What are the Different Types of Networks?
There are two types of networks displayed on this site. Both are two forms of gene co-expression networks:
Global Networks. A global network is built by combining all expression measurments (microarray samples) into a single compedium where all samples are normalized together and co-expression is determined through correlation of expression across all samples.
Gene Interaction Layer (GIL). Unlike a global network where all samples are used to build a single network, a GIL is contructed by first clustering the input samples by expression similarity. This clustering yields n groups of samples. Each group is then passed through the network construction pipeline to form n unique networks. Global networks cannot represent relationships that occur in only a few samples (experimental conditions) and can be heavily biased towards a specific condition when it is over-represented. Pre-clustering os samples is a mechanism to avoid those issues and capture as many meaningful interactions as possible.
What are the Different Types of Modules?
Modules are subsets of a network that contain highly connected nodes. Typically genes within a module are involved in similar biological processes. Functional enrichment analysis is one tool used to help identify potential function of modules. There are many different algorithms for determining modules within a network. The modules in this site have been constructed using WGCNA , MCL and link-community (LCM) methods.
Can I find Gene Set's Causal for Specific Phenotypes With This Database?
This database does not provide a set of genes as targets for phenotypes, but it will allow you to explore and potentially find gene sets that may be involved in a specific phenotypes. After exploration and identification of a potential gene set further tests in the laboratory would be needed to validate the gene set.