Submission

Read here in a point-by-point description, how to submit your list for predictions.

 

  • TransFind can predict transcription factors for gene groups of human and mouse origin. Thus, you need first to select the organism that you are interested in
Organism (set of studied genes):
human genes
mouse genes
  • TransFind optionally considers conservation between human and mouse. In this case you can either choose the consideration of minimum affinity of the ortholog sequences or average affinity. Minimum affinity is the more conservative approach, since it gives a higher weight to factors whose binding affinity did not change in the course of evolution.
Conservation (phylogenetic analysis)
no conservation considered
strong affinitify in both human and mouse (min. affinity ranked)
average affinity in human and mouse
  • TransFind needs to know which promoter set you want to use for prediction. We prepared two, one starting 800bp before putative Transcription Start Site (TSS), ending 200bp after, and the second 300 bp before TSS, ending at 100bp after. We recomend the second set, but you may also try both.
  • The set containing the regions from 700bp to 300bp upstream can be used as a pseudo negative set of similar sequence composition, assuming that the density of real binding sites is much higher directly upstream of the TSS.

Promoter set:
300 upstream ... 100 downstream of TSS (400nt, short putative promoters)
800 upstream ... 200 downstream of TSS (1000nt, long putative promoters)
700 upstream ... 300 upstream of TSS (400nt, upstream of the 400nt short putative promoters)

  • Next you can specify how many gene you think are regulated by one transcription factor. We do recommend to use the default setting, 500, but often, especially if your gene group is small, it is advisable to try also larger numbers here.

Number of genes with the highest predicted factor affinities to take:
50 100 200 500 1000 2000 5000

  • You can specify whether you want to restrict your analysis to one frequency matrix per factor:

Matrices representing the factors:
highest info. content for each factor (TRANSFAC, 210 matrices)
all vertebrate (TRANSFAC, 554 matrices)

  • In the last step, you need to submit the list of genes that you want to analyse. In the left window you need to paste the identifiers of genes for the genes of interest (e.g. up-regulated genes), or chose a file. The types of supported identifiers are: Entrez Gene ID, ensemble Gene ID, Entrez Gene Symbol. (For more information see Identifier Mapping). In the right window, you can submit a background list, which would typically be: all expressed genes. If no genes are submitted, all genes in Ensembl are taken as background. We do however strongly recommend to submit a background list, as expressed genes and non-expressed genes could vary in their sequence properties.
Gene IDs of regulated genes:

or a file with regulated-gene IDs:
Gene IDs of unregulated (or all) genes:

or a file with unregulated-gene IDs:
  • And finally, you need to submit the list of genes that you want to analyse, by pressing on the botton on the right hand! The bottons on the left hand provide example gene lists, in case you have no gene list at hand.