Selected Parameters

[%using_core_collection = 0%] [%IF using_core_collection == 1%] [%IF tax_groups%] [%END%] [%END%] [%IF tf_select_criteria == 'min_ic'%] [%ELSIF tf_select_criteria == 'specific'%] [%IF tf_set%] [%matrix_list = tf_set.get_matrix_list('name')%] [%END%] [%END%] [%IF result_sort_by == 'zscore'%] [%display_sort_by = 'Z-score'%] [%ELSIF result_sort_by == 'fisher_p_value'%] [%display_sort_by = 'Fisher 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%]
Number of genes submitted for analysis: [%num_t_gene_ids%]
Number of genes included in analysis: [%num_t_included_gene_ids%]
Number of genes missing from analysis: [%num_t_missing_gene_ids%]
Number of unique oPOSSUM genes in analysis: [%num_t_gids%]
JASPAR collection(s): [%FOREACH collection = collections%] [%IF collection == 'CORE'%] [%using_core_collection = 1%] [%END%] [%collection%]  [%END%]
Taxonomic supergroup(s): [%FOREACH tax_group = tax_groups%] [%tax_group%]  [%END%]
Anchoring TF: [%anchor_matrix.name()%]
Maximum Inter-Binding Distance: [%max_site_distance%]
Minimum profile specificity: [%min_ic%] bits
TFBS profiles: [%FOREACH matrix = matrix_list%] [%matrix.name()%] [%END%]
Conservation cutoff: [%min_conservation%]
Matrix score threshold: [%threshold*100%]%
Upstream sequence length: [%upstream_bp%]
Downstream sequence length: [%downstream_bp%]
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%] and a Fisher score >= [%fisher_cutoff%] sorted by [%display_sort_by%]

Target Genes

[%IF num_t_missing_gene_ids > 0%] [%END%]
Analyzed: [%FOREACH gene_id = t_included_gene_ids%] [%gene_id%][%END%]
Omitted: [%FOREACH gene_id = t_missing_gene_ids%] [%gene_id%][%END%]

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 = tf_set.get_tf(result.id)%] [%IF result.bg_gene_hits == 0 and result.t_gene_hits > 0%] [%ELSE%] [%END%] [%collection = tf.tag('collection')%] [%total_ic = formatf(3, tf.to_ICM.total_ic)%] [%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%] [%END%]
TF JASPAR ID Class Family Tax group IC GC Content Target gene hits Target gene non-hits Background gene hits Background gene non-hits Target TFBS hits Target TFBS nucleotide rate Background TFBS hits Background TFBS nucleotide rate Z-score Fisher score
*[%tf.name%][%tf.name%] [%IF collection != 'PENDING'%] [%tf.ID%] [%ELSE%] [%tf.ID%] [%END%] [%tf.class%] [%tf.tag('family')%] [%tf.tag('tax_group')%] [%IF total_ic > high_matrix_ic or total_ic < low_matrix_ic%] [%total_ic%] [%ELSE%] [%total_ic%] [%END%] [%IF gc > high_matrix_gc or gc < low_matrix_gc%] [%gc%] [%ELSE%] [%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)%]

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

View plot of Z-score vs. %GC content
View plot of Fisher 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

[%END%]