Hi Hanwen,

One strategy for finding direct gene targets could be to first knock out/knock down epc-1 and performing RNA-seq to determine genes that go down in expression. You'd have to followup with a ChIP-seq experiment for histone acetylation (in epc-1 WT and KO/KD background) or even better epc-1 itself in a WT background (assuming you have a good antibody or can generate a tagged gene) to confirm that the genes which go down in expression actually have corresponding histone acetylation peaks and epc-1 localization.

There are other genetic strategies for finding downstream targets of epc-1, but a combination of RNA-seq and ChIP-seq experiments should be the cornerstone of your study in finding the relevant targets.

Thanks,

Barry

Barry Zee

Hi Barry,

Thanks for your useful information. These will be very helpful for me to find the genes. And I also wondering are there any tools or website can search for the pathway a gene belongs to. Or I only can dig out the information from papers?

Thanks,

Hanwen

Hi Hanwen,

There are a number of websites that compile gene information, but the biggest determinant for you in choosing a website is probably the one with the most relevant and detailed information for your organism. Some general websites include Uniprot and NCBI.

If you have a set of genes that you want to identify pathways, GO-term searches can be helpful and can be acquired from websites like http://amigo.geneontology.org/amigo.

In the end, I think the best source of information would be searching the primary literature or reviews that cover your gene of interest. You can find literature in Web of Science, Pubmed, or even Google Scholar.

If your gene has never been studied before, there still are ways to get some hypotheses on relevant pathways, namely to search for sequence homologues of your gene in other organisms where there may be more information (websites such as BLAST or https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl).

Thanks,

Barry

Hi Barry,

Thanks for your useful information. This helps me a lot.

Thanks,

Hanwen