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/ Stat3 and CCAAT/enhancer binding protein beta (C/EBP-beta) regulate Jab1/CSN5 expression in mammary carcinoma cells. Stat3 and CCAAT/enhancer binding protein beta (C/EBP-beta) regulate Jab1/CSN5 expression in mammary carcinoma cells. Breast Cancer Res. (1465-5411) 2011 imex curation Shackleford T.J., Zhang Q., Tian L., Vu T.T., Korapati A.L., Baumgartner A.M., Le X.F., Liao W.S., Claret F.X. IBD - Inflammatory bowel disease They show that transfection of C/EBP-alpha, C/EBP-beta, GATA-1, GATA-2, GATA-3 (Fig. 4A) increases JAB1 promoter activity; however, they don’t mention the identity of the expression constructs. These would be causality statements that could be added to interactions of experiment EBI-9977008 if TF’s would be of human origin. Same is true for the C/EBP-alpha/Stat3 and C/EBP-beta/Stat3 cooperativity in Fig. 5A. I mailed corresponding author quite a while ago to clarify but never got a response...should I add a comment about what data is there but we don't know the origin of transfected proteins? - you can add a comment if you wish. If nothing else, if he suddenly dies get back to you, it will remind you what information you wished to add. fxclaret@mdanderson.org 22-Jan-2015: Contacted by IntAct-Help. Only protein-protein interactions human-mda_mb_231 Homo sapiens Caucasian breast adenocarcinoma mda_mb_231 Human Caucasian breast adenocarcinoma ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Shackleford T.J., Zhang Q., Tian L., Vu T.T., Korapati A.L., Baumgartner A.M., Le X.F., Liao W.S., Claret F.X. IBD - Inflammatory bowel disease They show that transfection of C/EBP-alpha, C/EBP-beta, GATA-1, GATA-2, GATA-3 (Fig. 4A) increases JAB1 promoter activity; however, they don’t mention the identity of the expression constructs. These would be causality statements that could be added to interactions of experiment EBI-9977008 if TF’s would be of human origin. Same is true for the C/EBP-alpha/Stat3 and C/EBP-beta/Stat3 cooperativity in Fig. 5A. I mailed corresponding author quite a while ago to clarify but never got a response...should I add a comment about what data is there but we don't know the origin of transfected proteins? - you can add a comment if you wish. If nothing else, if he suddenly dies get back to you, it will remind you what information you wished to add. For ChIP assays, MDA-MB-231 cells were transfected with empty control pcDNA vector or with C/EBP-beta2 (Rat) (P21272-2) expression vector. The identity of the C/EBP-beta2 construct was inferred from PMID:11573208 and PMID:2253878. fxclaret@mdanderson.org Accepted 2015-JAN-15 by ORCHARD Breast Cancer Res. (1465-5411) 2011 Only protein-protein interactions imex curation Stat3 and CCAAT/enhancer binding protein beta (C/EBP-beta) regulate Jab1/CSN5 expression in mammary carcinoma cells. Stat3 and CCAAT/enhancer binding protein beta (C/EBP-beta) regulate Jab1/CSN5 expression in mammary carcinoma cells. Breast Cancer Res. (1465-5411) 2011 imex curation Shackleford T.J., Zhang Q., Tian L., Vu T.T., Korapati A.L., Baumgartner A.M., Le X.F., Liao W.S., Claret F.X. IBD - Inflammatory bowel disease They show that transfection of C/EBP-alpha, C/EBP-beta, GATA-1, GATA-2, GATA-3 (Fig. 4A) increases JAB1 promoter activity; however, they don’t mention the identity of the expression constructs. These would be causality statements that could be added to interactions of experiment EBI-9977008 if TF’s would be of human origin. Same is true for the C/EBP-alpha/Stat3 and C/EBP-beta/Stat3 cooperativity in Fig. 5A. I mailed corresponding author quite a while ago to clarify but never got a response...should I add a comment about what data is there but we don't know the origin of transfected proteins? - you can add a comment if you wish. If nothing else, if he suddenly dies get back to you, it will remind you what information you wished to add. fxclaret@mdanderson.org 22-Jan-2015: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro emsa supershift electrophoretic mobility supershift assay emsa supershift autoradiography autoradiography Shackleford T.J., Zhang Q., Tian L., Vu T.T., Korapati A.L., Baumgartner A.M., Le X.F., Liao W.S., Claret F.X. IBD - Inflammatory bowel disease They show that transfection of C/EBP-alpha, C/EBP-beta, GATA-1, GATA-2, GATA-3 (Fig. 4A) increases JAB1 promoter activity; however, they don’t mention the identity of the expression constructs. These would be causality statements that could be added to interactions of experiment EBI-9977008 if TF’s would be of human origin. Same is true for the C/EBP-alpha/Stat3 and C/EBP-beta/Stat3 cooperativity in Fig. 5A. I mailed corresponding author quite a while ago to clarify but never got a response...should I add a comment about what data is there but we don't know the origin of transfected proteins? - you can add a comment if you wish. If nothing else, if he suddenly dies get back to you, it will remind you what information you wished to add. fxclaret@mdanderson.org Accepted 2015-JAN-15 by ORCHARD Breast Cancer Res. (1465-5411) 2011 Only protein-protein interactions imex curation Stat3 and CCAAT/enhancer binding protein beta (C/EBP-beta) regulate Jab1/CSN5 expression in mammary carcinoma cells. Stat3 and CCAAT/enhancer binding protein beta (C/EBP-beta) regulate Jab1/CSN5 expression in mammary carcinoma cells. Breast Cancer Res. (1465-5411) 2011 imex curation Shackleford T.J., Zhang Q., Tian L., Vu T.T., Korapati A.L., Baumgartner A.M., Le X.F., Liao W.S., Claret F.X. IBD - Inflammatory bowel disease They show that transfection of C/EBP-alpha, C/EBP-beta, GATA-1, GATA-2, GATA-3 (Fig. 4A) increases JAB1 promoter activity; however, they don’t mention the identity of the expression constructs. These would be causality statements that could be added to interactions of experiment EBI-9977008 if TF’s would be of human origin. Same is true for the C/EBP-alpha/Stat3 and C/EBP-beta/Stat3 cooperativity in Fig. 5A. I mailed corresponding author quite a while ago to clarify but never got a response...should I add a comment about what data is there but we don't know the origin of transfected proteins? - you can add a comment if you wish. If nothing else, if he suddenly dies get back to you, it will remind you what information you wished to add. fxclaret@mdanderson.org 22-Jan-2015: Contacted by IntAct-Help. Only protein-protein interactions human-mcf7 Homo sapiens mammary carcinoma cells mcf7 mammary carcinoma cells ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Shackleford T.J., Zhang Q., Tian L., Vu T.T., Korapati A.L., Baumgartner A.M., Le X.F., Liao W.S., Claret F.X. IBD - Inflammatory bowel disease Authors show that transfection of C/EBP-alpha, C/EBP-beta or GATA-1 increases JAB1 promoter activity (Fig. 4A); however, the origin of the expression constructs could not be determined, hence these causality statements are not captured here. They show that transfection of C/EBP-alpha, C/EBP-beta, GATA-1, GATA-2, GATA-3 (Fig. 4A) increases JAB1 promoter activity; however, they don’t mention the identity of the expression constructs. These would be causality statements that could be added to interactions of experiment EBI-9977008 if TF’s would be of human origin. Same is true for the C/EBP-alpha/Stat3 and C/EBP-beta/Stat3 cooperativity in Fig. 5A. I mailed corresponding author quite a while ago to clarify but never got a response...should I add a comment about what data is there but we don't know the origin of transfected proteins? - you can add a comment if you wish. If nothing else, if he suddenly dies get back to you, it will remind you what information you wished to add. fxclaret@mdanderson.org Accepted 2015-JAN-15 by ORCHARD Breast Cancer Res. (1465-5411) 2011 Only protein-protein interactions imex curation cebpb_human CCAAT/enhancer-binding protein beta CEBPB TCF5 PP9092 Liver activator protein Nuclear factor NF-IL6 Transcription factor 5 Liver-enriched inhibitory protein protein protein human Homo sapiens Human MQRLVAWDPACLPLPPPPPAFKSMEVANFYYEADCLAAAYGGKAAPAAPPAARPGPRPPAGELGSIGDHERAIDFSPYLEPLGAPQAPAPATATDTFEAAPPAPAPAPASSGQHHDFLSDLFSDDYGGKNCKKPAEYGYVSLGRLGAAKGALHPGCFAPLHPPPPPPPPPAELKAEPGFEPADCKRKEEAGAPGGGAGMAAGFPYALRAYLGYQAVPSGSSGSLSTSSSSSPPGTPSPADAKAPPTACYAGAAPAPSQVKSKAKKTVDKHSDEYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLSRELSTLRNLFKQLPEPLLASSGHC DIP protein P17676 original sequence version: 102 9B725BD6CCAA771D csn5_human_gata-site_dna-probe Human CSN5 gene promoter GATA binding site DNA probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human CAAACTTATCTCATTTAAGGTACC gata1_human Erythroid transcription factor GATA1 ERYF1 GF1 Eryf1 GATA-binding factor 1 NF-E1 DNA-binding protein protein protein human Homo sapiens Human MEFPGLGSLGTSEPLPQFVDPALVSSTPESGVFFPSGPEGLDAAASSTAPSTATAAAAALAYYRDAEAYRHSPVFQVYPLLNCMEGIPGGSPYAGWAYGKTGLYPASTVCPTREDSPPQAVEDLDGKGSTSFLETLKTERLSPDLLTLGPALPSSLPVPNSAYGGPDFSSTFFSPTGSPLNSAAYSSPKLRGTLPLPPCEARECVNCGATATPLWRRDRTGHYLCNACGLYHKMNGQNRPLIRPKKRLIVSKRAGTQCTNCQTTTTTLWRRNASGDPVCNACGLYYKLHQVNRPLTMRKDGIQTRNRKASGKGKKKRGSSLGGTGAAEGPAGGFMVVAGGSGSGNCGEVASGLTLGPPGTAHLYQGLGPVVLSGPVSHLMPFPGPLLGSPTGSFPTGPMPPTTSTTVVAPLSS DIP protein P15976 original sequence version: 163 DIP protein P15976 original sequence version: 113 DIP protein P15976 original sequence version: 146 822BD2DE14B908AD csn5_human_cebp-site_dna-probe Human CSN5 gene promoter C/EBP binding site DNA probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human CCTTACCTTTTAGTCTTTCAACAAACT csn5_human_gene COP9 signalosome complex subunit 5 (CSN5) human gene gene gene human Homo sapiens Human cebpa_human CCAAT/enhancer-binding protein alpha CEBPA CEBP protein protein human Homo sapiens Human MESADFYEAEPRPPMSSHLQSPPHAPSSAAFGFPRGAGPAQPPAPPAAPEPLGGICEHETSIDISAYIDPAAFNDEFLADLFQHSRQQEKAKAAVGPTGGGGGGDFDYPGAPAGPGGAVMPGGAHGPPPGYGCAAAGYLDGRLEPLYERVGAPALRPLVIKQEPREEDEAKQLALAGLFPYQPPPPPPPSHPHPHPPPAHLAAPHLQFQIAHCGQTTMHLQPGHPTPPPTPVPSPHPAPALGAAGLPGPGSALKGLGAAHPDLRASGGSGAGKAKKSVDKNSNEYRVRRERNNIAVRKSRDKAKQRNVETQQKVLELTSDNDRLRKRVEQLSRELDTLRGIFRQLPESSLVKAMGNCA 574C0A049E25BCAC stat3_human Signal transducer and activator of transcription 3 Acute-phase response factor STAT3 APRF protein protein human Homo sapiens Human MAQWNQLQQLDTRYLEQLHQLYSDSFPMELRQFLAPWIESQDWAYAASKESHATLVFHNLLGEIDQQYSRFLQESNVLYQHNLRRIKQFLQSRYLEKPMEIARIVARCLWEESRLLQTAATAAQQGGQANHPTAAVVTEKQQMLEQHLQDVRKRVQDLEQKMKVVENLQDDFDFNYKTLKSQGDMQDLNGNNQSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPIVQHRPMLEERIVELFRNLMKSAFVVERQPCMPMHPDRPLVIKTGVQFTTKVRLLVKFPELNYQLKIKVCIDKDSGDVAALRGSRKFNILGTNTKVMNMEESNNGSLSAEFKHLTLREQRCGNGGRANCDASLIVTEELHLITFETEVYHQGLKIDLETHSLPVVVISNICQMPNAWASILWYNMLTNNPKNVNFFTKPPIGTWDQVAEVLSWQFSSTTKRGLSIEQLTTLAEKLLGPGVNYSGCQITWAKFCKENMAGKGFSFWVWLDNIIDLVKKYILALWNEGYIMGFISKERERAILSTKPPGTFLLRFSESSKEGGVTFTWVEKDISGKTQIQSVEPYTKQQLNNMSFAEIIMGYKIMDATNILVSPLVYLYPDIPKEEAFGKYCRPESQEHPEADPGSAAPYLKTKFICVTPTTCSNTIDLPMSPRTLDSLMQFGNNGEGAEPSAGGQFESLTFDMELTSECATSPM 6C00632211C8012D DIP protein P40763 original sequence version: 157 DIP protein P40763-1 original sequence version: 147 DIP protein P40763-1 original sequence version: 135 DIP protein P40763-1 original sequence version: 157 DIP protein P40763 original sequence version: 165 DIP protein P40763 original sequence version: 182 DIP protein P40763 original sequence version: 135 6C00632211C8012D csn5-cebpb-1 2 7 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) 4 unspecified role unspecified role prey prey human-mcf7 Homo sapiens mammary carcinoma cells mcf7 mammary carcinoma cells physical association physical association Fig. 3c csn5-gata1-1 2 6 unspecified role unspecified role prey prey human-mcf7 Homo sapiens mammary carcinoma cells mcf7 mammary carcinoma cells 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 chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association Fig. 3c The sequence of the GATA-binding site probe in Fig. 3b is different from the one shown in Table 1, and neither of them matches the GATA1 site in the Jab1 promoter sequence shown in Fig. 1b. The sequence of the probe participating in this interaction was based on the GATA1 site in Fig. 1b. cebpa-csn5-1 3 9 unspecified role unspecified role bait bait 8 unspecified role unspecified role prey prey promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Fig. 4d cebpb-csn5-1 3 8 unspecified role unspecified role prey prey promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 4 unspecified role unspecified role bait bait association association Fig. 4d gata1-csn5-1 3 8 unspecified role unspecified role prey prey promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 6 unspecified role unspecified role bait bait association association Fig. 4d stat3-csn5-1 1 8 unspecified role unspecified role prey prey promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 10 unspecified role unspecified role bait bait association association Fig. 5c P21272-2 More CSN5/JAB1 promoter DNA co-precipitated with anti-Stat3 antibody from cells transfected with Rat C/EBP-beta2 (P21272-2) compared to cells transfected with empty control vector. P40763 increases expression at RNA level of ENSG00000121022 P40763 increases expression at protein level of ENSG00000121022 P21272-2 increases binding of P40763 to ENSG00000121022