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

NetworkAnalyst
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  • 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.

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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)?

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

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

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Hello Nikhil,

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

Guangyan