IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ Multiple activating and repressive cis-promoter regions regulate TNFSF15 expression in human primary mononuclear cells. Multiple activating and repressive cis-promoter regions regulate TNFSF15 expression in human primary mononuclear cells. Cytokine 2013 imex curation Gonsky R., Deem RL., Targan SR. IBD - Inflammatory bowel disease Monocytes were isolated from PBMC using negative selection by depletion with magnetic beads. Stephan.Targan@cshs.org 17-Sep-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-monocyte Human mononuclear cells monocyte Monocyte, mononuclear cell ch-ip chromatin immunoprecipitation assay ch-ip q-pcr quantitative pcr q-pcr Gonsky R., Deem RL., Targan SR. IBD - Inflammatory bowel disease Info given for this ChIp even more confusing than usual;I think they mean that p65 does not bind at all - the error bars are almost bigger than the "result" ? (No idea what "UT" and "P/I" mean.) Monocytes were isolated from PBMC using negative selection by depletion with magnetic beads. Stephan.Targan@cshs.org Accepted 2015-JUL-30 by ORCHARD Cytokine 2013 Only protein-protein interactions imex curation imex curation Multiple activating and repressive cis-promoter regions regulate TNFSF15 expression in human primary mononuclear cells. Multiple activating and repressive cis-promoter regions regulate TNFSF15 expression in human primary mononuclear cells. Cytokine 2013 imex curation Gonsky R., Deem RL., Targan SR. IBD - Inflammatory bowel disease Monocytes were isolated from PBMC using negative selection by depletion with magnetic beads. Stephan.Targan@cshs.org 17-Sep-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa tag fluorescence tag visualisation by fluorescence tag fluorescence Gonsky R., Deem RL., Targan SR. IBD - Inflammatory bowel disease No further details are available for Promega supplied c-Jun, as the product is no longer available. Stephan.Targan@cshs.org Accepted 2015-JUL-30 by ORCHARD Cytokine 2013 imex curation jun_human Transcription factor AP-1 JUN Activator protein 1 Proto-oncogene c-Jun V-jun avian sarcoma virus 17 oncogene homolog p39 protein protein human Homo sapiens Human MTAKMETTFYDDALNASFLPSESGPYGYSNPKILKQSMTLNLADPVGSLKPHLRAKNSDLLTSPDVGLLKLASPELERLIIQSSNGHITTTPTPTQFLCPKNVTDEQEGFAEGFVRALAELHSQNTLPSVTSAAQPVNGAGMVAPAVASVAGGSGSGGFSASLHSEPPVYANLSNFNPGALSSGGGAPSYGAAGLAFPAQPQQQQQPPHHLPQQMPVQHPRLQALKEEPQTVPEMPGETPPLSPIDMESQERIKAERKRMRNRIAASKCRKRKLERIARLEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNHVNSGCQLMLTQQLQTF DIP protein P05412 original sequence version: 119 DIP protein P05412 original sequence version: 114 DIP protein P05412 original sequence version: 185 DIP protein P05412 original sequence version: 145 DIP protein P05412 original sequence version: 202 DIP protein P05412 original sequence version: 206 DIP protein P05412 original sequence version: 163 DIP protein P05412 original sequence version: 175 DIP protein P05412 original sequence version: 189 DIP protein P05412 original sequence version: 169 0695E23AC4D33561 p19838-pro_0000030311 Nuclear factor NF-kappa-B p50 subunit NFKB1 DNA-binding factor KBF1 EBP-1 Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 protein protein human Homo sapiens Human MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHG 1 433 5D027BB8EBCAA33A tnf15_human_gene Tumor necrosis factor ligand superfamily member 15 TNFSF15 TL1 VEGI gene gene human Homo sapiens Human tnfsf15_ap-1_site_probe TNFSF15_5-prime_UTR_AP-1_site dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human GGTGACTTTAATCACTCAGTCTCC ap1-consensus_probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid chemical synthesis Chemical synthesis (Chemical synthesis) CGCTTGATGACTCAGCCGGAA tnfsf15_ap_1 site_probe-jun-1 2 3 unspecified role unspecified role prey prey 6 unspecified role unspecified role bait bait 5-prime fluorescent dye fluorescent dye label fluorescent dye certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction 3C tnfsf15_ap_1_site_probe-ap1_consensus_probe-1 2 7 inhibitor inhibitor prey prey C13T,A14G mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain CA TG chemical synthesis Chemical synthesis (Chemical synthesis) 3 unspecified role unspecified role prey prey 6 unspecified role unspecified role bait bait 5-prime fluorescent dye fluorescent dye label fluorescent dye certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction 3Ci tnfsf15_ap_1_site_probe-ap1_consensus_probe-2 2 6 inhibitor inhibitor prey prey chemical synthesis Chemical synthesis (Chemical synthesis) 3 unspecified role unspecified role prey prey 6 unspecified role unspecified role bait bait 5-prime fluorescent dye fluorescent dye label fluorescent dye certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction 3Cii jun-tnfsf15-1 1 5 unspecified role unspecified role prey prey 5-prime_UTR_AP1_binding site sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 3 unspecified role unspecified role bait bait association association 4 P05412 increases expression at RNA level of ENSG00000181634 I cannot add causality statements for TAT-TI-JIP and SN50 as they are peptides/synthetic/fusion proteins of some description - so cannot enter into Chebi(?) (CHEBI:87077 = MG132). Results from Fig 5 use PBMCs - which are only ~30% monocytes- so no causality statements entered. CHEBI:87077 indirectly decreases expression at RNA level of ENSG00000181634 CHEBI:87077 indirectly decreases expression at protein level of ENSG00000181634 jun-tnfsf15-2 1 5 unspecified role unspecified role prey prey 5-prime_UTR_−210 bp_NFKb_binding_site sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 4 unspecified role unspecified role bait bait association association 4i