Instructions here
This protocol describes a network analysis workflow in Cytoscape for a set of differentially expressed genes. Points covered:
Ovarian serous cystadenocarcinoma is a type of epithelial ovarian cancer which accounts for ~90% of all ovarian cancers. The data used in this protocol are from The Cancer Genome Atlas, in which multiple subtypes of serous cystadenocarcinoma were identified and characterized by mRNA expression.
We will focus on the differential gene expression between two subtypes: Mesenchymal and Immunoreactive.
For convenience, the data has already been analyzed and pre-filtered, using log fold change value and adjusted p-value.
Many public databases and multiple Cytoscape apps allow you to retrieve a network or pathway relevant to your data. For this workflow, we will use the STRING app. Some other options include:
To identify a relevant network, we will use the STRING database in two different ways:
Query STRING protein with the list of differentially expressed genes.
Query STRING disease for a keyword; ovarian cancer.
The two examples are split into two separate workflows on the following slides.
When I set the column to logFC and the color mapping, it doesn’t show up on the network. All the nodes are gray.
I didn’t have the red-blue colors option…