Selected Parameters

[%IF user_seq_file%] [%END%] [%IF user_peak_pos_file%] [%END%] [%IF user_bg_seq_file%] [%ELSIF bg_seq_set_name%] [%END%] [%IF user_bg_peak_pos_file%] [%END%] [%IF tf_db%] [%END%] [%IF cl_db%] [%END%] [%IF collections%] [%END%] [%IF user_tf_family_file%] [%END%] [%IF tf_families%] [%END%] [%IF tax_groups%] [%END%] [%IF min_ic%] [%END%] [%IF result_sort_by == 'zscore'%] [%display_sort_by = 'Z-score'%] [%ELSIF result_sort_by == 'fisher_p_value'%] [%display_sort_by = 'Fisher score'%] [%ELSIF result_sort_by == 'ks_p_value'%] [%display_sort_by = 'KS score'%] [%ELSE%] [%display_sort_by = result_sort_by%] [%END%] [%IF result_type == 'top_x_results'%] [%IF num_display_results == 'All'%] [%ELSE%] [%END%] [%ELSIF result_type == 'significant_hits'%] [%END%]
Job ID: [%job_id%]
Target sequence file: [%user_seq_file%]
Target sequence MCP position file: [%user_peak_pos_file%]
Background sequence file: [%user_bg_seq_file%]
Background sequence set: [%bg_seq_set_name%]
Background sequence MCP position file: [%user_bg_peak_pos_file%]
Number of target sequences: [%num_t_seqs%]
Number of background sequences: [%num_bg_seqs%]
Total target sequence length: [%t_seq_len%]
Total background sequence length: [%bg_seq_len%]
Target sequence GC content: [%IF t_seq_gc_content > high_seq_gc or t_seq_gc_content < low_seq_gc%] [%t_seq_gc_content%] [%ELSE%] [%t_seq_gc_content%] [%END%]
Background sequence GC content: [%IF bg_seq_gc_content > high_seq_gc or bg_seq_gc_content < low_seq_gc%] [%bg_seq_gc_content%] [%ELSE%] [%bg_seq_gc_content%] [%END%]
TFBS profile matrix source: [%tf_db%]
TFBS cluster source: [%cl_db%]
JASPAR collection(s): [%FOREACH collection = collections%][%collection%] [%END%]
TF family file: [%user_tf_family_file%]
TFBS families: [%FOREACH family = tf_families%][%family%] [%END%]
Taxonomic supergroup(s): [%FOREACH tax_group = tax_groups%][%tax_group%] [%END%]
Min. IC: [%min_ic%] bits
Matrix score threshold: [%threshold%]
Results returned:All results sorted by [%display_sort_by%]Top [%num_display_results%] results sorted by [%display_sort_by%]All results with a Z-score >= [%zscore_cutoff%] / Fisher score >= [%fisher_cutoff%] / KS p-value <= [%ks_cutoff%] sorted by [%display_sort_by%]
The results will be sent to the following email: [%email%]

Results - click column headers to sort by that column

[%IF message%]

[%message%]

[%ELSIF results%] [%IF warn_zero_bg_hits%]

Warning: The provided background set resulted in zero binding sites for one or more TF clusters. These cases are highlighted in red. In cases where there were also zero binding sites for the target set, the Z-score is undefined (NA). In cases where there were one or more binding sites in the target set, the Z-score is infinite (Inf). However, the result may or may not be considered significant. Results for which this was the case are marked with an asterisk (*).

[%END%] [%FOREACH result = results%] [%cl = tf_cluster_set.get_tf_cluster(result.id)%] [%IF result.bg_gene_hits == 0 and result.t_gene_hits > 0%] [%ELSE%] [%END%] [%IF result.bg_gene_hits == 0%] [%IF result.zscore == 'inf' or result.zscore == 'Inf'%] [%ELSE%] [%END%] [%ELSE%] [%END%] [%IF result.fisher_p_value == 'inf' or result.fisher_p_value == 'Inf'%] [%ELSE%] [%END%] [%IF result.ks_p_value == 'inf' or result.ks_p_value == 'Inf'%] [%ELSE%] [%END%] [%END%]
TFBS cluster name Target seq. hits Target seq. non-hits Background seq. hits Background seq. non-hits Target cluster hits Target cluster nucleotide rate Background cluster hits Background cluster nucleotide rate Z-score Fisher score KS score
*[%cl.name%][%cl.name%] [%IF result.t_gene_hits > 0%] [%result.t_gene_hits%] [%ELSE%] [%result.t_gene_hits%] [%END%] [%result.t_gene_no_hits%] [%IF result.bg_gene_hits == 0%] [%result.bg_gene_hits%] [%ELSE%] [%result.bg_gene_hits%] [%END%] [%result.bg_gene_no_hits%] [%IF result.t_cluster_hits > 0%] [%result.t_cluster_hits%] [%ELSE%] [%result.t_cluster_hits%] [%END%] [%formatg(3, result.t_cluster_rate)%] [%IF result.bg_gene_hits == 0%] [%result.bg_cluster_hits%] [%ELSE%] [%result.bg_cluster_hits%] [%END%] [%IF result.bg_gene_hits == 0%] [%formatg(3, result.bg_cluster_rate)%] [%ELSE%] [%formatg(3, result.bg_cluster_rate)%] [%END%] InfNA[%formatf(3, result.zscore)%]Inf[%formatf(3, result.fisher_p_value)%]Inf[%formatf(3, result.ks_p_value)%]

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Consult the help file for an explanation of the column headings.

[%ELSE%]

No TFBS clusters were found which matched your search criteria

[%END%]