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 user_matrix_file%] [%ELSE%] [%IF tf_db%] [%END%] [%IF tf_select_criteria == 'specific'%] [%IF tf_set%] [%matrix_list = tf_set.get_matrix_list('name')%] [%END%] [%ELSIF tf_select_criteria == 'min_ic'%] [%IF collection%] [%END%] [%IF tax_groups%] [%END%] [%IF min_ic%] [%END%] [%END%] [%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 file: [%user_matrix_file%]
TFBS profile matrix source: JASPAR
TFBS profiles: [%FOREACH matrix = matrix_list%][%matrix.name()%] [%END%]
JASPAR collection(s): [%FOREACH collection = collections%][%collection%] [%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 TFs. 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%] [%tf_id = result.id%] [%tf = tf_set.get_matrix(tf_id)%] [%IF result.bg_gene_hits == 0 and result.t_gene_hits > 0%] [%ELSE%] [%END%] [%IF tf.class%] [%ELSE%] [%END%] [%IF tf.tag('family')%] [%ELSE%] [%END%] [%IF tf.tag('tax_group')%] [%ELSE%] [%END%] [%gc = tf.tag('gc_content')%] [%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%]
TF Name TF ID Class Family Tax group IC GC Content Target seq. hits Target seq. non-hits Background seq. hits Background seq. non-hits Target TFBS hits Target TFBS nucleotide rate Background TFBS hits Background TFBS nucleotide rate Z-score Fisher score KS score
*[%tf.name%][%tf.name%] [%IF tf_db%] [%collection = tf.tag('collection')%] [%IF collection != 'PENDING'%] [%tf.ID%] [%ELSE%] [%tf.ID%] [%END%] [%ELSE%] [%tf.ID%] [%END%] [%tf.class%]NA[%tf.tag('family')%]NA[%tf.tag('tax_group')%]NA [%IF tf.isa('TFBS::Matrix::PFM')%] [%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%] [%ELSE%] NA [%END%] [%IF gc > high_matrix_gc or gc < low_matrix_gc%] [%formatf(3, gc)%] [%ELSE%] [%formatf(3, gc)%] [%END%] [%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_tfbs_hits > 0%] [%result.t_tfbs_hits%] [%ELSE%] [%result.t_tfbs_hits%] [%END%] [%formatg(3, result.t_tfbs_rate)%] [%IF result.bg_gene_hits == 0%] [%result.bg_tfbs_hits%] [%ELSE%] [%result.bg_tfbs_hits%] [%END%] [%IF result.bg_gene_hits == 0%] [%formatg(3, result.bg_tfbs_rate)%] [%ELSE%] [%formatg(3, result.bg_tfbs_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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View plot of Z-score vs. %GC content
View plot of Fisher score vs. %GC content
View plot of KS score vs. %GC content

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

[%ELSE%]

No TFBSs were found which matched your search criteria

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