EEADannot

This repository holds the scripts and data files used for the manual curation of DNA motifs and cis regulatory sites, mostly from plants, that are eventually added as a separate library/collection in the database footprintDB, also available at RSAT::Plants, which are part of the INB/ELIXIR-ES resources portfolio.

Citation

Contreras-Moreira B, Sebastian A. FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces. Methods Mol Biol. 2016; 1482:259-77. doi: 10.1007/978-1-4939-6396-6_17. PMID: 27557773.

Example motif in TRANSFAC format

MO  EREBP1
NA  Os02g54160.1
P0      A      C      G      T
01   1.00   0.00   0.00   0.00
02   0.00   0.00   1.00   0.00
03   0.00   1.00   0.00   0.00
04   0.50   0.50   0.00   0.00
05   0.00   0.00   1.00   0.00
06   0.00   0.50   0.50   0.00
07   0.00   1.00   0.00   0.00
RX  PUBMED:23703395
RL  Serra TS et al (2013) OsRMC, a negative regulator of salt stress response in rice...Plant Mol Biol 82(4-5): 439-455
RX  PUBMED:12913152
RL  Cheong YH et al (2003) BWMK1, a rice mitogen-activated protein kinase... Plant Physiol 132(4):1961-72
XX
FA  EREBP1
NA  Ethylene-responsive transcription factor 1; EREBP1; OsEREBP1; ERF1_ORYSJ; Q6K7E6; Q9SE28
SQ  MCGGAIIHHLKGHPEGSRRATEGLLWPEKKKPRWGGGGRRHFGGFVEEDDEDFEADFEEFEVDSGDSDLELGEEDDDDVVEI...
OS  Oryza sativa
CC  family:AP2/ERF
XX
SI  EREBP1_1
SQ  gAGCCGCCa
XX
SI  EREBP1_2
SQ  gAGCAGGCa
XX
//

Production steps

• Add new TFs to TFsequences.faa

  • Make sure 'FullName' has no blanks.

• Add new motifs to PWM.tab.

  • In name line, 1st word is motif name [no spaces], 2nd is 1+ TF names separated by commas [,].

  • Make sure separators among weights/columns are TABs.

  • To convert MEME/HOMER motifs you can use a one liner such as:

    perl -ane 'next if(/^>/ || /^#/); $f++; for $c (1 .. @F){ $data[$f][$c]=$F[$c-1] }; $maxc=@F if(@F>$maxc); END{ for $c (1 .. $maxc){ for $ff (1 .. $f){ printf("%1.3f\t",$data[$ff][$c]) } print "\n"} }' motif.meme

  • If you need to convert a PNG logo check https://www.biostars.org/p/9537076/#9607522 followed by:

    cat enoLogo.txt | perl -lne 'if(/^([ACGT])/){ s/^([ACGT])/$1:/; tr/AT/TA/; s/(\d+.\d{3})\d+/$1/g; push(@pwm,"$_\n")} END{ print sort(@pwm)}'

• Add individual sites, if any, to sites.tab.

• Add new papers to references.tab

  • Make sure 1st field matches a motif name in PWM.tab.
  • Second field is one or more TF name/primary key separated by commas [,].
  • Third field is PubMed id.

• Actually format the library in footprintDB format (will try to use Plant-TFClass to assign TFs to families):

  $ perl create_library4footprintdb.pl