[ HELP ]
Paste gene IDs (max. [%max_target_genes%] gene IDs): [%FOREACH in_t_gene_id = in_t_gene_ids%][%in_t_gene_id%] [%END%] OR upload a file containing a list of gene identifiers (max. [%max_target_genes%] gene IDs):
All [%total_genes%] genes in the oPOSSUM database OR a random set of genes from the oPOSSUM database OR paste gene IDs: [%FOREACH in_bg_gene_id = in_bg_gene_ids%][%in_bg_gene_id%] [%END%] OR upload a file containing a list of gene identifiers:
All TFBS clusters OR select specific TF famlies:
[%UNLESS species == 'yeast'%] Conservation cutoff: [%FOREACH level = cl_levels%] [%cl = cl_hash.$level%] [%cl.min_conservation()%] [%END%] [%END%] Matrix score threshold: [%FOREACH level = thl_levels%] [%thl = thl_hash.$level%] [%thl.threshold()*100%]% [%END%] OR enter score threshold [%dflt_threshold = thl_hash.$thl_dflt_level.threshold()%] % (min. = [%db_info.min_threshold()*100%]%) [%IF species == 'yeast'%] Amount of upstream sequence: [%FOREACH level = srl_levels%] [%srl = srl_hash.$level%] [%srl.upstream_bp()%] [%END%] OR enter custom values [%dflt_upstream_bp = srl_hash.$srl_dflt_level.upstream_bp()%] bp (max. = [%db_info.max_upstream_bp%]) [%ELSE%] Amount of upstream / downstream sequence: [%FOREACH level = srl_levels%] [%srl = srl_hash.$level%] [%srl.upstream_bp()%] / [%srl.downstream_bp()%] [%END%] OR enter custom values [%dflt_upstream_bp = srl_hash.$srl_dflt_level.upstream_bp()%] [%dflt_downstream_bp = srl_hash.$srl_dflt_level.downstream_bp()%] / bp (max. = [%db_info.max_upstream_bp%] / [%db_info.max_upstream_bp%]) [%END%] Maximum inter-binding distance (max. = [%max_inter_binding_dist%]) Number of results to return: Top [%FOREACH num = nresults%] [%num%] [%END%] results OR only results with Z-score >= [%FOREACH cutoff = zcutoffs%] [%cutoff%] [%END%] and Fisher score >= [%FOREACH cutoff = fcutoffs%] [%cutoff%] [%END%] (Default values have been chosen based on empirical studies) Sort results by: Z-score Fisher score
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Press the Submit button to perform the analysis or Reset to reset the analysis parameters to their default values. Notification will be sent to the e-mail address you provided once the analysis is complete. Depending on parameters selected and server load, the analysis may take anywhere from a few minutes to several hours to complete.