[%INCLUDE "sample_genes.html"%]

STEP 1: Enter target (co-expressed) genes

[ HELP ]

Paste gene IDs (max. [%max_target_genes%] gene IDs):




OR upload a file containing a list of gene identifiers (max. [%max_target_genes%] gene IDs):




STEP 2: Enter background genes

[ HELP ]

All [%total_genes%] genes in the oPOSSUM database

OR a random set of  genes from the oPOSSUM database

OR paste gene IDs:



OR upload a file containing a list of gene identifiers:




STEP 3: Select transcription factor binding site profiles

[ HELP ]

JASPAR CORE Profiles

Select anchoring TF
[%tf_list = tf_set.get_matrix_list('name')%]
[%tax_group_list%]

Select TFs to find in combination with anchoring TF
[%IF num_tax_groups > 1%] All profiles from the following tax groups:
[%first_tax_group = 1%] [%FOREACH tax = tax_groups%]   [%tax%] [%first_tax_group = 0%] [%END%]  with a minimum specificity of  [%ELSE%] All [%tax_group_list%] profiles with a minimum specificity of  [%END%] bits (min. [%db_info.min_ic()%] bits)

[%IF num_tax_groups > 1%] OR select specific profiles: [%ELSE%] OR select specific [%tax_group_list%] profiles: [%END%]
[%IF num_tax_groups > 1%] [%FOREACH tax = tax_groups%] [%IF tax_tf_sets.$tax.size > 0%] [%END%] [%END%] [%END%] [%FOREACH tax = tax_groups%] [%IF tax_tf_sets.$tax.size > 0%] [%tf_list = tax_tf_sets.$tax.get_matrix_list('name')%] [%END%] [%END%]
[%tax%]




STEP 4: Select TFBS search parameters

[ HELP ]

[%UNLESS species == 'yeast'%] Conservation cutoff:


[%END%] Matrix score threshold:
OR enter score threshold [%dflt_threshold = thl_hash.$thl_dflt_level.threshold()%] % (min. = [%db_info.min_threshold()*100%]%)

[%IF species == 'yeast'%] Amount of upstream sequence: OR enter custom values [%dflt_upstream_bp = srl_hash.$srl_dflt_level.upstream_bp()%] bp (max. = [%db_info.max_upstream_bp%]) [%ELSE%] Amount of upstream / downstream sequence:
OR enter custom values [%dflt_upstream_bp = srl_hash.$srl_dflt_level.upstream_bp()%] [%dflt_downstream_bp = srl_hash.$srl_dflt_level.downstream_bp()%] / bp (max. = [%db_info.max_upstream_bp%] / [%db_info.max_upstream_bp%]) [%END%]

Maximum inter-binding distance (max. = [%max_inter_binding_dist%])

Number of results to return:
Top results
OR only results with Z-score >= and Fisher score >= (Default values have been chosen based on empirical studies)

Sort results by:
Z-score Fisher score



Please enter your e-mail address:

Press the Submit button to perform the analysis or Reset to reset the analysis parameters to their default values.
Notification will be sent to the e-mail address you provided once the analysis is complete.
Depending on parameters selected and server load, the analysis may take anywhere from a few minutes to several hours to complete.