B Cell Interactome
The B cell interactome (BCI) is a network of protein-protein, protein-DNA and modulatory interactions in human B cells. The network contains known interactions (reported in public databases) and predicted interactions by a Bayesian evidence integration framework which integrates a variety of generic and context specific experimental clues about protein-protein and protein-DNA interactions - such as a large collection of B cell expression profiles - with inferences from different reverse engineering algorithms, such as GeneWays and ARACNE. Modulatory interactions are predicted by the MINDY, an algorithm for the prediction of modulators of transcriptional interactions (please refer to the publication section for more information).
The BCI contains 21,156 protein-protein interactions, 41,568 protein-DNA interactions and 1,925 modulatory interactions.
The BCI can be downloaded as one tab delimited file containing the complete network (BCI.txt) with each type of interaction explicitly defined.
Documentation and Support
BCI.txt: describes the Interations from the B cell Interactome. Three type of interactions are describe: ppi for protein-protein interactions, pdi for protein-DNA interactions and tfmi for transcription factor-modulator interactions (identified by the algorithm MINDy).
BCI.txt is tab-delimited and contains 7 columns: - Entrez Gene ID 1 (Transcription Factor if PDI) - Gene Name 1 - Entrez Gene ID 2 (Target if PDI, Modulator if TFMI) - Gene Name 2 - Interaction Type (ppi, pdi, tfmi) - Probability as computed with a Naive Bayes Classifier - 0 means the interaction was not detected by this method but is described in at least one of the public databases used in this analysis. - Type: 1 if the interaction is reported in a public database, 0 otherwise.
Lefebvre C, Lim WK, Basso K, Dalla Favera R, and Califano A. A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells. Lecture Notes in Computer Science. 2007;4532:42-56.
Wang K, Banerjee N, Margolin AA, Nemenman I, Califano A. Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes. Lecture Notes in Computer Science. 2006;3909:348-362.