DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

Table 1 Comparison of interactions confirmed in RegulonDB and identified by ChIP-chip experiments, CLR, SEREND and DISTILLER for five global regulators

For each method, the identified interactions that were known as compared to RegulonDB were selected. For all known interactions, we indicate whether (ChIP-chip) or not (Not ChIP-chip) the interactions were found in a corresponding ChIP-chip experiment. The recall (TP/TP + FN) and precision (TP/TP + FP) were calculated using the ChIP-chip data as a gold standard. Interactions identified by either CLR, SEREND or DISTILLER and confirmed by a ChIP-chip experiment were considered to be true positives (TP); interactions confirmed by a ChIP-chip experiment but not identified by either CLR, SEREND or DISTILLER were considered false negatives (FN); interactions identified by either CLR, SEREND or DISTILLER but not confirmed in a ChIP-chip experiment were considered false positives (FP). Note that since all interactions of RegulonDB are recovered by SEREND by definition (algorithmic consequence of using RegulonDB as a training set), a comparison with SEREND was not possible here.

ISSN: 1474-760X