Fig. 2

The SimSearch App. Pattern selection: Tracks can be loaded in IGB from local or remote files, a DAS server, or a Quickload server (like the one we have prepared so as to provide quick access to peak regions for histone marks and transcription factor bindings in several cell lines (a)). A query pattern can be built based on the selection of tracks or track regions (b) (with the possibility to select different regions of the same track), or by selecting a pre-defined pattern (c). Pattern editing: For each track, the type of matching, the relative distance between regions, and the usage of region attributes can be modified; in particular, the type of each pattern track (see Table 1) can be specified (d). Finding matching regions: The pattern matchings found are displayed in a table (e) showing score and features of each identified matching; a visual representation of the pattern matching corresponding to the table row selected is shown on the right of the table (f). Analysis and visualization: A new track is created (g), allowing visual analyses of the results. In this example, the “Strong_enhancer” track, including the result found by SimSearch, shows a region matching the pattern, which overlaps with a similar result from ChromHMM (light yellow: state 7_Enh, Enhancer; dark green: state 5_TxWk, Weak transcription). It is possible to further analyze the results based on annotations from PANTHER [22] or from another IGB track (h), or on the composition of the pattern matchings (i). j Comparison of matchings found for the “Active Promoter” pattern (from ENCODE) in the K562 (light blue background) and HeLa (light yellow background) cell lines. Only in K562 the pattern is found at the TSS of the MEIOB gene, which encodes a chromatin-associated protein required for meiotic recombination and synapsis, in line with the gene expression measured in the two cell lines: 13 FPKM in K562, no expression in HeLa (from the Expression Atlas [23])