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/ Smad3 and NFAT cooperate to induce Foxp3 expression through its enhancer. Smad3 and NFAT cooperate to induce Foxp3 expression through its enhancer. Nature immunology 2008 imex curation Tone Y., Furuuchi K., Kojima Y., Tykocinski ML., Greene MI., Tone M. IBD - Inflammatory bowel disease Results from Pull Down Assays - Figure 6 cannot be included as the origin of the HA-Smad3 construct cannot be traced. Supplementary fig 5C also cannot be annotated due to lack of antibody specificity. causality statements from Fig 1 (no protein statement for T cells), fig 5B, fig7 ( I suspect the HA-Smad3 construct might well be Human - as there seem to be some of these around, but no mouse ones) mtone@mail.med.upenn.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation mouse-t-cell Mouse T cell t-cell Peripheral blood T-lymphocytes ch-ip chromatin immunoprecipitation assay ch-ip q-pcr quantitative pcr q-pcr Tone Y., Furuuchi K., Kojima Y., Tykocinski ML., Greene MI., Tone M. IBD - Inflammatory bowel disease Results from Pull Down Assays - Figure 6 cannot be included as the origin of the HA-Smad3 construct cannot be traced. Supplementary fig 5C also cannot be annotated due to lack of antibody specificity. causality statements from Fig 1 (no protein statement for T cells), fig 5B, fig7 ( I suspect the HA-Smad3 construct might well be Human - as there seem to be some of these around, but no mouse ones) CD4+CD25+ Treg cells and CD4+CD25- T cells. CD4+CD25- T cells were treated with anti-CD3/28 and TGF-beta1 to induce Foxp3 expression. mtone@mail.med.upenn.edu Accepted 2015-SEP-11 by ORCHARD Nature immunology 2008 Only protein-protein interactions imex curation imex curation as before - ; I have altered the SIS3 chebi identifier in this expt- and the other one, as requested. As Anti-CD3/28 antibodies are used, in effect, as a mitogen (as in many expts using antigen-specific TCD4+/TCD8+ cells -a standard protocol) - without these abs you would not see much cell division, and the cells might die, or not respond to any other stimulus(??). So I did not think it appropriate to add the comment you suggest; - The CD3/28 presence for the non-TReg cells is already stated in the Exp. Mod. for both Expts. Also anti-CD3 has an effect with TGF-beta alone, without anti-CD28 (Fig 1C +others?) - so I cannot add a simple statement to the effect that "TGF-Beta only has an effect in the presence of anti-CD3/28 in CD4+CD25- T cells " . Anti-CD3/Cd28 + TGF-beta are not used/needed for the naturally occurring TReg cells experiment - so not relevant in this instance (Fig 8D). If you still think I should add a comment regarding presence of anti-CD3/CD28 -get back to me. (though I cannot think what I would put) I had not add the ChIPs for Figs 7D and 8C/D for some reason (omitted). So have added these here to existing interaction. Smad3 and NFAT cooperate to induce Foxp3 expression through its enhancer. Smad3 and NFAT cooperate to induce Foxp3 expression through its enhancer. Nature immunology 2008 imex curation Tone Y., Furuuchi K., Kojima Y., Tykocinski ML., Greene MI., Tone M. IBD - Inflammatory bowel disease Results from Pull Down Assays - Figure 6 cannot be included as the origin of the HA-Smad3 construct cannot be traced. Supplementary fig 5C also cannot be annotated due to lack of antibody specificity. causality statements from Fig 1 (no protein statement for T cells), fig 5B, fig7 ( I suspect the HA-Smad3 construct might well be Human - as there seem to be some of these around, but no mouse ones) mtone@mail.med.upenn.edu 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 weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Tone Y., Furuuchi K., Kojima Y., Tykocinski ML., Greene MI., Tone M. IBD - Inflammatory bowel disease Results from Pull Down Assays - Figure 6 cannot be included as the origin of the HA-Smad3 construct cannot be traced. Supplementary fig 5C also cannot be annotated due to lack of antibody specificity. causality statements from Fig 1 (no protein statement for T cells), fig 5B, fig7 ( I suspect the HA-Smad3 construct might well be Human - as there seem to be some of these around, but no mouse ones) CD4+CD25+ Treg cells and CD4+CD25- T cells. CD4+CD25- T cells were treated with anti-CD3/28 and TGF-beta1 to induce Foxp3 expression. mtone@mail.med.upenn.edu Accepted 2015-SEP-11 by ORCHARD Nature immunology 2008 Only protein-protein interactions imex curation imex curation as before - ; I have altered the SIS3 chebi identifier in this expt- and the other one, as requested. As Anti-CD3/28 antibodies are used, in effect, as a mitogen (as in many expts using antigen-specific TCD4+/TCD8+ cells -a standard protocol) - without these abs you would not see much cell division, and the cells might die, or not respond to any other stimulus(??). So I did not think it appropriate to add the comment you suggest; - The CD3/28 presence for the non-TReg cells is already stated in the Exp. Mod. for both Expts. Also anti-CD3 has an effect with TGF-beta alone, without anti-CD28 (Fig 1C +others?) - so I cannot add a simple statement to the effect that "TGF-Beta only has an effect in the presence of anti-CD3/28 in CD4+CD25- T cells " . Anti-CD3/Cd28 + TGF-beta are not used/needed for the naturally occurring TReg cells experiment - so not relevant in this instance (Fig 8D). If you still think I should add a comment regarding presence of anti-CD3/CD28 -get back to me. (though I cannot think what I would put) I had not add the ChIPs for Figs 7D and 8C/D for some reason (omitted). So have added these here to existing interaction. Smad3 and NFAT cooperate to induce Foxp3 expression through its enhancer. Smad3 and NFAT cooperate to induce Foxp3 expression through its enhancer. Nature immunology 2008 imex curation Tone Y., Furuuchi K., Kojima Y., Tykocinski ML., Greene MI., Tone M. IBD - Inflammatory bowel disease Results from Pull Down Assays - Figure 6 cannot be included as the origin of the HA-Smad3 construct cannot be traced. Supplementary fig 5C also cannot be annotated due to lack of antibody specificity. causality statements from Fig 1 (no protein statement for T cells), fig 5B, fig7 ( I suspect the HA-Smad3 construct might well be Human - as there seem to be some of these around, but no mouse ones) mtone@mail.med.upenn.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation mouse-el4 Mus musculus el4 Mouse ascites lymphoma lymphoblast line ch-ip chromatin immunoprecipitation assay ch-ip q-pcr quantitative pcr q-pcr Tone Y., Furuuchi K., Kojima Y., Tykocinski ML., Greene MI., Tone M. IBD - Inflammatory bowel disease Results from Pull Down Assays - Figure 6 cannot be included as the origin of the HA-Smad3 construct cannot be traced. Supplementary fig 5C also cannot be annotated due to lack of antibody specificity. causality statements from Fig 1 (no protein statement for T cells), fig 5B, fig7 ( I suspect the HA-Smad3 construct might well be Human - as there seem to be some of these around, but no mouse ones) EL4 - LAF cells - a subclone of EL4. All cells were treated with anti-CD3/28 and TGF-beta1 to induce Foxp3 expression. mtone@mail.med.upenn.edu Accepted 2015-SEP-11 by ORCHARD Nature immunology 2008 Only protein-protein interactions imex curation imex curation as before - ; I have altered the SIS3 chebi identifier in this expt- and the other one, as requested. As Anti-CD3/28 antibodies are used, in effect, as a mitogen (as in many expts using antigen-specific TCD4+/TCD8+ cells -a standard protocol) - without these abs you would not see much cell division, and the cells might die, or not respond to any other stimulus(??). So I did not think it appropriate to add the comment you suggest; - The CD3/28 presence for the non-TReg cells is already stated in the Exp. Mod. for both Expts. Also anti-CD3 has an effect with TGF-beta alone, without anti-CD28 (Fig 1C +others?) - so I cannot add a simple statement to the effect that "TGF-Beta only has an effect in the presence of anti-CD3/28 in CD4+CD25- T cells " . Anti-CD3/Cd28 + TGF-beta are not used/needed for the naturally occurring TReg cells experiment - so not relevant in this instance (Fig 8D). If you still think I should add a comment regarding presence of anti-CD3/CD28 -get back to me. (though I cannot think what I would put) I had not add the ChIPs for Figs 7D and 8C/D for some reason (omitted). So have added these here to existing interaction. 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 p2_probe_foxp3_enhancer_region dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid mouse Mus musculus Mouse GCTTCATTTTTTCCATTTACTGCAGAG nfac1_mouse Nuclear factor of activated T-cells, cytoplasmic 1 Nfatc1 Nfat2 Nfatc NFAT transcription complex cytosolic component protein protein mouse Mus musculus Mouse MPNTSFPVPSKFPLGPPAAVCGSGETLRPAPPSGGTMKAAEEEHYSYVSPSVTSTLPLPTAHSALPAACHDLQTSTPGISAVPSANHPPSYGGAVDSGPSGYFLSSGNTRPNGAPTLESPRIEITSYLGLHHGSGQFFHDVEVEDVLPSCKRSPSTATLHLPSLEAYRDPSCLSPASSLSSRSCNSEASSYESNYSYPYASPQTSPWQSPCVSPKTTDPEEGFPRSLGACHLLGSPRHSPSTSPRASITEESWLGARGSRPTSPCNKRKYSLNGRQPSCSPHHSPTPSPHGSPRVSVTEDTWLGNTTQYTSSAIVAAINALTTDSTLDLGDGVPIKSRKTALEHAPSVALKVEPAGEDLGTTPPTSDFPPEEYTFQHLRKGAFCEQYLSVPQASYQWAKPKSLSPTSYMSPSLPALDWQLPSHSGPYELRIEVQPKSHHRAHYETEGSRGAVKASAGGHPIVQLHGYLENEPLTLQLFIGTADDRLLRPHAFYQVHRITGKTVSTTSHEIILSNTKVLEIPLLPENNMRAIIDCAGILKLRNSDIELRKGETDIGRKNTRVRLVFRVHIPQPNGRTLSLQVASNPIECSQRSAQELPLVEKQSTDSYPVIGGKKMVLSGHNFLQDSKVIFVEKAPDGHHVWEMEAKTDRDLCKPNSLVVEIPPFRNQRITSPAQVSFYVCNGKRKRSQYQRFTYLPANGNSVFLTLSSESELRGGFY mint Plays a role in the inducible expression of cytokine genes in T-cells, especially in the induction of the IL-2 or IL-4 gene transcription. Also controls gene expression in embryonic cardiac cells. Could regulate not only the activation and proliferation but also the differentiation and programmed death of T-lymphocytes as well as lymphoid and non-lymphoid cells 58837C6CC085268D h4_mouse Histone H4 H4c11 H4c12 H4c14 H4c2 H4c3 H4c4 H4c6 H4c8 H4c9 H4f16 Hist1h4a Hist4h4 Hist1h4b Hist1h4c Hist1h4d Hist1h4f Hist1h4h Hist1h4i Hist1h4j Hist1h4k Hist2h4a Hist2h4 Hist1h4m H4-53 H4-12 H4c1 protein protein mouse Mus musculus Mouse MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG DIP protein P62806 original sequence version: 108 A9E5DFD3F8B97598 hist1h4h-foxp3-3 1 8 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 4 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 enhancer_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 2 F/G, 3C/D, 5A,6F,7D, 8C/D. P01137 increases binding of P62806 to ENSMUSG00000039521 Human TGF-beta1 (P01137) P01137 increases expression at RNA level of ENSMUSG00000039521 SIS3 ( CHEBI:87461) : a selective inhibitor of TGF-beta1-dependent Smad3 phosphorylation CHEBI:4031 decreases binding of P62806 to ENSMUSG00000039521 Cyclosporin A (CHEBI:4031 ): an immunosuppressant; it can inhibit antigen and mitogen triggered T cell activation In both naturally occurring and induced (anti-CD3/28 + TGF-beta) TReg cells, Histone H4 molecules near the NFAT- and Smad3-binding sequences (in the homologous region of the enhancer ) were highly acetylated. hist1h4h-foxp3-4 3 8 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 4 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 enhancer_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 2 F/G, 3C/D, 5A/D P01137 increases binding of P62806 to ENSMUSG00000039521 Human TGF-beta1 (P01137) P01137 increases expression at RNA level of ENSMUSG00000039521 P01137 increases expression at protein level of ENSMUSG00000039521 CHEBI:87461 increases expression at RNA level of ENSMUSG00000039521 CHEBI:4031 decreases expression at RNA level of ENSMUSG00000039521 p2_probe_foxp3_enhancer_region-nfatc1-1 2 7 unspecified role unspecified role prey prey subcellular prep subcellular preparation subcellular prep mouse-t-cell Mouse T cell t-cell Peripheral blood T-lymphocytes 6 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 physical association physical association 4C p2_probe_foxp3_enhancer_region-nfatc1-2 2 7 unspecified role unspecified role prey prey mouse-el4 Mus musculus el4 Mouse ascites lymphoma lymphoblast line 6 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 physical association physical association 4Ci nfatc1-foxp3-2 1 7 unspecified role unspecified role bait bait 4 unspecified role unspecified role prey prey enhancer_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 4D smad3-foxp3-3 1 5 unspecified role unspecified role bait bait 4 unspecified role unspecified role prey prey enhancer_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 6D Smad3 binding to the enhancer region was detected stimulated for 0.5–12 h, but not for longer durations.