C[%anchor_cluster.id%] ([%anchor_tf_name%])

Class: [%anchor_cluster.class%]
Family: [%anchor_cluster.family%]

C[%tf_cluster.id%]

Class: [%tf_cluster.class%]
Family: [%tf_cluster.family%]

C[%anchor_cluster.id%] - C[%tf_cluster.id%] Binding Site Combinations

[%UNLESS gene_id_type == dflt_gene_id_type%] [%END%] [%IF has_operon%] [%END%] [%FOREACH gene = genes%] [%gid = gene.id%] [%promoters = gene.promoters()%] [%IF gene.strand == 1%] [%prom_start = gene.tss%] [%prom_end = gene.end%] [%ELSE%] [%prom_start = gene.start%] [%prom_end = gene.tss%] [%END%] [%IF has_operon and operon_genes.$gid%] [%UNLESS gene_id_type == dflt_gene_id_type%] [%FOREACH input_gene = operon_genes.$gid%] [%input_gid = input_gene.id%] [%gene_ids = gid_gene_ids.$input_gid%] [%END%] [%END%] [%ELSE%] [%UNLESS gene_id_type == dflt_gene_id_type%] [%gene_ids = gid_gene_ids.$gid%] [%END%] [%END%] [%IF has_operon%] [%IF gene.operon%] [%ELSE%] [%END%] [%END%] [%first = 1%] [%FOREACH sitepair = gid_sitepairs.$gid%] [%anchor = sitepair.anchor_site%] [%site = sitepair.cluster_site%] [%distance = sitepair.distance%] [%anchor_start = gene.start + anchor.start - 1%] [%anchor_end = gene.start + anchor.end - 1%] [%site_start = gene.start + site.start - 1%] [%site_end = gene.start + site.end - 1%] [%anchor_closest_tss = gene.tss%] [%site_closest_tss = gene.tss%] [%min_anchor_tss_dist = 999999%] [%min_site_tss_dist = 999999%] [%FOREACH promoter = promoters%] [%tss = promoter.tss()%] [%anchor_start_tss_dist = anchor_start - tss%] [%anchor_end_tss_dist = anchor_end - tss%] [%IF anchor_start_tss_dist < 0%] [%anchor_start_tss_dist = anchor_start_tss_dist * -1%] [%END%] [%IF anchor_end_tss_dist < 0%] [%anchor_end_tss_dist = anchor_end_tss_dist * -1%] [%END%] [%IF anchor_start_tss_dist < min_anchor_tss_dist%] [%min_anchor_tss_dist = anchor_start_tss_dist%] [%anchor_closest_tss = tss%] [%END%] [%IF anchor_end_tss_dist < min_anchor_tss_dist%] [%min_anchor_tss_dist = anchor_end_tss_dist%] [%anchor_closest_tss = tss%] [%END%] [%END%] [%IF gene.strand == 1%] [%anchor_rel_start = anchor_start - anchor_closest_tss%] [%IF anchor_start >= anchor_closest_tss%] [%anchor_rel_start = anchor_rel_start + 1%] [%END%] [%anchor_rel_end = anchor_end - anchor_closest_tss%] [%IF anchor_end >= anchor_closest_tss%] [%anchor_rel_end = anchor_rel_end + 1%] [%END%] [%site_rel_start = site_start - anchor_closest_tss%] [%IF site_start >= anchor_closest_tss%] [%site_rel_start = site_rel_start + 1%] [%END%] [%site_rel_end = site_end - anchor_closest_tss%] [%IF site_end >= anchor_closest_tss%] [%site_rel_end = site_rel_end + 1%] [%END%] [%ELSE%] [%anchor_rel_start = anchor_closest_tss - anchor_start%] [%IF anchor_start <= anchor_closest_tss%] [%anchor_rel_start = anchor_rel_start + 1%] [%END%] [%anchor_rel_end = anchor_closest_tss - anchor_end%] [%IF anchor_end <= anchor_closest_tss%] [%anchor_rel_end = anchor_rel_end + 1%] [%END%] [%temp = anchor_rel_end%] [%anchor_rel_end = anchor_rel_start%] [%anchor_rel_start = temp%] [%site_rel_start = anchor_closest_tss - site_start%] [%IF site_start <= anchor_closest_tss%] [%site_rel_start = site_rel_start + 1%] [%END%] [%site_rel_end = anchor_closest_tss - site_end%] [%IF site_end <= anchor_closest_tss%] [%site_rel_end = site_rel_end + 1%] [%END%] [%temp = site_rel_end%] [%site_rel_end = site_rel_start%] [%site_rel_start = temp%] [%END%] [%UNLESS first == 1%] [%IF has_operon%] [%END%] [%UNLESS gene_id_type == dflt_gene_id_type%] [%END%] [%END%] [%first = 0%] [%END%] [%END%]
Gene ID(s)Ensembl IDOperon IDChr Gene Start Gene End Strand Nearest TSS Anchoring TFBS Cluster Start End Rel. Start Rel. End Strand %Score Sequence Anchored TFBS Cluster Start End Rel. Start Rel. End Strand %Score Sequence Distance
[%FOREACH gene_id = gene_ids%][%gene_id%] [%END%] [%FOREACH input_gene = operon_genes.$gid%] [%input_gene.ensembl_id%]  [%END%] [%FOREACH gene_id = gene_ids%][%gene_id%] [%END%] [%gene.ensembl_id%][%gene.operon.symbol%]NA[%gene.chr%] [%prom_start%] [%prom_end%] [%IF gene.strand == 1%]+[%ELSE%]-[%END%]
[%anchor_closest_tss%] C[%anchor_cluster.id()%] [%anchor_start%] [%anchor_end%] [%anchor_rel_start%] [%anchor_rel_end%] [%IF anchor.strand() == 1%]+[%ELSE%]-[%END%] [%formatf(1, anchor.rel_score() * 100)%]% [%anchor.seq()%] C[%tf_cluster.id()%] [%site_start%] [%site_end%] [%site_rel_start%] [%site_rel_end%] [%IF site.strand() == 1%]+[%ELSE%]-[%END%] [%formatf(1, site.rel_score() * 100)%]% [%site.seq()%] [%distance%]

Download as a tab delimited text file (results will be kept on the server for [%result_retain_days%] days after analysis)

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