[%anchor_matrix.name%]

JASPAR ID: [%anchor_matrix.ID%]
Class: [%anchor_matrix.class%]
Family: [%anchor_matrix.tag('family')%]
Tax group: [%anchor_matrix.tag('tax_group')%]
Information content: [%total_ic = formatf(3, anchor_matrix.to_ICM.total_ic)%] [%IF total_ic > high_matrix_ic or total_ic < low_matrix_ic%] [%total_ic%] [%ELSE%] [%total_ic%] [%END%]
GC content: [%gc = formatf(3, anchor_matrix.tag('gc_content'))%] [%IF gc > high_matrix_gc or gc < low_matrix_gc%] [%gc%] [%ELSE%] [%gc%] [%END%]

[%tf.name%]

JASPAR ID: [%tf.ID%]
Class: [%tf.class%]
Family: [%tf.tag('family')%]
Tax group: [%tf.tag('tax_group')%]
Information content: [%total_ic = formatf(3, tf.to_ICM.total_ic)%] [%IF total_ic > high_matrix_ic or total_ic < low_matrix_ic%] [%total_ic%] [%ELSE%] [%total_ic%] [%END%]
GC content: [%gc = formatf(3, tf.tag('gc_content'))%] [%IF gc > high_matrix_gc or gc < low_matrix_gc%] [%gc%] [%ELSE%] [%gc%] [%END%]

[%anchor_matrix.name%] - [%tf.name%] Binding Site Combinations

[%UNLESS gene_id_type == dflt_gene_id_type%] [%END%] [%IF has_operon%] [%END%] [%FOREACH gene = genes%] [%gid = gene.id%] [%ensembl_id = gene.ensembl_id()%] [%chr = gene.chr()%] [%gene_start = gene.start()%] [%gene_end = gene.end()%] [%strand = gene.strand()%] [%tss = gene.tss()%] [%promoters = gene.fetch_promoters()%] [%IF has_operon%] [%operon = gene.fetch_operon()%] [%END%] [%IF operon%] [%operon_start = operon.start()%] [%operon_end = operon.end()%] [%IF strand == 1%] [%prom_start = tss%] [%prom_end = operon_end%] [%ELSE%] [%prom_start = operon_start%] [%prom_end = tss%] [%END%] [%ELSE%] [%IF strand == 1%] [%prom_start = tss%] [%prom_end = gene_end%] [%ELSE%] [%prom_start = gene_start%] [%prom_end = tss%] [%END%] [%END%] [%IF has_operon and operon_genes.$gid%] [%UNLESS gene_id_type == dflt_gene_id_type%] [%id_str = ''%] [%first_id = 1%] [%FOREACH input_gene = operon_genes.$gid%] [%input_gid = input_gene.id%] [%gene_ids = gid_gene_ids.$input_gid%] [%FOREACH gene_id = gene_ids%] [%UNLESS first_id%] [%id_str = id_str _ ','%] [%END%] [%first_id = 0%] [%id_str = id_str _ gene_id%] [%END%] [%END%] [%END%] [%id_str = ''%] [%first_id = 1%] [%FOREACH input_gene = operon_genes.$gid%] [%UNLESS first_id%] [%id_str = id_str _ ','%] [%END%] [%first_id = 0%] [%id_str = id_str _ input_gene.ensembl_id()%] [%END%] [%ELSE%] [%UNLESS gene_id_type == dflt_gene_id_type%] [%id_str = ''%] [%first_id = 1%] [%gene_ids = gid_gene_ids.$gid%] [%FOREACH gene_id = gene_ids%] [%UNLESS first_id%] [%id_str = id_str _ ','%] [%END%] [%first_id = 0%] [%id_str = id_str _ gene_id%] [%END%] [%END%] [%END%] [%IF has_operon%] [%IF operon%] [%ELSE%] [%END%] [%END%] [%first = 1%] [%FOREACH sitepair = gid_sitepairs.$gid%] [%anchor = sitepair.anchor_site%] [%site = sitepair.tf_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 TF Start End Rel. Start Rel. End Strand Score %Score Sequence Anchored TF Start End Rel. Start Rel. End Strand Score %Score Sequence Distance
[%id_str%][%id_str%][%id_str%][%ensembl_id%][%operon.symbol()%]NA[%chr%] [%prom_start%] [%prom_end%] [%IF strand == 1%]+[%ELSE%]-[%END%]
[%anchor_closest_tss%] [%anchor_matrix.name()%] [%anchor_start%] [%anchor_end%] [%anchor_rel_start%] [%anchor_rel_end%] [%IF anchor.strand() == 1%]+[%ELSE%]-[%END%] [%anchor.score()%] [%anchor.rel_score() * 100%]% [%anchor.seq()%] [%tf.name()%] [%site_start%] [%site_end%] [%site_rel_start%] [%site_rel_end%] [%IF site.strand() == 1%]+[%ELSE%]-[%END%] [%site.score()%] [%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)

Back to top