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/ Human CYP2C8 is transcriptionally regulated by the nuclear receptors constitutive androstane receptor, pregnane X receptor, glucocorticoid receptor, and hepatic nuclear factor 4alpha. Human CYP2C8 is transcriptionally regulated by the nuclear receptors constitutive androstane receptor, pregnane X receptor, glucocorticoid receptor, and hepatic nuclear factor 4alpha. Mol. Pharmacol. (0026-895X) 2005 imex curation Ferguson S.S., Chen Y., LeCluyse E.L., Negishi M., Goldstein J.A. Ulcerative colitis - Interactions of proteins identified as having a link to ulcerative colitis IBD - Inflammatory bowel disease There's causality statements about CAR and PXR affecting CYP2C9 RNA expression (Fig. 3/6), and RXR affecting binding of CAR and PXR to CYP2C8 and CYP2C9 DNA (and vice versa) (Fig. 2/5), which can be added to interactions in the emsa experiment; however, I wasn't sure if these interactions meet the conditions to allow annotating causalities, as there are two prey proteins? The molecule "RXR" has been entered as RXRA, as this was the molecule detected in figure 5. It has been assumed to have been used elsewhere in this publication. goldste1@niehs.nih.gov 22-Jan-2015: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa autoradiography autoradiography Ferguson S.S., Chen Y., LeCluyse E.L., Negishi M., Goldstein J.A. Ulcerative colitis - Interactions of proteins identified as having a link to ulcerative colitis There's causality statements about CAR and PXR affecting CYP2C9 RNA expression (Fig. 3/6), and RXR affecting binding of CAR and PXR to CYP2C8 and CYP2C9 DNA (and vice versa) (Fig. 2/5), which can be added to interactions in the emsa experiment; however, I wasn't sure if these interactions meet the conditions to allow annotating causalities, as there are two prey proteins? The molecule "RXR" has been entered as RXRA, as this was the molecule detected in figure 5. It has been assumed to have been used elsewhere in this publication. goldste1@niehs.nih.gov Accepted 2015-JAN-19 by MGT Mol. Pharmacol. (0026-895X) 2005 Only protein-protein interactions imex curation Human CYP2C8 is transcriptionally regulated by the nuclear receptors constitutive androstane receptor, pregnane X receptor, glucocorticoid receptor, and hepatic nuclear factor 4alpha. Human CYP2C8 is transcriptionally regulated by the nuclear receptors constitutive androstane receptor, pregnane X receptor, glucocorticoid receptor, and hepatic nuclear factor 4alpha. Mol. Pharmacol. (0026-895X) 2005 imex curation Ferguson S.S., Chen Y., LeCluyse E.L., Negishi M., Goldstein J.A. Ulcerative colitis - Interactions of proteins identified as having a link to ulcerative colitis IBD - Inflammatory bowel disease There's causality statements about CAR and PXR affecting CYP2C9 RNA expression (Fig. 3/6), and RXR affecting binding of CAR and PXR to CYP2C8 and CYP2C9 DNA (and vice versa) (Fig. 2/5), which can be added to interactions in the emsa experiment; however, I wasn't sure if these interactions meet the conditions to allow annotating causalities, as there are two prey proteins? The molecule "RXR" has been entered as RXRA, as this was the molecule detected in figure 5. It has been assumed to have been used elsewhere in this publication. goldste1@niehs.nih.gov 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 Ferguson S.S., Chen Y., LeCluyse E.L., Negishi M., Goldstein J.A. Ulcerative colitis - Interactions of proteins identified as having a link to ulcerative colitis There's causality statements about CAR and PXR affecting CYP2C9 RNA expression (Fig. 3/6), and RXR affecting binding of CAR and PXR to CYP2C8 and CYP2C9 DNA (and vice versa) (Fig. 2/5), which can be added to interactions in the emsa experiment; however, I wasn't sure if these interactions meet the conditions to allow annotating causalities, as there are two prey proteins? The molecule "RXR" has been entered as RXRA, as this was the molecule detected in figure 5. It has been assumed to have been used elsewhere in this publication. goldste1@niehs.nih.gov Accepted 2015-JAN-19 by MGT Mol. Pharmacol. (0026-895X) 2005 Only protein-protein interactions imex curation cp2c8_human_hnf4a-site_dna-probe Human CP2C8 gene promoter HNF4-alpha binding site (-154) DNA probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human CATGGGCCAAAGTCCACTC nr1i2_human Nuclear receptor subfamily 1 group I member 2 NR1I2 PXR Orphan nuclear receptor PAR1 Orphan nuclear receptor PXR Pregnane X receptor Steroid and xenobiotic receptor protein protein human Homo sapiens Human MEVRPKESWNHADFVHCEDTESVPGKPSVNADEEVGGPQICRVCGDKATGYHFNVMTCEGCKGFFRRAMKRNARLRCPFRKGACEITRKTRRQCQACRLRKCLESGMKKEMIMSDEAVEERRALIKRKKSERTGTQPLGVQGLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGITGS 1DF6A2AE3109C4DA cp2c9_human_car-re_dna-probe Human CP2C9 gene promoter CAR response element proximal/-1839 DNA probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human AACCAAACTCTTCTGACCTCTC hnf4a_human Hepatocyte nuclear factor 4-alpha Transcription factor HNF-4 Nuclear receptor subfamily 2 group A member 1 Transcription factor 14 HNF4A HNF4 NR2A1 TCF14 protein protein human Homo sapiens Human MRLSKTLVDMDMADYSAALDPAYTTLEFENVQVLTMGNDTSPSEGTNLNAPNSLGVSALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERDRISTRRSSYEDSSLPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGGSPSDAPHAHHPLHPHLMQEHMGTNVIVANTMPTHLSNGQMCEWPRPRGQAATPETPQPSPPGGSGSEPYKLLPGAVATIVKPLSAIPQPTITKQEVI 5F1309B89D95DCAF cp2c8_human_dr5-site_dna-probe Human CP2C8 gene promoter proximal/-2796 DR-5 element DNA probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human AGTAAACCCTATGTGAACTTC rxra_human Retinoic acid receptor RXR-alpha RXRA NR2B1 Retinoid X receptor alpha Nuclear receptor subfamily 2 group B member 1 protein protein human Homo sapiens Human MDTKHFLPLDFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQMT DIP protein P19793 original sequence version: 177 DIP protein P19793 original sequence version: 107 DIP protein P19793 original sequence version: 153 DIP protein P19793 original sequence version: 131 DIP protein P19793 original sequence version: 136 DIP protein P19793 original sequence version: 169 DIP protein P19793 original sequence version: 161 DIP protein P19793 original sequence version: 139 7F952B580AD84C42 cp2c8_human_dr4-site_dna-probe Human CP2C8 gene promoter distal/-8806 DR-4 element DNA probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human AGTCAACTTTGATGACCCCA nr1i3_human Nuclear receptor subfamily 1 group I member 3 NR1I3 CAR Constitutive androstane receptor Constitutive activator of retinoid response Orphan nuclear receptor MB67 protein protein human Homo sapiens Human MASREDELRNCVVCGDQATGYHFNALTCEGCKGFFRRTVSKSIGPTCPFAGSCEVSKTQRRHCPACRLQKCLDAGMRKDMILSAEALALRRAKQAQRRAQQTPVQLSKEQEELIRTLLGAHTRHMGTMFEQFVQFRPPAHLFIHHQPLPTLAPVLPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQNFLCGPLRYTIEDGARVSPTVGFQVEFLELLFHFHGTLRKLQLQEPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGYQIQHIQGLSAMMPLLQEICS 73B060FE4950D519 cp2c8-rxra 2 8 unspecified role unspecified role prey prey in vitro In vitro 7 unspecified role unspecified role bait bait dctp 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. 5 cp2c8-rxra-1 2 9 unspecified role unspecified role bait bait dctp 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 in vitro In vitro physical association physical association Fig. 5 cp2c8-hnf4a 2 6 unspecified role unspecified role prey prey in vitro In vitro 3 unspecified role unspecified role bait bait dctp 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. 10a P41235 increases expression at RNA level of ENSG00000138115 cp2c8-hnf4a-1 1 6 unspecified role unspecified role prey prey in vitro In vitro 3 unspecified role unspecified role bait bait dctp 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. 10a cp2c8-cp2c8 1 6 unspecified role unspecified role prey prey in vitro In vitro 3 unspecified role unspecified role bait bait dctp 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 3 competitor competitor competitor prey prey c8g_a9t_a10t_a11t_g12c_t13a mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) association association Fig. 10a cp2c8-nr1i3 1 10 unspecified role unspecified role prey prey in vitro In vitro 9 unspecified role unspecified role bait bait dctp 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 in vitro In vitro association association Fig. 4, 5 cp2c8-cp2c8-1 1 10 unspecified role unspecified role prey prey in vitro In vitro 8 unspecified role unspecified role prey prey in vitro In vitro 9 competitor competitor competitor prey prey chemical synthesis Chemical synthesis (Chemical synthesis) 9 unspecified role unspecified role bait bait dctp 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) association association Fig. 4, 5 cp2c8-cp2c8-2 1 4 unspecified role unspecified role prey prey in vitro In vitro 8 unspecified role unspecified role prey prey in vitro In vitro 9 competitor competitor competitor prey prey chemical synthesis Chemical synthesis (Chemical synthesis) 9 unspecified role unspecified role bait bait dctp 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) association association Fig. 4, 5 cp2c8-nr1i2 1 9 unspecified role unspecified role bait bait dctp 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 in vitro In vitro 4 unspecified role unspecified role prey prey in vitro In vitro association association Fig. 4, 5 cp2c8-nr1i2-1 1 4 unspecified role unspecified role prey prey in vitro In vitro 7 unspecified role unspecified role bait bait dctp 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 in vitro In vitro association association Fig. 5 cp2c8-cp2c8-3 1 7 unspecified role unspecified role bait bait dctp 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 in vitro In vitro 7 competitor competitor competitor prey prey chemical synthesis Chemical synthesis (Chemical synthesis) 4 unspecified role unspecified role prey prey in vitro In vitro association association Fig. 5 cp2c8-cp2c8-4 1 10 unspecified role unspecified role prey prey in vitro In vitro 8 unspecified role unspecified role prey prey in vitro In vitro 7 unspecified role unspecified role bait bait dctp 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 7 competitor competitor competitor prey prey chemical synthesis Chemical synthesis (Chemical synthesis) association association Fig. 5 cp2c8-nr1i3-1 1 10 unspecified role unspecified role prey prey in vitro In vitro 7 unspecified role unspecified role bait bait dctp 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 in vitro In vitro association association Fig. 5 cp2c9-nr1i3 1 10 unspecified role unspecified role prey prey in vitro In vitro 5 unspecified role unspecified role bait bait dctp 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 in vitro In vitro association association Fig. 2 cp2c9-cp2c9-2 1 10 unspecified role unspecified role prey prey in vitro In vitro 8 unspecified role unspecified role prey prey in vitro In vitro 5 competitor competitor competitor prey prey chemical synthesis Chemical synthesis (Chemical synthesis) 5 unspecified role unspecified role bait bait dctp 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) association association Fig. 2 cp2c9-cp2c9-3 1 8 unspecified role unspecified role prey prey in vitro In vitro 4 unspecified role unspecified role prey prey in vitro In vitro 5 unspecified role unspecified role bait bait dctp 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 5 competitor competitor competitor prey prey chemical synthesis Chemical synthesis (Chemical synthesis) association association Fig. 2 cp2c9-nr1i2 1 5 unspecified role unspecified role bait bait dctp 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 in vitro In vitro 8 unspecified role unspecified role prey prey in vitro In vitro association association Fig. 2