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/ Molecular mechanisms underlying FOXP3 induction in human T cells. Molecular mechanisms underlying FOXP3 induction in human T cells. Journal of immunology (Baltimore, Md. : 1950) 2006 imex curation Mantel PY., Ouaked N., Rückert B., Karagiannidis C., Welz R., Blaser K., Schmidt-Weber CB. IBD - Inflammatory bowel disease Carsten.schmidt-weber@siaf.unizh.ch 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Mantel PY., Ouaked N., Rückert B., Karagiannidis C., Welz R., Blaser K., Schmidt-Weber CB. IBD - Inflammatory bowel disease Figure 8 is found after Figure 5 in the body of the publication and on magnifying the top of the image states "Figure 6". Naive (CD45RA+), resting (CD25−), activated (CD25−) or regulatory (CD25+) T cells. [ref 20 states that "activation" includes treatment with anti-CD3/28] Carsten.schmidt-weber@siaf.unizh.ch Accepted 2015-OCT-14 AT 08:15 BST AT 08:15 BST by ORCHARD Journal of immunology (Baltimore, Md. : 1950) 2006 imex curation Molecular mechanisms underlying FOXP3 induction in human T cells. Molecular mechanisms underlying FOXP3 induction in human T cells. Journal of immunology (Baltimore, Md. : 1950) 2006 imex curation Mantel PY., Ouaked N., Rückert B., Karagiannidis C., Welz R., Blaser K., Schmidt-Weber CB. IBD - Inflammatory bowel disease Carsten.schmidt-weber@siaf.unizh.ch 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Mantel PY., Ouaked N., Rückert B., Karagiannidis C., Welz R., Blaser K., Schmidt-Weber CB. IBD - Inflammatory bowel disease Figure 8 is found after Figure 5 in the body of the publication and on magnifying the top of the image states "Figure 6". Carsten.schmidt-weber@siaf.unizh.ch Accepted 2015-OCT-14 AT 08:15 BST AT 08:15 BST by ORCHARD Journal of immunology (Baltimore, Md. : 1950) 2006 imex curation Molecular mechanisms underlying FOXP3 induction in human T cells. Molecular mechanisms underlying FOXP3 induction in human T cells. Journal of immunology (Baltimore, Md. : 1950) 2006 imex curation Mantel PY., Ouaked N., Rückert B., Karagiannidis C., Welz R., Blaser K., Schmidt-Weber CB. IBD - Inflammatory bowel disease Carsten.schmidt-weber@siaf.unizh.ch 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro emsa supershift electrophoretic mobility supershift assay emsa supershift autoradiography autoradiography Mantel PY., Ouaked N., Rückert B., Karagiannidis C., Welz R., Blaser K., Schmidt-Weber CB. IBD - Inflammatory bowel disease Probe sequence for -124- -173 GC box probe was taken from core promoter sequence in Fig 1. Carsten.schmidt-weber@siaf.unizh.ch Accepted 2015-OCT-14 AT 08:15 BST AT 08:15 BST by ORCHARD Journal of immunology (Baltimore, Md. : 1950) 2006 imex curation nfac2_human Nuclear factor of activated T-cells, cytoplasmic 2 T-cell transcription factor NFAT1 NFAT pre-existing subunit NFATC2 NFAT1 NFATP protein protein human Homo sapiens Human MNAPERQPQPDGGDAPGHEPGGSPQDELDFSILFDYEYLNPNEEEPNAHKVASPPSGPAYPDDVLDYGLKPYSPLASLSGEPPGRFGEPDRVGPQKFLSAAKPAGASGLSPRIEITPSHELIQAVGPLRMRDAGLLVEQPPLAGVAASPRFTLPVPGFEGYREPLCLSPASSGSSASFISDTFSPYTSPCVSPNNGGPDDLCPQFQNIPAHYSPRTSPIMSPRTSLAEDSCLGRHSPVPRPASRSSSPGAKRRHSCAEALVALPPGASPQRSRSPSPQPSSHVAPQDHGSPAGYPPVAGSAVIMDALNSLATDSPCGIPPKMWKTSPDPSPVSAAPSKAGLPRHIYPAVEFLGPCEQGERRNSAPESILLVPPTWPKPLVPAIPICSIPVTASLPPLEWPLSSQSGSYELRIEVQPKPHHRAHYETEGSRGAVKAPTGGHPVVQLHGYMENKPLGLQIFIGTADERILKPHAFYQVHRITGKTVTTTSYEKIVGNTKVLEIPLEPKNNMRATIDCAGILKLRNADIELRKGETDIGRKNTRVRLVFRVHIPESSGRIVSLQTASNPIECSQRSAHELPMVERQDTDSCLVYGGQQMILTGQNFTSESKVVFTEKTTDGQQIWEMEATVDKDKSQPNMLFVEIPEYRNKHIRTPVKVNFYVINGKRKRSQPQHFTYHPVPAIKTEPTDEYDPTLICSPTHGGLGSQPYYPQHPMVAESPSCLVATMAPCQQFRTGLSSPDARYQQQNPAAVLYQRSKSLSPSLLGYQQPALMAAPLSLADAHRSVLVHAGSQGQSSALLHPSPTNQQASPVIHYSPTNQQLRCGSHQEFQHIMYCENFAPGTTRPGPPPVSQGQRLSPGSYPTVIQQQNATSQRAAKNGPPVSDQKEVLPAGVTIKQEQNLDQTYLDDVNEIIRKEFSGPPARNQT DIP protein Q13469 original sequence version: 99 DIP protein Q13469 original sequence version: 100 DIP protein Q13469 original sequence version: 167 8DAE86855CCB58D3 nf-at-328_oligo_probe_foxp3_promoter dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human CTATACACTTTTGTTTTAAAAACTGTGGGAGCTCATGAGCCCTATTATCTCATTGATACC nf-at-383_oligo_probe_foxp3_promoter nucleic acid nucleic acid human Homo sapiens Human GTTGGCCCTGTGATTTATTTTAGTTCTCGAGCCTTGTTTTTTTTTTTTCAAACT h4_human Histone H4 H4-16 H4C1 H4C11 H4C12 H4C13 H4C14 H4C15 H4C2 H4C3 H4C4 H4C5 H4C6 H4C8 H4C9 H4/A H4/B H4/C H4/D H4/E H4/G H4/H H4/I H4/J H4/K H4/M H4/N H4/O H4F2 H4FA H4FB H4FC H4FD H4FE H4FG H4FH H4FI H4FJ H4FK H4FM H4FN H4FO HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4 HIST2H4A HIST2H4B HIST4H4 protein protein human Homo sapiens Human MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG DIP protein P62805 original sequence version: 68 DIP protein P62805 original sequence version: 111 DIP protein P62805 original sequence version: 94 DIP protein P62805 original sequence version: 97 DIP protein P62805 original sequence version: 116 DIP protein P62805 original sequence version: 105 DIP protein P62805 original sequence version: 120 DIP protein P62805 original sequence version: 144 DIP protein P62805 original sequence version: 150 DIP protein P62805 original sequence version: 154 DIP protein P62805 original sequence version: 156 DIP protein P62805 original sequence version: 112 DIP protein P62805 original sequence version: 121 DIP protein P62805 original sequence version: 123 DIP protein P62805 original sequence version: 126 DIP protein P62805 original sequence version: 132 DIP protein P62805 original sequence version: 136 DIP protein P62805 original sequence version: 119 A9E5DFD3F8B97598 sp3_human Transcription factor Sp3 SPR-2 SP3 protein protein human Homo sapiens Human MTAPEKPVKQEEMAALDVDSGGGGGGGGGHGEYLQQQQQHGNGAVAAAAAAQDTQPSPLALLAATCSKIGPPSPGDDEEEAAAAAGAPAAAGATGDLASAQLGGAPNRWEVLSATPTTIKDEAGNLVQIPSAATSSGQYVLPLQNLQNQQIFSVAPGSDSSNGTVSSVQYQVIPQIQSADGQQVQIGFTGSSDNGGINQESSQIQIIPGSNQTLLASGTPSANIQNLIPQTGQVQVQGVAIGGSSFPGQTQVVANVPLGLPGNITFVPINSVDLDSLGLSGSSQTMTAGINADGHLINTGQAMDSSDNSERTGERVSPDINETNTDTDLFVPTSSSSQLPVTIDSTGILQQNTNSLTTSSGQVHSSDLQGNYIQSPVSEETQAQNIQVSTAQPVVQHLQLQESQQPTSQAQIVQGITPQTIHGVQASGQNISQQALQNLQLQLNPGTFLIQAQTVTPSGQVTWQTFQVQGVQNLQNLQIQNTAAQQITLTPVQTLTLGQVAAGGAFTSTPVSLSTGQLPNLQTVTVNSIDSAGIQLHPGENADSPADIRIKEEEPDPEEWQLSGDSTLNTNDLTHLRVQVVDEEGDQQHQEGKRLRRVACTCPNCKEGGGRGTNLGKKKQHICHIPGCGKVYGKTSHLRAHLRWHSGERPFVCNWMYCGKRFTRSDELQRHRRTHTGEKKFVCPECSKRFMRSDHLAKHIKTHQNKKGIHSSSTVLASVEAARDDTLITAGGTTLILANIQQGSVSGIGTVNTSATSNQDILTNTEIPLQLVTVSGNETME DCFD4363509DB49D foxp3_human_gene Forkhead box protein P3 (FOXP3) human gene gene gene human Homo sapiens Human sp1_human Transcription factor Sp1 SP1 TSFP1 protein protein human Homo sapiens Human MSDQDHSMDEMTAVVKIEKGVGGNNGGNGNGGGAFSQARSSSTGSSSSTGGGGQESQPSPLALLAATCSRIESPNENSNNSQGPSQSGGTGELDLTATQLSQGANGWQIISSSSGATPTSKEQSGSSTNGSNGSESSKNRTVSGGQYVVAAAPNLQNQQVLTGLPGVMPNIQYQVIPQFQTVDGQQLQFAATGAQVQQDGSGQIQIIPGANQQIITNRGSGGNIIAAMPNLLQQAVPLQGLANNVLSGQTQYVTNVPVALNGNITLLPVNSVSAATLTPSSQAVTISSSGSQESGSQPVTSGTTISSASLVSSQASSSSFFTNANSYSTTTTTSNMGIMNFTTSGSSGTNSQGQTPQRVSGLQGSDALNIQQNQTSGGSLQAGQQKEGEQNQQTQQQQILIQPQLVQGGQALQALQAAPLSGQTFTTQAISQETLQNLQLQAVPNSGPIIIRTPTVGPNGQVSWQTLQLQNLQVQNPQAQTITLAPMQGVSLGQTSSSNTTLTPIASAASIPAGTVTVNAAQLSSMPGLQTINLSALGTSGIQVHPIQGLPLAIANAPGDHGAQLGLHGAGGDGIHDDTAGGEEGENSPDAQPQAGRRTRREACTCPYCKDSEGRGSGDPGKKKQHICHIQGCGKVYGKTSHLRAHLRWHTGERPFMCTWSYCGKRFTRSDELQRHKRTHTGEKKFACPECPKRFMRSDHLSKHIKTHQNKKGGPGVALSVGTLPLDSGAGSEGSGTATPSALITTNMVAMEAICPEGIARLANSGINVMQVADLQSINISGNGF DIP protein P08047 original sequence version: 185 DIP protein P08047 original sequence version: 187 DIP protein P08047 original sequence version: 181 DIP protein P08047 original sequence version: 162 DIP protein P08047 original sequence version: 161 43893DBF6518B9EA gc_box_foxp3_promoter_probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human GAGAAAAAAAAAACTATGAGAACCCCCCCCCACCCCGTGATTATC hist1h4a-foxp3_human_gene-3 1 7 unspecified role unspecified role bait bait region ac1res monoacetylated residue Acetyl Acetylation (N terminus, N epsilon of Lysine, O of Serine) (Ac) Acetylation Ac1Res undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined observed-ptm observed-ptm observed ptm observed-ptm 9 unspecified role unspecified role prey prey core_promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 2B Histone hyperacetylation was detectable, particularly in activated or nTReg cells, showing that the FOXP3 promoter region is in an open conformation and accessible to the transcription machinery in the CD4+CD25− cells. gc_box_foxp3_promoter_probe-sp1-1 3 11 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 10 unspecified role unspecified role prey prey human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ physical association physical association 4D gc_box_foxp3_promoter_probe-sp1-2 3 11 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 8 unspecified role unspecified role prey prey human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ physical association physical association 4Di nf_at_383_oligo_probe_foxp3_promoter-nfatc2-1 2 6 unspecified role unspecified role bait bait region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined C28T,G29C,A30T,G31T mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain CGAG TCTT chemical synthesis Chemical synthesis (Chemical synthesis) 4 unspecified role unspecified role prey prey human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ physical association physical association 6/8B nf_at_383_oligo_probe_foxp3_promoter-nfatc2-2 2 5 unspecified role unspecified role bait bait region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined G29T,A30T,G31T mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain GAG TTT chemical synthesis Chemical synthesis (Chemical synthesis) 4 unspecified role unspecified role prey prey human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ physical association physical association 6/8C nfatc2-foxp3_human_gene-1 1 4 unspecified role unspecified role bait bait 9 unspecified role unspecified role prey prey core_promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 6/8D Q13469 increased the expression at RNA level of ENSG00000049768 CD4+CD25− T cells activated using anti-CD3 and anti-CD28 were used. CHEBI:4031 decreased the expression at RNA level of ENSG00000049768 CHEBI:4031 decreased the expression at protein level of ENSG00000049768 Causality statements from Fig6. (CsA is shown in other publications to stop expression/binding to Foxp3 promoter although this would seem counter-intuitive as CsA is an immunosuppressant.