Plot showing the positions of co-occurring motifs

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We plotted the positions of the co-occurring motifs within a module along the upstream regions. These positions were estimated using the positional weight matrix for the 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 number of co-occurrences is shown to the right of each line). The Locus Link id of each gene is shown to the left.

Each symbol (shown in a different color) represents a different motif.

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.

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 75. The putative binding sites 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