Web servers for DNA motif analysis and Gene Ontology

1. MEME: https://meme-suite.org/meme/

2. DAVID: https://david.ncifcrf.gov

3. Bioprofiling.de

4. Homer: http://homer.ucsd.edu/homer/motif/

5. TFmotifView (http://bardet.u-strasbg.fr/tfmotifview/)

6. http://motifmap.ics.uci.edu

7. https://www.hsls.pitt.edu/obrc/index.php?page=sequence_motif_search_alignment_manipulation

8. http://www.geneinfinity.org/sp/sp_motif.html

9. http://cisbp.ccbr.utoronto.ca/TFTools.php

10. http://drimust.technion.ac.il

11. P-MATCH: http://gene-regulation.com

12. CiiiDER: http://ciiider.com

13. Bioinformatics.psb.ugent.be

14. https://www.cbioportal.org

15. https://www.telis.ucla.edu

16. https://meme-suite.org/meme/tools/tgene

17. http://lcbb.swjtu.edu.cn/EnhancerDB/

18. http://cisbp.ccbr.utoronto.ca/TFTools.php

19. http://bardet.u-strasbg.fr/tfmotifview/?results=Kq2tPLN2sv5zgN

20. InnateDB (www.innatedb.com) analysis platform used for GO

21. https://thebiogrid.org (database for protein-protein interaction)

22. http://www.beaconlab.it/pscan [Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are significantly over- or under-represented, providing thus hints on which transcription factors could be common regulators of the genes studied, together with the location of their candidate binding sites in the sequences]

23. http://bioinfo.wilmer.jhu.edu/tiger/ (Tissue-specific Gene expression and regulation)

24. https://molbiol-tools.ca/Motifs.htm (many tools, including logo, drawings, etc.)

25. http://biogps.org/#goto=welcome

26. https://tabula-muris.ds.czbiohub.org

Others:

TF databases search machines

FactorNet

TFImpute

TBiNet