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This plot illustrates the positions of all modules of co-occurring motifs along the upstream regions. The format of this figure is very similar to the plot showing the positions of each module in each transcript.
The motif positions were estimated using the positional weight matrix for each motif (see Binding sites for details).
The x-axis shows the position with respect to the translation initiation ATG signal at the 3' end.
Each line corresponds to a separate transcript (the transcript index number as well as the LocusLink id of each gene is shown to the left).
Each symbol-color represents a different motif (Note that, for the sake of clarity, we imposed a maximum of 20 different symbols for this plot).
Note that in many cases, a given motif may appear several times within the same module. This may be biologically very relevant since it increases the probability of binding for a transcription factor.
Note that in some cases, there are overlaps of the motif positions or module positions. We did not perform any clustering of the modules but this plot allows to visualize specific modules that should be grouped together. In some cases, different modules occur in the same transcript at distinct locations. This may be biologically relevant as it has been described that specific modules may fulfilll different regulatory functions.
Positional conservation with respect to the ATG across different transcripts in the same species would show up here as a vertical accumulation of motif binding sites.
For clarity, we restricted the number of transcripts shown to 50. The putative binding sites of every module in every transcript are reported in a text list under a separate link in the main page. The x-axis label indicates the number of transcripts plotted as well as the total number of transcripts.
Questions? Click here to email Gabriel Kreiman