TFBS Hits Summary Table

This table contains the gene and promoter information where the TFBS predictions are found, along with individual TFBS hit locations.

The table is preceded by a header section listing the TF name, JASPAR ID, structural class and family, taxonomic group, information content and GC content of the TFBS profile for the anchoring TF and the anchored (paired) TF.

Note that a gene may have multiple alternative promoters. In some cases, the region upstream of one TSS overlaps with the downstream region of an adjacent TSS (depending on the promoter upstream and downstream parameters selected).

For operon genes in the C. elegans genome, the operon ID is displayed.

Gene ID(s)

This column only appears if you specified gene IDs other than Ensembl IDs. Shows the gene ID/symbol of the gene for which the TFBS is predicted. Since there can be a many-to-one mapping between gene IDs and Ensembl IDs, this may be a comma separated list of IDs

Ensembl ID(s)

The Ensembl gene ID for which the TFBS is predicted.

Operon ID (for C. elegans)

The ID for the operon containing the gene. When a gene occurs as part of an operon, the TFBSs upstream of the first gene in the operon apply to all genes in the operon.

Chr

The chromosome on which the gene is located.

Strand

The chromosome strand on which the gene is located.

Gene Start

The annotated start position of the gene.

Gene End

The annotated end position of the gene.

Nearest TSS

The annotated transcription start site (TSS) position located closest to the given TFBS hit.

Anchoring TF

The anchoring TF name.

Start

The start position of the predicted anchoring TFBS.

End

The end position of the predicted anchoring TFBS.

Rel. Start

The relative start position of the predicted anchoring TFBS to the neareset TSS.

Rel. End

The relative end position of the predicted anchoring TFBS to the nearest TSS.

Strand

The chromosome strand on which the predicted anchoring TFBS is located.

Score

The absolute score of the predicted binding site sequence given the anchoring TFBS weight matrix profile.

% Score

The relative (percent) score of the predicted binding site sequence given the anchoring TFBS weight matrix profile.

Sequence

The predicted binding site sequence of the anchoring TF. Note that if the anchoring TFBS strand is negative, the sequence reported is based on the antisense strand

Anchored TF

The anchored TF name (paired with the anchoring TF).

Start

The start position of the predicted anchored TFBS.

End

The end position of the predicted anchored TFBS.

Rel. Start

The relative start position of the predicted anchored TFBS to the neareset TSS.

Rel. End

The relative end position of the predicted anchored TFBS to the nearest TSS.

Strand

The chromosome strand on which the predicted anchored TFBS is located.

Score

The absolute score of the predicted binding site sequence given the anchored TFBS weight matrix profile.

% Score

The relative (percent) score of the predicted binding site sequence given the anchored TFBS weight matrix profile.

Sequence

The predicted binding site sequence of the anchored TF. Note that if the anchored TFBS strand is indicated to be negative, the sequence reported is based on the antisense strand.

Distance

The distance between the anchoring TFBS and the anchored TFBS.