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/ A distal cis-regulatory element, CNS-9, controls NFAT1 and IRF4-mediated IL-10 gene activation in T helper cells. A distal cis-regulatory element, CNS-9, controls NFAT1 and IRF4-mediated IL-10 gene activation in T helper cells. Molecular immunology 2009 imex curation Lee CG., Kang KH., So JS., Kwon HK., Son JS., Song MK., Sahoo A., Yi HJ., Hwang KC., Matsuyama T., Yui K., Im SH. IBD - Inflammatory bowel disease imsh@gist.ac.kr 19-Jan-2016: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro emsa supershift electrophoretic mobility supershift assay emsa supershift autoradiography autoradiography Lee CG., Kang KH., So JS., Kwon HK., Son JS., Song MK., Sahoo A., Yi HJ., Hwang KC., Matsuyama T., Yui K., Im SH. IBD - Inflammatory bowel disease imsh@gist.ac.kr Accepted 2015-DEC-02 AT 09:13 GMT AT 09:13 GMT by ORCHARD Molecular immunology 2009 Only protein-protein interactions imex curation imex curation A distal cis-regulatory element, CNS-9, controls NFAT1 and IRF4-mediated IL-10 gene activation in T helper cells. A distal cis-regulatory element, CNS-9, controls NFAT1 and IRF4-mediated IL-10 gene activation in T helper cells. Molecular immunology 2009 imex curation Lee CG., Kang KH., So JS., Kwon HK., Son JS., Song MK., Sahoo A., Yi HJ., Hwang KC., Matsuyama T., Yui K., Im SH. IBD - Inflammatory bowel disease imsh@gist.ac.kr 19-Jan-2016: Contacted by IntAct-Help. Only protein-protein interactions imex curation mouse-t-cell_th2 mouse helper T-lymphocyte Th2 Mouse t-cell_th2 T-helper cell 2 ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Lee CG., Kang KH., So JS., Kwon HK., Son JS., Song MK., Sahoo A., Yi HJ., Hwang KC., Matsuyama T., Yui K., Im SH. IBD - Inflammatory bowel disease ChIP is stated to have been carried out using NFAT2 antibodies, but no results are shown in Figure 2E. The text also states:-"NFAT1 binding to the reported IL-4 and IFN-gamma promoter regions are shown as positive controls for the NFAT1 ChIP in Th1 and Th2 cells, respectively." However Fig 2E shows binding with NFAT1 in Th1 cells for the IFN-gamma promoter and the IL4 promoter in Th2 cells. please check I am not misinterpreting what they are saying - in my comment. Cells were purified from the lymph nodes and spleen. Cells were stimulated with PMA and ionomycin. imsh@gist.ac.kr Accepted 2015-DEC-02 AT 09:13 GMT AT 09:13 GMT by ORCHARD Molecular immunology 2009 Only protein-protein interactions imex curation imex curation A distal cis-regulatory element, CNS-9, controls NFAT1 and IRF4-mediated IL-10 gene activation in T helper cells. A distal cis-regulatory element, CNS-9, controls NFAT1 and IRF4-mediated IL-10 gene activation in T helper cells. Molecular immunology 2009 imex curation Lee CG., Kang KH., So JS., Kwon HK., Son JS., Song MK., Sahoo A., Yi HJ., Hwang KC., Matsuyama T., Yui K., Im SH. IBD - Inflammatory bowel disease imsh@gist.ac.kr 19-Jan-2016: Contacted by IntAct-Help. Only protein-protein interactions imex curation mouse-t-cell_th1 Mouse T helper cell Th1 t-cell_th1 T-helper cell 1 ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Lee CG., Kang KH., So JS., Kwon HK., Son JS., Song MK., Sahoo A., Yi HJ., Hwang KC., Matsuyama T., Yui K., Im SH. IBD - Inflammatory bowel disease ChIP is stated to have been carried out using NFAT2 antibodies, but no results are shown in Figure 2E. The text also states:-"NFAT1 binding to the reported IL-4 and IFN-gamma promoter regions are shown as positive controls for the NFAT1 ChIP in Th1 and Th2 cells, respectively." However Fig 2E shows binding with NFAT1 in Th1 cells for the IFN-gamma promoter and the IL4 promoter in Th2 cells. please check I am not misinterpreting what they are saying - in my comment. Cells were purified from the lymph nodes and spleen. Cells were stimulated with PMA and ionomycin. imsh@gist.ac.kr Accepted 2015-DEC-02 AT 09:13 GMT AT 09:13 GMT by ORCHARD Molecular immunology 2009 Only protein-protein interactions imex curation imex curation 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 cns9c_enhancer_il10_gene_probe ds dna double stranded deoxyribonucleic acid ds DNA ds dna mouse Mus musculus Mouse ACGGCGAGAAGGAAACACAGGTGAACACGC ifng_mouse_gene Interferon gamma Ifng gene gene mouse Mus musculus Mouse il10_mouse_gene Interleukin-10 gene gene gene mouse Mus musculus Mouse 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 irf4_mouse Interferon regulatory factor 4 Irf4 Spip Lymphocyte-specific interferon regulatory factor NF-EM5 PU.1 interaction partner Transcriptional activator PIP protein protein mouse Mus musculus Mouse MNLETGSRGSEFGMSAVSCGNGKLRQWLIDQIDSGKYPGLVWENEEKSVFRIPWKHAGKQDYNREEDAALFKAWALFKGKFREGIDKPDPPTWKTRLRCALNKSNDFEELVERSQLDISDPYKVYRIVPEGAKKGAKQLTLDDTQMAMGHPYPMTAPYGSLPAQQVHNYMMPPHDRSWRDYAPDQSHPEIPYQCPVTFGPRGHHWQGPSCENGCQVTGTFYACAPPESQAPGIPIEPSIRSAEALALSDCRLHICLYYRDILVKELTTTSPEGCRISHGHTYDVSNLDQVLFPYPDDNGQRKNIEKLLSHLERGLVLWMAPDGLYAKRLCQSRIYWDGPLALCSDRPNKLERDQTCKLFDTQQFLSELQVFAHHGRPAPRFQVTLCFGEEFPDPQRQRKLITAHVEPLLARQLYYFAQQNTGHFLRGYELPEHVTTPDYHRSLRHSSIQE DIP protein Q64287 original sequence version: 111 5FD94CA6C453869C cns9a_enhancer_il10_gene_probe ds dna double stranded deoxyribonucleic acid ds DNA ds dna mouse Mus musculus Mouse CTCACAACGAAACTGCAACCTCAAAGCACC il4_mouse_gene Interleukin-4 Il4 Il-4 gene gene mouse Mus musculus Mouse cns9c_enhancer_il10_gene_probe-nfatc2-2 1 8 unspecified role unspecified role prey prey mouse-el4 Mus musculus el4 Mouse ascites lymphoma lymphoblast line 5 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 in vitro In vitro physical association physical association 2C cns9c_enhancer_il10_gene_probe-nfatc2-1 1 4 unspecified role unspecified role prey prey mouse-el4 Mus musculus el4 Mouse ascites lymphoma lymphoblast line 5 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 in vitro In vitro physical association physical association 2C-2 CHEBI:63954 and CHEBI:37537 increase the expression at RNA level of ENSMUSG00000016529 O88942 and Q60591 increase the expression at RNA level of ENSMUSG00000016529 causality from 1b/4B: cell line is EL4 (no chips for this line) cns9a_enhancer_il10_gene_probe-irf4-1 1 9 unspecified role unspecified role prey prey mouse-t-cell_th2 mouse helper T-lymphocyte Th2 Mouse t-cell_th2 T-helper cell 2 10 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 in vitro In vitro physical association physical association 2D nfatc2-ifng-1 3 6 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 8 unspecified role unspecified role bait bait association association 2E positive control causality from fig 1E CHEBI:63954 and CHEBI:37537 increase the expression at RNA level of ENSMUSG00000055170 nfatc2-il10_mouse_gene-1 2 7 unspecified role unspecified role prey prey cns9_enhancer_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 8 unspecified role unspecified role bait bait association association 2E CHEBI:63954 and CHEBI:37537 increase the expression at RNA level of ENSMUSG00000016529 CHEBI:4031 decreases the expression at RNA level of ENSMUSG00000016529 Q60591 increases the expression at RNA level of ENSMUSG00000016529 causality from Fig 1D/3A/3C nfatc2-il10_mouse_gene-2 2 8 unspecified role unspecified role bait bait 11 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 2E-2 positive control CHEBI:63954 and CHEBI:37537 increase the expression at RNA level of ENSMUSG00000000869 casuality from fig 1E nfatc2-il10_mouse_gene-3 2 7 unspecified role unspecified role prey prey cns9_enhancer_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 9 unspecified role unspecified role bait bait association association 2Ei irf4-il4-1 2 9 unspecified role unspecified role bait bait 11 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 2E-2i weak interaction