 715430 transcription factor binding sites in 10 non-model animals. There were 77486 TFBS in chicken, 46326 TFBS in cattle, 38771 TFBS in dog, 178696 TFBS in duck, 17915 TFBS in goat, 7304 TFBS in horse, 134517 TFBS in pig, 166 327 TFBS in rabbit, 46 986 TFBS in sheep and 1 102 TFBS in turkey. The TFBS targets 61591 target genes and 3175 highly similar TF motifs, and 7124797 pairs of TF-TFBS-Gene transcriptional regulatory networks.
3. When should I use NMATFBS?
The NMATFBS database may be used in the following situations: 1. Hope to build a relevant regulatory network through data; 2. People who are interested in TF and its vital regulatory disorders; 3. People who are interested in the study of coregulation of transcription factor binding sites; 4. Individuals who wish to conduct computer analysis of the cis-regulatory components of animals provided by NMATFBS.
4. Data sources and bioinformatics tools
| Data | Source | URL |
|---|---|---|
| Promoter sequence | UCSC | http://genome.ucsc.edu/ |
| Promoter sequence | Ensemble | http://asia.ensembl.org/index.html |
| Transcript factors | JASPAR | http://jaspar.genereg.net/ |
| Transcript factors | TFBSshape | https://rohslab.usc.edu/TFBSshape/ |
| Transcript factors | CIS-BP | http://cisbp.ccbr.utoronto.ca/ |
| Whole genome sequence | Ensemble | ftp://ftp.ensembl.org/pub/release-98/fasta |
| Tool | Usage | URL |
| MEME | Search TFBS motif | http://meme-suite.org/ |
| bedtools | Search TFBS target genes | https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html/ |
| CentriMo | Motif Enrichment | http://meme-suite.org/tools/centrimo/ |
| FIMO | Search motif | http://meme-suite.org/tools/fimo/ |
| TOMTOM | Motif alignment | http://meme-suite.org/tools/tomtom/ |