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/ Development of Foxp3(+) regulatory t cells is driven by the c-Rel enhanceosome. Development of Foxp3(+) regulatory t cells is driven by the c-Rel enhanceosome. Immunity 2009 imex curation Ruan Q., Kameswaran V., Tone Y., Li L., Liou HC., Greene MI., Tone M., Chen YH. IBD - Inflammatory bowel disease yhc@mail.med.upenn.edu 03-Dec-2015: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Ruan Q., Kameswaran V., Tone Y., Li L., Liou HC., Greene MI., Tone M., Chen YH. IBD - Inflammatory bowel disease A subclone of mouse EL4 T lymphoma cells EL4/ LAF cells. yhc@mail.med.upenn.edu Accepted 2015-NOV-26 AT 08:48 GMT AT 08:48 GMT by ORCHARD Immunity 2009 Only protein-protein interactions imex curation I have amalgamated the 2 SMAD3 interactions - there should be no pCREB interaction. Development of Foxp3(+) regulatory t cells is driven by the c-Rel enhanceosome. Development of Foxp3(+) regulatory t cells is driven by the c-Rel enhanceosome. Immunity 2009 imex curation Ruan Q., Kameswaran V., Tone Y., Li L., Liou HC., Greene MI., Tone M., Chen YH. IBD - Inflammatory bowel disease yhc@mail.med.upenn.edu 03-Dec-2015: Contacted by IntAct-Help. Only protein-protein interactions mouse-t-cell Mouse T cell t-cell Peripheral blood T-lymphocytes ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr time in hours 2.0 8 19 0.5 TNF-beta 0 + Ruan Q., Kameswaran V., Tone Y., Li L., Liou HC., Greene MI., Tone M., Chen YH. IBD - Inflammatory bowel disease TGF-beta affected primarily the recruitment of Smad to the Foxp3 promoter while having little effect on recruitment of other transcription factors tested. Interactions with "p-CREB" have not been included as the antibody target is not known. 1] causality statements based on Fig 2, Supp Fig2 2] if I thought I was imagining a band might be present I have NOT added it e.g. at 0.5 hrs for many baits. 3] Santa Cruz sell antibodies to pCREB-1, pCREB-2 4] Cant add any Causality statements for TGF-beta as no species mentioned. CD4+CD25− T cells cultured under Treg cell-inducing conditions and in the presence (A) or absence (B) of recombinant TGF-beta. yhc@mail.med.upenn.edu Accepted 2015-NOV-26 AT 08:48 GMT AT 08:48 GMT by ORCHARD Immunity 2009 Only protein-protein interactions imex curation I have amalgamated the 2 SMAD3 interactions - there should be no pCREB interaction. Development of Foxp3(+) regulatory t cells is driven by the c-Rel enhanceosome. Development of Foxp3(+) regulatory t cells is driven by the c-Rel enhanceosome. Immunity 2009 imex curation Ruan Q., Kameswaran V., Tone Y., Li L., Liou HC., Greene MI., Tone M., Chen YH. IBD - Inflammatory bowel disease yhc@mail.med.upenn.edu 03-Dec-2015: Contacted by IntAct-Help. Only protein-protein interactions mouse-t-cell Mouse T cell t-cell Peripheral blood T-lymphocytes ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr time in hours 2.0 8 19 0.5 TNF-beta 0 + Ruan Q., Kameswaran V., Tone Y., Li L., Liou HC., Greene MI., Tone M., Chen YH. IBD - Inflammatory bowel disease Interactions with "p-CREB" have not been included as the antibody target is not known. if I thought I was imagining a band might be present I have NOT added it e.g. at 0.5 hrs for many baits. Santa Cruz sell antibodies to CREB-1, CREB-2;there are also other possible targets- less likely. CD4+CD25− T cells cultured under Treg cell-inducing conditions and in the presence (A) or absence (B) of recombinant TGF-beta. RE-ChIP/Sequential ChIp experiment; the Bait of the first IP becomes a Prey in the second IP. It allows for the identification of multiple (concurrently binding) proteins on a single DNA sequence. yhc@mail.med.upenn.edu Accepted 2015-NOV-26 AT 08:48 GMT AT 08:48 GMT by ORCHARD Immunity 2009 Only protein-protein interactions imex curation I have amalgamated the 2 SMAD3 interactions - there should be no pCREB interaction. mouse-rel-nfat_oligo_foxp3_promoter_382 ss dna single stranded deoxyribonucleic acid ss DNA ss dna mouse Mus musculus Mouse TTGTGATTTGACTTATTTTCCCTCAGTTTTTTT tf65_mouse Transcription factor p65 Nuclear factor NF-kappa-B p65 subunit Rela Nfkb3 Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3 protein protein mouse Mus musculus Mouse MDDLFPLIFPSEPAQASGPYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLVTKDPPHRPHPHELVGKDCRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQRIQTNNNPFHVPIEEQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDNRAPNTAELKICRVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPYADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPDTDDRHRIEEKRKRTYETFKSIMKKSPFNGPTEPRPPTRRIAVPTRNSTSVPKPAPQPYTFPASLSTINFDEFSPMLLPSGQISNQALALAPSSAPVLAQTMVPSSAMVPLAQPPAPAPVLTPGPPQSLSAPVPKSTQAGEGTLSEALLHLQFDADEDLGALLGNSTDPGVFTDLASVDNSEFQQLLNQGVSMSHSTAEPMLMEYPEAITRLVTGSQRPPDPAPTPLGTSGLPNGLSGDEDFSSIADMDFSALLSQISS DIP protein Q04207 original sequence version: 158 DIP protein Q04207 original sequence version: 117 DIP protein Q04207-1 original sequence version: 117 DIP protein Q04207-1 original sequence version: 118 DIP protein Q04207 original sequence version: 119 DIP protein Q04207 original sequence version: 141 DIP protein Q04207-1 original sequence version: 141 DIP protein Q04207-1 original sequence version: 149 DIP protein Q04207 original sequence version: 149 DIP protein Q04207 original sequence version: 168 DIP protein Q04207 original sequence version: 125 BDF1673D2FE398B9 nfac2_mouse Nuclear factor of activated T-cells, cytoplasmic 2 T-cell transcription factor NFAT1 NFAT pre-existing subunit Nfatc2 Nfat1 Nfatp protein protein mouse Mus musculus Mouse MDVPEPQPDPDGGDGPGHEPGGSPQDELDFSILFDYDYLNPIEEEPIAHKAISSPSGLAYPDDVLDYGLKPCNPLASLSGEPPGRFGEPDSIGFQNFLSPVKPAGASGPSPRIEITPSHELMQAGGALRGRDAGLSPEQPALALAGVAASPRFTLPVPGYEGYREPLCLSPASSGSSASFISDTFSPYTSPCVSPNNAGPDDLCPQFQNIPAHYSPRTSPIMSPRTSLAEDSCLGRHSPVPRPASRSSSPGAKRRHSCAEALVAPLPAASPQRSRSPSPQPSPHVALQDDSIPAGYPPTAGSAVLMDALNTLATDSPCGIPSKIWKTSPDPTPVSTAPSKAGLARHIYPTVEFLGPCEQEERRNSAPESILLVPPTWPKQLVPAIPICSIPVTASLPPLEWPLSNQSGSYELRIEVQPKPHHRAHYETEGSRGAVKAPTGGHPVVQLHGYMENKPLGLQIFIGTADERILKPHAFYQVHRITGKTVTTTSYEKIVGNTKVLEIPLEPKNNMRATIDCAGILKLRNADIELRKGETDIGRKNTRVRLVFRVHVPEPSGRIVSLQAASNPIECSQRSAHELPMVERQDMDSCLVYGGQQMILTGQNFTAESKVVFMEKTTDGQQIWEMEATVDKDKSQPNMLFVEIPEYRNKHIRVPVKVNFYVINGKRKRSQPQHFTYHPVPAIKTEPSDEYEPSLICSPAHGGLGSQPYYPQHPMLAESPSCLVATMAPCQQFRSGLSSPDARYQQQSPAAALYQRSKSLSPGLLGYQQPSLLAAPLGLADAHRSVLVHAGSQGQGQGSTLPHTSSASQQASPVIHYSPTNQQLRGGGHQEFQHIMYCENFGPSSARPGPPPINQGQRLSPGAYPTVIQQQTAPSQRAAKNGPSDQKEALPTGVTVKQEQNLDQTYLDDVNEIIRKEFSGPPSRNQT F21E7BABE7DBB40F foxp3_mouse_gene Forkhead box protein P3 Foxp3 gene gene mouse Mus musculus Mouse smad3_mouse Mothers against decapentaplegic homolog 3 Smad3 Madh3 SMAD family member 3 protein protein mouse Mus musculus Mouse MSSILPFTPPIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNVNTKCITIPRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHYQRVETPVLPPVLVPRHTEIPAEFPPLDDYSHSIPENTNFPAGIEPQSNIPETPPPGYLSEDGETSDHQMNHSMDAGSPNLSPNPMSPAHNNLDLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNSERFCLGLLSNVNRNAAVELTRRHIGRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS DIP protein Q8BUN5 original sequence version: 57 46DF5E8B371321AC rel_mouse Proto-oncogene c-Rel Rel protein protein mouse Mus musculus Mouse MASSGYNPYVEIIEQPRQRGMRFRYKCEGRSAGSIPGERSTDNNRTYPSVQIMNYYGKGKIRITLVTKNDPYKPHPHDLVGKDCRDGYYEAEFGPERRPLFFQNLGIRCVKKKEVKGAIILRISAGINPFNVGEQQLLDIEDCDLNVVRCVFMFFLPDEDGNFTTALPPIVSNPIYDNRAPNTAELRICRVNKNCGSVRGGDEIFLLCDKVQKDDIEVRFVLNDWEARGVFSQADVHRQVAIVFKTPPYCKAILEPVTVKMQLRRPSDQEVSESMDFRYLPDEKDAYGNKSKKQKTTLIFQKLLQDCGHFTEKPRTAPLGSTGEGRFIKKESNLFSHGTVLPEMPRSSGVPGQAEPYYSSCGSISSGLPHHPPAIPSVAHQPTSWPPVTHPTSHPVSTNTLSTFSAGTLSSNSQGILPFLEGPGVSDLSASNSCLYNPDDLARMETPSMSPTDLYSISDVNMLSTRPLSVMAPSTDGMGDTDNPRLVSINLENPSCNARLGPRDLRQLHQMSPASLSAGTSSSSVFVSQSDAFDRSNFSCVDNGLMNEPGLSDDANNPTFVQSSHYSVNTLQSEQLSDPFTYGFFKI DIP protein P15307 original sequence version: 88 98FC237B6D140416 mouse-rel-nfat_oligo_foxp3_promoter_327 ss dna single stranded deoxyribonucleic acid ss DNA ss dna mouse Mus musculus Mouse TTTAAGAAATTGTGGTTTCTCATGAGCCCTGTT mouse_rel_nfat_oligo_foxp3_promoter_382-1 1 16 unspecified role unspecified role bait bait region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined T_C_C19-21G_G_A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain TCC GGA chemical synthesis Chemical synthesis (Chemical synthesis) 21 unspecified role unspecified role prey prey mouse-el4 Mus musculus el4 Mouse ascites lymphoma lymphoblast line physical association physical association 4A mouse_rel_nfat_oligo_foxp3_promoter_382-rel-1 1 16 unspecified role unspecified role bait bait region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined T_C_C19-21G_G_A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain TCC GGA chemical synthesis Chemical synthesis (Chemical synthesis) 18 unspecified role unspecified role prey prey mouse-el4 Mus musculus el4 Mouse ascites lymphoma lymphoblast line physical association physical association 4Ai mouse_rel_nfat_oligo_foxp3_promoter_382-rel-2 1 22 unspecified role unspecified role bait bait region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined G12C,T16C,T17G,T18C,C19A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain TTTC CGCA certain certain sequence position certain certain certain sequence position certain G C chemical synthesis Chemical synthesis (Chemical synthesis) 21 unspecified role unspecified role prey prey mouse-el4 Mus musculus el4 Mouse ascites lymphoma lymphoblast line physical association physical association 4Aii mouse_rel_nfat_oligo_foxp3_promoter_327-rel-1 1 22 unspecified role unspecified role bait bait region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined G12C,T16C,T17G,T18C,C19A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain TTTC CGCA certain certain sequence position certain certain certain sequence position certain G C chemical synthesis Chemical synthesis (Chemical synthesis) 18 unspecified role unspecified role prey prey mouse-el4 Mus musculus el4 Mouse ascites lymphoma lymphoblast line physical association physical association 4Aiii smad3-foxp3-1 2 20 unspecified role unspecified role bait bait 19 unspecified role unspecified role prey prey promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined enhancer1_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 8 3 8 6 4 A/B-1 rel-foxp3-1 2 21 unspecified role unspecified role bait bait 19 unspecified role unspecified role prey prey promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 4 7 7 6 3 7 5 7 8 3 8 4 4 A/B-2 P15307 increases expression at RNA level ENSMUSG00000039521 CHEBI:63954 and CHEBI:37537 increases expression at RNA level ENSMUSG00000039521 rela-foxp3-1 2 17 unspecified role unspecified role bait bait 19 unspecified role unspecified role prey prey promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 4 7 7 6 3 7 5 7 8 3 8 4 8 5 4 A/B-3 Q04207 increases expression at RNA level ENSMUSG00000039521 nfatc2-foxp3-1 2 18 unspecified role unspecified role bait bait 19 unspecified role unspecified role prey prey promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 4 7 7 6 3 7 5 7 8 3 8 4 8 5 4 A/B-4 rel-foxp3-2 9 18 unspecified role unspecified role bait bait 21 unspecified role unspecified role prey prey 19 unspecified role unspecified role prey prey promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 4 7 7 6 3 7 5 7 8 3 8 4 4 A/B-2 smad3-foxp3-7 2 20 unspecified role unspecified role bait bait 19 unspecified role unspecified role prey prey promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined enhancer1_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 8 6 8 3 4 A/B-1