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:
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: ABI4 Agamous AGL3 Ar Arnt Arnt-Ahr ARR10 Athb-1 ATHB5 Bapx1 Broad-complex_1 Broad-complex_3 Broad-complex_4 bZIP910 bZIP911 cEBP CF2-II CFI-USP Chop-cEBP CREB1 deltaEF1 Dof2 Dof3 Dorsal_1 Dorsal_2 E2F1 E74A ELK1 ELK4 ESR1 Evi1 Fos Foxa2 FOXD1 Foxd3 FOXF2 FOXI1 Foxq1 GABPA GAMYB Gfi HAND1-TCF3 HLF HMG-1 HMG-IY HNF4 Hox11-CTF1 Hunchback IRF1 IRF2 MAX MEF2A MNB1A Myb MYB.ph3 MYC-MAX Mycn Myf NF-kappaB NF-Y NFIL3 NFKB1 NHLH1 Nkx2-5 NR1H2-RXR NR2F1 NR3C1 Pax4 Pax5 Pax6 PBF Pbx PPARG PPARG-RXRA Prrx2 REL RELA Roaz RORA RORA1 RREB1 RUNX1 RXR-VDR Snail Sox17 Sox5 SOX9 SP1 SPIB Spz1 SQUA SRF SRY Staf SU_h T TAL1-TCF3 TBP TCF1 TEAD TP53 USF1 YY1 ZNF42_1-4 ZNF42_5-13 STEP 3: Select parameters Level of conservation ? Top 30% of conserved regions (min. conservation 60%) Top 20% of conserved regions (min. conservation 65%) Top 10% of conserved regions (min. conservation 70%) Matrix match threshold ? 75% 80% 85% Matrix classification method ? CompareACE mat_align Amount of upstream/downstream sequence ? bp (max. 10000)/ bp (max 10000) Cardinality of combinations ? 2 3 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:
Level of conservation ? Top 30% of conserved regions (min. conservation 60%) Top 20% of conserved regions (min. conservation 65%) Top 10% of conserved regions (min. conservation 70%) Matrix match threshold ? 75% 80% 85% Matrix classification method ? CompareACE mat_align Amount of upstream/downstream sequence ? bp (max. 10000)/ bp (max 10000) Cardinality of combinations ? 2 3 Maximum inter-binding site distance ? bp Minimum multiplicity ? Class combination score threshold ?
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.
