Our network-based enrichment (NBE) methods are available as part of our software package, Biorithm.
The following zipped directory contains the universal network, the interesting network, and the gene sets (i.e., functional annotations) used as inputs to our NBE methods for analysis of the B Cell Interactome (BCI). Additionally, we provide a post-processed version of the NBE results achieved using these inputs. Download supplementary files for BCI analysis.
The following zipped directory contains the universal network, the interesting network, and the gene sets (i.e., functional annotations) used as inputs to our NBE methods for our analysis of two hepatic cultures (hepatocyte monolayer versus collagen sandwich). Additionally, we provide a post-processed version of the NBE results achieved using these inputs. Download supplementary files for hepatic culture analysis.
The following zipped file contains the universal network, the two interesting networks (one without the 14,421 genetic interactions reported by Collins et al. [1] and the other including these genetic interactions), and the gene sets (i.e., functional annotations) used as inputs to our NBE methods for determining functions whose NBE score improves after including the genetic interactions. Additionally, we provide a post-processed version of the NBE results achieved using these inputs. Download supplementary files for analysis of the the GI study.