[%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

[%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 core_tf_sets.$tax.size > 0%] [%END%] [%END%] [%END%] [%FOREACH tax = tax_groups%] [%IF core_tf_sets.$tax.size > 0%] [%core_tf_list = core_tf_sets.$tax.get_matrix_list('name')%] [%END%] [%END%]
[%tax%]

[%UNLESS species == 'yeast'%]

JASPAR PBM Profiles

All profiles with a minimum specificity of bits (min. [%db_info.min_ic()%] bits)

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

[%END%] [%IF species == 'worm'%]

JASPAR PENDING Profiles

All profiles with a minimum specificity of bits (min. [%db_info.min_ic()%] bits)

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

[%END%]



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%]

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



Press the Submit button to perform the analysis or Reset to reset the analysis parameters to their default values.
Depending on parameters selected and server load, the analysis may take anywhere from a few seconds to several minutes to perform.