TY - JOUR AU - Hendrix, Willam AU - Rocha, Andrea M. AU - Padmanabhan, Kanchana AU - Choudhary, Alok AU - Scott, Kathleen AU - Mihelcic, James R. AU - Samatova, Nagiza F. PY - 2011 DA - 2011/10/24 TI - DENSE: efficient and prior knowledge-driven discovery of phenotype-associated protein functional modules JO - BMC Systems Biology SP - 172 VL - 5 IS - 1 AB - Identifying cellular subsystems that are involved in the expression of a target phenotype has been a very active research area for the past several years. In this paper, cellular subsystem refers to a group of genes (or proteins) that interact and carry out a common function in the cell. Most studies identify genes associated with a phenotype on the basis of some statistical bias, others have extended these statistical methods to analyze functional modules and biological pathways for phenotype-relatedness. However, a biologist might often have a specific question in mind while performing such analysis and most of the resulting subsystems obtained by the existing methods might be largely irrelevant to the question in hand. Arguably, it would be valuable to incorporate biologist's knowledge about the phenotype into the algorithm. This way, it is anticipated that the resulting subsytems would not only be related to the target phenotype but also contain information that the biologist is likely to be interested in. SN - 1752-0509 UR - https://doi.org/10.1186/1752-0509-5-172 DO - 10.1186/1752-0509-5-172 ID - Hendrix2011 ER -