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 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.
