Hi everyone,
I have done the Differential analysis of genes involved in osteoclasts physiology. My goal is to find out new genes in osteoclast that are related to osteoporosis. I have done with gene ontology using David as a tool. Now, I am confused that how to use KEGG information to look at the new genes. As most of the paper, I went through mentioned the selection of a bunch of genes that they are using for further analysis.
Kindly give me your suggestions.
Thanks.
Dear Sarah,
You might take the help of the attached publication for the in-detail methodology, regardless of the type of disease.
Title: Integrated bioinformatics analysis for the screening of hub genes and therapeutic drugs in ovarian cancer
Link: https://ovarianresearch.biomedcentral.com/articles/10.1186/s13048-020-0613-2
To discover new genes in any related disease:
1. Use the latest version of Cytoscape software
2. Choose a string disease query (at the top left corner if you are using version 3.9.0).
3. Type your disease name and search. You will get a PPI network specifically for your inquiry.
4. Choose from Apps “ STRING enrichment” then “retrieve functional analysis” and “retrieve enriched publications”.
5. Map another PPI network from your DEGs (Analyze it in detail)
NOTE: it is so important to carefully choose and compare your DEGs datasets. It is preferred to overlap two or more datasets and filter them according to your Cut-off criteria.
6. Compare the available genes in the string disease query with your mapped PPI network to find out the new ones.
I am just a beginner in enrichment analysis, but I hope these answers might be helpful.
Sarah Hassanein thanks.I will follow these steps. Thanks for sharing the information.