Human Combination Site Analysis

Version 2.0

Select Analysis Parameters

STEP 1: Enter a list of co-expressed genes ?

Species:
human mouse

Gene ID type:
Ensembl HUGO/MGI Symbol/Alias RefSeq Entrez Gene

Paste gene IDs:



OR upload a file containing a list of gene identifiers:



STEP 2: Select transcription factor binding sites ?

All profiles with a minimum specificity of bits (min. 8 bits)
OR select TF from taxonomic supergroup: plant  vertebrate  insect 

For combinations of binding sites:
All possible combinations
OR select profiles that must be included in combinations:



STEP 3: Select parameters

Level of conservation ?


Matrix match threshold ?

Matrix classification method ?

Amount of upstream/downstream sequence ? bp (max. 10000)/ bp (max 10000)

Cardinality of combinations ?

Maximum inter-binding site distance ? bp

Minimum multiplicity ?

Class combination score threshold ?



STEP 4: Enter e-mail address ?

Send notification to this e-mail address once analysis is complete:

Press the Submit button below to perform the analysis or Reset to reset the analysis parameters to their default values. Your job will be put into a queue on our server and you will be notified of its completion by an e-mail sent to the above address. Depending on server load, the analysis may take anywhere from fifteen minutes to an hour or more to perform. Please be patient.

Citing oPOSSUM CSA Results

When citing results produced by the oPOSSUM CSA tool, please reference:
Huang SS, Fulton DL, Arenillas DJ, Perco P, Ho Sui SJ, Mortimer JR, Wasserman WW. Identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes. In: Series on Advances in Bioinformatics and Computational Biology Volume 3 - Proceedings of the 4th Asia-Pacific Bioinformatics Conference: 2006; Taipei, Taiwan: Imperial College Press, London UK; 2006:247-256.