Differential Gene Expression Analysis

Your Possible Next Steps

IPA software, IPA training
Quickly visualize and understand RNA-seq data and perform insightful data analysis and interpretation by placing your experimental results within the context of biological systems.
IPA also allows for transcription factor analysis
You can book IPA through the CMCB booking system once you have gone through a registration process. Please check out this README for detailed instructions about the registration process.

Determine whether groups of functionally related genes are significantly over-represented in your list of differentially expressed genes.
EnrichR
g:Profiler
Webgestalt

GSEA software
Determine whether groups of functionally related genes tend to occur at the top or bottom of your ranked gene list.
A lot of our clients like this option, so you might want to try it.
Use the normalized counts as input. In addition, load all phenotype label files that may be of interest for comparisons.
You can either choose one of the pre-defined gene sets from MsigDB or set up your own gene set.
For human and mouse data, genes are identified by their Ensembl IDs; select “Human_Ensembl_Gene_ID_*” and “Mouse_Ensembl_Gene_ID_*” as chip platform, respectively.
For other species, Ensembl IDs cannot be used and genes need to be identified by their symbols; use “Human_Gene_Symbol_with_Remapping_*” if the gene symbols are all in upper case and “Mouse_Gene_Symbol_with_Remapping_*” if only the first letter is in upper case.

Morpheus software
This is a very simple tool that you can use to explore and visualize smaller parts of your data in a heatmap.
You can use our provided z-scores and select your genes of interest. You can upload your selected table to the Morpheus website.
In addition, you can add sample annotations to view your conditions.