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how to identify TATA box in a gene list

Hi everybody,

Is the first time that I've tried to look for TATA box in a gene list. I used homer (findMotif.pl) to do that, but I don't know how to read the results. Is there any way in which I can identify only the TATA boxes for a set of gene list? Ideally, I would like to know the frequency of the genes in my gene list with TATA box.

Thank you very much in advance!

tata homer gene
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updated by Ram Ram • written by Lila M Lila M

Please, can you be more clear on what you mean with "gene list"? If it is a FASTA file with the sequences of the genes of your organism, like a transcriptome, you won't find TATA boxes (or maybe you will find only false positives) because it usually resides before the startpoint of transcription.

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written by Matteo Schiavinato Matteo Schiavinato

No, How can create this "motif file"?

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written by Lila M Lila M

Yes, I did, but for me is not very intuitive, what I am trying is download the TATA motif and use it at <motif file=""> , could that work?

findMotifs.pl gene human  -find motif_TATA.motif > TATA_results

Thank you!

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written by Lila M Lila M

I can't tell unless you paste what is inside the motif_TATA.motif...

I assume you have to specify a motif name one per line, didn't the second link help on that?

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written by Matteo Schiavinato Matteo Schiavinato

Yes, and I assume that is the same, right? 

>CCTTTTATAGNC   TATA-Box(TBP)/Promoter/Homer,BestGuess:TATA-Box(TBP)/Promoter/Homer(1.000)  5.682591    -3.995489e+02   0   124715.9,9565.0,11407.0,1769.0,0.00e+00
0.025   0.606   0.283   0.086
0.006   0.85    0.004   0.14
0.091   0.125   0.001   0.783
0.001   0.048   0.001   0.95
0.297   0.001   0.001   0.701
0.234   0.001   0.001   0.764
0.964   0.034   0.001   0.001
0.351   0.001   0.172   0.476
0.704704704704705   0.00900900900900901 0.285285285285285   0.001001001001001
0.042   0.2 0.716   0.042
0.178178178178178   0.355355355355355   0.328328328328328   0.138138138138138
0.117   0.51    0.304   0.069
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written by Lila M Lila M

Was this created with seq2profile.pl ?

seq2profile.pl <consensus> [# mismatches] [name] > output.motif

i.e. seq2profile.pl TATA 0 ets > output.motif

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written by Matteo Schiavinato Matteo Schiavinato

I think that is not necessary, If I downloaded the matrix from HOMER (paste above), is can be recognized.

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written by Lila M Lila M

So please, provide us the output that you're not able to understand and we can see if someone of us does! ;)

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written by Matteo Schiavinato Matteo Schiavinato

The output of the result! As in it I can see the sequence, is not exactly the TATA sequence (I don't know if HOMER only report the most similar one) so How can be sure that the genes that the output report has TATA boxes? 

GeneID  PromoterID  Offset  Sequence    Motif Name  Strand  MotifScore  Unigene Refseq  Ensembl Name    Alias   Orf Chr Description Type
644353  NM_001143978    -276    CGGTCTAAAAGC    TATA-Box(TBP)/Promoter/Homer,BestGuess:TATA-Box(TBP)/Promoter/Homer(1.000)  -   8.308651    Hs.648338   NM_001143978    ENSG00000166707 ZCCHC18 PNMA7B|SIZN2    -   Xq22.2  zinc finger CCHC-type containing 18 protein-coding
25771   NM_014346   -66 CCTTTAATAACG    TATA-Box(TBP)/Promoter/Homer,BestGuess:TATA-Box(TBP)/Promoter/Homer(1.000)  +   7.344113    Hs.435044   NM_014346   ENSG00000054611 TBC1D22A    C22orf4|HSC79E021   -   22q13.31    TBC1 domain family member 22A   protein-coding
23464   NM_014291   -63 CTTTTTAAGCGA    TATA-Box(TBP)/Promoter/Homer,BestGuess:TATA-Box(TBP)/Promoter/Homer(1.000)  +   6.041534    Hs.54609    NM_014291   ENSG00000100116 GCAT    KBL -   22q13.1 glycine C-acetyltransferase protein-coding
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written by Lila M Lila M

These kind of predictions usually come with an e-Value or a probability score. In this case, you have a lod-score (logarithm of the odds) that is associated to every line, present in field number 6 as "MotifScore". The documentation you provided says, at some point:

"Motif Score (log odds score of the motif matrix, higher scores are better matches)"

A good approach would be to plot all the lod-scores and see the distribution to infer which ones are the good ones are which ones are not.

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written by Matteo Schiavinato Matteo Schiavinato

You are right, but for me "higher scores are better matches" is not much informative (what is considered higher and lower?, how can I set a proper cut-off? in my opinion there is not much information and is a bit complicate be sure about the result...

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written by Lila M Lila M

Thank you very much for the information! :)

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written by Lila M Lila M

1 answer

https://www.dnalc.org/resources/geneboy.html

Put your sequence in geneboy to find the tatabox.

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written by theobroma22 theobroma22

As I said previously, I don't have any sequence, I only have gene IDs

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written by Lila M Lila M

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