Gene-List Network Enrichment Analysis (GeLiNEA) takes a gene list (e.g., from a screening experiment), a gene set (from a corpus of curated gene sets, e.g., MSigDB), and a protein-protein association network (e.g., STRING) and evaluates the significance of connections between the gene list and the gene set in the network under a null model of degree-preserving random gene lists.
Use sbt (https://www.scala-sbt.org/) to run GeLiNEA:
sbt> run -n <network_file> -s <gene_sets_file> -l <gene_list_file> -o <results_file> -b <bin_size>
File formats:
- network file: tab-separated text file with a header row, and containing node ids in the first two columns
- gene-sets file: GMT file format, ids must match ids in the network file
- gene-list file: text file with a header row containing one node id per row
- results file: tab-separated text file with the following columns:
- geneSet - name of a gene set
- overlap - number of genes common to the gene list and the gene set.
- nConnections - number of commections between the gene list and the gene set in the network
- pValue - significance of connections between the gene list and the gene set in the network under a null model of degree-preserving random gene lists
Notes:
- you can use
-O <results_file>to overwite an existing results file - sugested bin size: 50
To cite your use of the GeLiNEA please reference Yilong Zou et al.: Plasticity of polyunsaturated ether phospholipids promotes ferroptosis susceptibility and evasion. Nature (2020).