/Transcription-Factor-Databases

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Transcription-Factor-Databases

Current (05/15/2019) Transcription Factor Data Source

  1. (1,639) List of ‘All’ Known TFs (Ref 1 & 2) Incorpates Following Sources:

    • CIS-BP Database: Catalog of Inferred Sequence Binding Preferences
    • CISBP-RNA Database: Catalog of Inferred Sequence Binding Preferences of RNA binding proteins
    • TRANSFAC motif database
    • JASPAR motif database
    • HocoMoco motif database
    • Uniprobe PBM database
    • Vaquerizas et al TF census
    • TFCat
    • TFClass
    • Protein Data Bank (PDB)
    • Pfam
    • SMART
    • Interpro
    • Gene Ontology

  2. TF Expression Specifity (Ref 1 & 2)

  3. Trust v2 DB = (~800) Transcription Factor & Target Binding (8,444) (Ref 3)

    • Automated literature search then Manually curated literature based TF & Targets
    • 3 Category Types for Targets: Repressive, Activating, Unknown
    • GMT files within directory

Future To Add or Consider:

  1. Harmonizome (Ref 4)
    • Download Datasets: harmonizomedownloader.py
    • 10 entries (http://amp.pharm.mssm.edu/Harmonizome/download) as of 05/15/2019 for Transcription Factors
    • 7 entries (TFs & Targets) are not listed as incorporated in dataset for Transcription Factors used
      • CHEA
      • MotifMap
      • ENCODE
  2. https://saezlab.github.io/DoRothEA/
    • Additional database
    • Garcia-Alonso, Luz, et al. "Benchmark and integration of resources for the estimation of human transcription factor activities." BioRxiv (2018): 337915

Current Folder Structure & Explaination

  • Trust V2 data & paper
  • TF_Paper_Data = (Ref 1 & 2) raw data

References

  1. http://humantfs.ccbr.utoronto.ca/allTFs.php
  2. Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., ... & Weirauch, M. T. (2018). The human transcription factors. Cell, 172(4), 650-665.
  3. Han, H., Cho, J. W., Lee, S., Yun, A., Kim, H., Bae, D., ... & Lee, S. (2017). TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. Nucleic acids research, 46(D1), D380-D386.
  4. Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford). 2016 Jul 3;2016. pii: baw100.