What are the differences between the TF-gene interactions databases?

  • ENCODE: TF-gene interactions are inferred from ENCODE ChIP-seq data using the BETA algorithm. BETA integrates factor binding and differential expression analysis to predict whether a TF has an activating or a repressing effect, to infer the gene targets, and to identify the binding motif.

  • JASPAR: uses a collection of position frequency matrices to predict TF binding sites on the DNA.

  • ChEA: collected ChIP-X (including ChIP-chip, ChIP-seq, ChIP-PET, and DamID) data from the literature to describe the binding of TFs to target genes in mammalian species.


Hi, I could not find this TF-binding analyse in the new ExpressAnalyst website…
(which I have used in the previous NetworkAnalyst so I would like to repeat the results now…)
Could you please help to find where it is now (not sure if you still keep this function in the new version)?

Hello Sunny, this is a mistake of mine, the TF-gene analysis are now in NetworkAnalyst which is accessed using gene list upload.

1 Like

Hi, how to differentiate between activating and repressing TFs? Is it possible to get a directed network using network analyst for TF-Gene interactions?

Hello Nikhil,

The current version doesn’t have activation/repression information in the database. We will consider it for future releases.