I used MEME to find few conserved motifs upstream to a set of genes. But I am unable to find good hits using TOMTOM (which searches for proteins binding to similar motifs). What are the alternative reliable tools? Also is there any way to connect RNAseq data for these species to the presence or absence of the motifs found in the upstream region.
1. To validate your DNA motif try to align with putative orthologs and check for the consensus sequence.
2. To find proteins that recognize a similar DNA motif check for :
http://floresta.eead.csic.es/3dfootprint/
Which gets updated on weekly basis..
3. For the use RNA seq data for the motif enrichment try AME, which is part of MEME suite. Before that use STIF algorithm (in house prog) to predict upstream region.
Hope the following points might help you..
Cheers :-)
Naseer
1. To validate your DNA motif try to align with putative orthologs and check for the consensus sequence.
2. To find proteins that recognize a similar DNA motif check for :
http://floresta.eead.csic.es/3dfootprint/
Which gets updated on weekly basis..
3. For the use RNA seq data for the motif enrichment try AME, which is part of MEME suite. Before that use STIF algorithm (in house prog) to predict upstream region.
Hope the following points might help you..
Cheers :-)
Naseer
Dear Naseer,
I used 3dfootprint as suggested by you but it gives output of proteins for which structures are available, but sadly I could not find a good motif hit in that. I am finding some motifs in the human database using footprintdb (http://floresta.eead.csic.es/footprintdb/?databases).
As STIF works using the TFs from plants I do not think it will be useful for me. I will try AME.
I cant try your first suggestion of looking into orthologs of these genes in other organisms. Only t finding the location of many of these orthologous genes is not a straightforward task.
Thank you for your inputs!
Regards,
Snehal
Hi Snehal,
Regarding your first question, you can try to match the motif you found to one of the several ones we have determined experimentally via PBMs, using our "Motif Scan" tool at http://cisbp.ccbr.utoronto.ca/TFTools.php. Comparison is also via TomTom, but it will use our database to compare.
Good luck.
-A
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