May you give more info about your experiments? Is it ChIP/ChIP-sec or qRNA/RNA-seq etc.? Is it about specific gene(s) or something else? It is impossible to answer your question without clarification.

It is from the scRNA seq with time series. When the GeneA (a transcrtion factor) goes up, the Gene B goes down. vice versa. Perfect match.

Same regulated was confirmed by qPCR. If knocking out the GeneA, the expression of Gene B goes down.

Keep in mind that the interaction you are observing may either the direct (transcription Factor A binds regulatory region of gene B and modulates expression) or indirect (transcription Factor A influences expression of one or more genes other than gene B, and these gene products influence expression of gene B).

What else do you know about your two genes? Many transcription factors are well-studied and we often know something about their consensus sequences for binding. You could look for this sequence in the regulatory regions of gene B.

Thank you Amy Klocko ! is there any database or tools that I can check the target genes of transcription Factor A? or the the regulatory regions of gene B?

Hello Qin,

Well, it really depends on your organism and what databases have been created. For example, eplant has interaction viewers for plants, I believe there is something similar for yeast and fruit flies as well.

Here is the plant site

ePlant (utoronto.ca)

What organism are you working on?

Thank you! Amy Klocko I am looking for mice and human. Any recommendation?

I'm not as familiar with those field (plant geneticist here).

Found some citations with a google search for "mouse interactome network," should be enough to get started with

Predicted mouse interactome and network-based interpretation of differentially expressed genes - PubMed (nih.gov)

Amy Klocko Thank you so much! I appreciate it!