Chromatin Help

Regions of chromatin accessibility (ATAseq) around a chosen gene within ImmGen cell-types.

(1) Select the type of data to browse (currently ImmGen ATACseq, more coming)

(2) Select the subset of ImmGen cell-types you wish to survey

(3) Choose the gene neighborhood to survey (enter as official Gene Symbol)

(4) Set the width of the region to display around the gene of interest

(5) Click to display ATACseq expression profiles at their chromosome location on the UCSC genome browser (once there, use all the functionalities of the UCSC browser to zoom or move around the genome, to change the representation parameters (scale, relative position), or to put the data in relation to the wealth of additional information is available there.
For more details on the UCSC browser :

(6) Click there to view a table with detailed information on the significant peaks in the region (position, intensity in the chosen cell-types, etc; the page also gives information on transcription factor binding motifs that might be present in these peaks, as are predicted by the FIMO algorithm. The top 3 motifs with the highest FIMO scores are shown.
More details on FIMO :