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Search

  • 1 Enter either an HGNC gene symbol or Ensembl transcript id.
  • 2 Select id type.
  • 3 Submit search.

Search – Transcript Table

If you have searched by HGNC gene symbol, now choose your transcript of interest for your gene.

  • ensembl trancript id – Unique and stable identification number used by the Ensembl database to catalog distinct transcripts.
  • ensembl prot id – Unique and stable identification number used by the Ensembl database to catalog distinct proteins.  Parent protein of target transcript id.
  • ensembl gene id – Unique and stable identification number used by the Ensembl database to catalog distinct genes.  Parent gene of target transcript id and protein id.
  • gene name – HGNC identifier of gene.
  • transcript name – HGNC identifier + Ensembl internal name for unique transcript.
  • chromosome/strand/start/end – Human genomic location of the current feature.
  • description – Description of gene of target transcript.

Results – Mapped Promoter

  • A Ensembl transcript name, HGNC identifier + Ensembl internal name for unique transcript.
  • B Color coded top 10 transcription factors predicted to bind to this promoter.
  • C Graphical representation of promoter of transcript, predicted binding sites are indicated by bars.  Bar height represents number of species that the prediction is supported in.  Positive y-axis indicates +strand and negative y-axis representes -strand.
  • D Conservation of mammal nucleotide sequences in alignment analyzed.
  • E Vertical lines represent CpG locations.  Red line describes CpG ratio of human promoter sequence over a 100 nt window.
  • F Nucleotide position relative to Ensembl defined transcription start site of human sequence.  Applies to C, D, and E.

Results – Predictions Table

  • ensembl trancript id – Unique and stable identification number used by the Ensembl database to catalog distinct transcripts.
  • binding protein – Transcription factor which is predicted to bind to human sequence at the given location.
  • start/end – Locations where transcription factor is predicted to bind to human sequence, with reference to the TSS.
  • strand – Strand on which the binding protein is predicted to bind, with reference to +1 indicating the same strand as the transcript feature.
  • score – Log odds weight score for the relevant binding protein on the human sequence at the location indicated.
  • support – Number of species for which a prediction of the relevant binding protein scored higher than the required threshold, includes human.
  • combined affinity score – A summation of log odds weight scores for all species which have a prediction of the relevant binding protein at the same position in the alignment as the human prediction, includes human.
  • motif – The human nucleotide sequence which the relevant binding protein is predicted to bind to at the relevant location.
  • p_value – P-value of the score of the found motif in the human sequence.