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/ http://www.ebi.ac.uk/ wang-2004h-1 Binding at and transactivation of the COX-2 promoter by nuclear tyrosine kinase receptor ErbB-2. human-bt474 Homo sapiens breast ductal carcinoma cell line bt474 Human breast ductal carcinoma cell line BT474 Human breast ductal carcinoma cell line established from a solid, invasive ductal carcinoma of the breast obtained from a 60-year-old woman. ch-ip chromatin immunoprecipitation assay ch-ip nucleotide sequence nucleotide sequence identification sequence cloning sequence cloning nucleotide sequence Wang S.C., Lien H.C., Xia W., Chen I.F., Lo H.W., Wang Z., Ali-Seyed M., Lee D.F., Bartholomeusz G., Ou-Yang F., Giri D.K., Hung M.C. Cancer - Interactions investigated in the context of cancer DNA fragments associated with ErbB-2 were processed, cloned, and identified by sequencing. Figure S8A has not been added as the cell line used is not stated. mhung@mdanderson.org Cancer Cell (1535-6108) 2004 mimix curation wang-2004h-5 Binding at and transactivation of the COX-2 promoter by nuclear tyrosine kinase receptor ErbB-2. human-mcf7 Homo sapiens mammary carcinoma cells mcf7 mammary carcinoma cells ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Wang S.C., Lien H.C., Xia W., Chen I.F., Lo H.W., Wang Z., Ali-Seyed M., Lee D.F., Bartholomeusz G., Ou-Yang F., Giri D.K., Hung M.C. Cancer - Interactions investigated in the context of cancer DNA fragments associated with ErbB-2 were processed, cloned, and identified by sequencing. Figure S8A has not been added as the cell line used is not stated. mhung@mdanderson.org Cancer Cell (1535-6108) 2004 mimix curation wang-2004h-2 Binding at and transactivation of the COX-2 promoter by nuclear tyrosine kinase receptor ErbB-2. human-skbr3 Homo sapiens SKBR3 skbr3 SKBR3 Species: human; Tissue: breast; Tumor: adenocarcinoma; Derived from: metastatic site: pleural effusion ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Wang S.C., Lien H.C., Xia W., Chen I.F., Lo H.W., Wang Z., Ali-Seyed M., Lee D.F., Bartholomeusz G., Ou-Yang F., Giri D.K., Hung M.C. Cancer - Interactions investigated in the context of cancer DNA fragments associated with ErbB-2 were processed, cloned, and identified by sequencing. Figure S8A has not been added as the cell line used is not stated. mhung@mdanderson.org Cancer Cell (1535-6108) 2004 mimix curation wang-2004h-3 Binding at and transactivation of the COX-2 promoter by nuclear tyrosine kinase receptor ErbB-2. human-bt474 Homo sapiens breast ductal carcinoma cell line bt474 Human breast ductal carcinoma cell line BT474 Human breast ductal carcinoma cell line established from a solid, invasive ductal carcinoma of the breast obtained from a 60-year-old woman. ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Wang S.C., Lien H.C., Xia W., Chen I.F., Lo H.W., Wang Z., Ali-Seyed M., Lee D.F., Bartholomeusz G., Ou-Yang F., Giri D.K., Hung M.C. Cancer - Interactions investigated in the context of cancer DNA fragments associated with ErbB-2 were processed, cloned, and identified by sequencing. Figure S8A has not been added as the cell line used is not stated. mhung@mdanderson.org Cancer Cell (1535-6108) 2004 mimix curation wang-2004h-4 Binding at and transactivation of the COX-2 promoter by nuclear tyrosine kinase receptor ErbB-2. human-skov_3 Homo sapiens ovarian adenocarcinoma cell line skov_3 Human ovarian adenocarcinoma cell line Derived from the ascitic fluid from a 64 year old caucasian female with an ovarian tumour. Forms moderately well-differentiated adenocarcinoma consistent with ovarian primary cells. ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Wang S.C., Lien H.C., Xia W., Chen I.F., Lo H.W., Wang Z., Ali-Seyed M., Lee D.F., Bartholomeusz G., Ou-Yang F., Giri D.K., Hung M.C. Cancer - Interactions investigated in the context of cancer DNA fragments associated with ErbB-2 were processed, cloned, and identified by sequencing. Figure S8A has not been added as the cell line used is not stated. mhung@mdanderson.org Cancer Cell (1535-6108) 2004 mimix curation wang-2004h-6 Binding at and transactivation of the COX-2 promoter by nuclear tyrosine kinase receptor ErbB-2. in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Wang S.C., Lien H.C., Xia W., Chen I.F., Lo H.W., Wang Z., Ali-Seyed M., Lee D.F., Bartholomeusz G., Ou-Yang F., Giri D.K., Hung M.C. Cancer - Interactions investigated in the context of cancer DNA fragments associated with ErbB-2 were processed, cloned, and identified by sequencing. Figure S8A has not been added as the cell line used is not stated. mhung@mdanderson.org Cancer Cell (1535-6108) 2004 mimix curation wang-2004h-7 Binding at and transactivation of the COX-2 promoter by nuclear tyrosine kinase receptor ErbB-2. human-hct116 Human colon carcinoma HCT116 cells hct116 Human colon carcinoma line HCT116 ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Wang S.C., Lien H.C., Xia W., Chen I.F., Lo H.W., Wang Z., Ali-Seyed M., Lee D.F., Bartholomeusz G., Ou-Yang F., Giri D.K., Hung M.C. Cancer - Interactions investigated in the context of cancer DNA fragments associated with ErbB-2 were processed, cloned, and identified by sequencing. Figure S8A has not been added as the cell line used is not stated. mhung@mdanderson.org Cancer Cell (1535-6108) 2004 mimix curation wang-2004h-8 Binding at and transactivation of the COX-2 promoter by nuclear tyrosine kinase receptor ErbB-2. in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Wang S.C., Lien H.C., Xia W., Chen I.F., Lo H.W., Wang Z., Ali-Seyed M., Lee D.F., Bartholomeusz G., Ou-Yang F., Giri D.K., Hung M.C. Cancer - Interactions investigated in the context of cancer DNA fragments associated with ErbB-2 were processed, cloned, and identified by sequencing. Figure S8A has not been added as the cell line used is not stated. mhung@mdanderson.org Cancer Cell (1535-6108) 2004 mimix curation wang-2004h-9 Binding at and transactivation of the COX-2 promoter by nuclear tyrosine kinase receptor ErbB-2. human-breast_cancer Homo sapiens breast cancer tissue breast_cancer Breast cancer tissue ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Wang S.C., Lien H.C., Xia W., Chen I.F., Lo H.W., Wang Z., Ali-Seyed M., Lee D.F., Bartholomeusz G., Ou-Yang F., Giri D.K., Hung M.C. Cancer - Interactions investigated in the context of cancer DNA fragments associated with ErbB-2 were processed, cloned, and identified by sequencing. Figure S8A has not been added as the cell line used is not stated. mhung@mdanderson.org Cancer Cell (1535-6108) 2004 mimix curation pgh2_human_gene PTGS2/COX2/Prostaglandin G/H synthase 2 gene gene human Homo sapiens Human erbb2_human Receptor tyrosine-protein kinase erbB-2 p185erbB2 MLN19 Proto-oncogene c-ErbB-2 Tyrosine kinase-type cell surface receptor HER2 Proto-oncogene Neu ERBB2 HER2 NEU NGL Metastatic lymph node gene 19 protein protein protein human Homo sapiens Human MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHRHRSSSTRSGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAKGLQSLPTHDPSPLQRYSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLGLDVPV prpk_human_gene TP53RK/PRPK Human gene gene gene human Homo sapiens Human mmp16_human_gene MMP16 HUMAN GENE gene gene human Homo sapiens Human ddx10_human_gene DDX10 HUMAN GENE gene gene human Homo sapiens Human tff1_human_gene PS2/TFFI HUMAN GENE gene gene human Homo sapiens Human esr1_human Estrogen receptor ESR1 ESR NR3A1 Estradiol receptor ER-alpha Nuclear receptor subfamily 3 group A member 1 protein protein human Homo sapiens Human MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANAQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLENEPSGYTVREAGPPAFYRPNSDNRRQGGRERLASTNDKGSMAMESAKETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRRGGRMLKHKRQRDDGEGRGEVGSAGDMRAANLWPSPLMIKRSKKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAPTSRGGASVEETDQSHLATAGSTSSHSLQKYYITGEAEGFPATV has_oligonucleotide_probe(cox2/ptgs2_promoter) HER-2-Associated Qequence -from COX2/PTGS2 promoter dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human ATAAACTTCAAATTTCAGTA erbb2-pgh2 1272106 n/a 1272115 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 false promoter_region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1272116 unspecified role unspecified role bait bait association association false false false S2A/2A The sequence was named "HER-2-associated sequence (HAS)", and is located 1750 nucleotides upstream from the transcriptional start site in this gene. erbb2-prpk 1272106 n/a 1272117 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 false n/a 1272116 unspecified role unspecified role bait bait association association false false false S2A/2A The sequence was named "HER-2-associated sequence (HAS)", and is located 1750 nucleotides upstream from the transcriptional start site in this gene. erbb2-mmp16 1272106 n/a 1272118 unspecified role unspecified role prey prey intron_1 binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1272116 unspecified role unspecified role bait bait association association false false false S2A/2A The sequence was named "HER-2-associated sequence (HAS)", and is located 1750 nucleotides upstream from the transcriptional start site in this gene. erbb2-ddx10 1272106 n/a 1272119 unspecified role unspecified role prey prey intron_4 binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1272116 unspecified role unspecified role bait bait association association false false false S2A/2A The sequence was named "HER-2-associated sequence (HAS)", and is located 1750 nucleotides upstream from the transcriptional start site in this gene. erbb2-pgh2-4 1272107 n/a 1272115 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 false n/a 1272116 unspecified role unspecified role bait bait P04626:p.Lys753Met mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate range range range range false association association false false false 2D, 2G, 3A, 3B, S3B. Herceptin, tyrosine kinase inhibitor AG825. The ERBB2 kinase-dead mutant has been entered as K753M, but this is not stated in this paper. er1-ps2 1272107 n/a 1272120 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 false n/a 1272121 unspecified role unspecified role bait bait association association false false false 2D The estrogen receptor was recruited to the pS2 promoter, a documented target of ER. erbb2-pgh2-1 1272108 n/a 1272116 unspecified role unspecified role bait bait n/a 1272115 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 false association association false false false 2C erbb2-pgh2-2 1272109 n/a 1272115 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 false n/a 1272116 unspecified role unspecified role bait bait association association false false false 2C erbb2-pgh2-3 1272110 n/a 1272115 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 false n/a 1272116 unspecified role unspecified role bait bait association association false false false 2C erbb2-has 1272111 n/a 1272122 unspecified role unspecified role bait bait tcaaatttc_sequence required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1272116 unspecified role unspecified role prey prey human-mcf7_her2 Human MCF7 cells overexpressing HER2 mcf7_her2 MCF7 cells overexpressing HER2 physical association physical association false false false 2H, 4C-E. Table 1. Radiolabeled HAS oligonucleotide formed a specific complex with nuclear ErbB-2, which was abolished by cold HAS, core oligonucleotides or anti-ErbB-2 antibodies. erbb2-pgh2-6 1272112 n/a 1272116 unspecified role unspecified role bait bait n/a 1272115 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 false association association false false false S3A has-erbb2 1272113 n/a 1272122 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 false tcaaatttc_sequence required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1272116 unspecified role unspecified role prey prey human-mcf7_her2 Human MCF7 cells overexpressing HER2 mcf7_her2 MCF7 cells overexpressing HER2 physical association physical association false false false 4F mutant (ATAAACTGACCCGGGAAGTA) HAS showed greatly reduced binding to ERBB2. erbb2-pgh2-7 1272114 n/a 1272116 unspecified role unspecified role bait bait n/a 1272115 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 false association association false false false 6B