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/ Inhibition of de novo NAD(+) synthesis by oncogenic URI causes liver tumorigenesis through DNA damage. Inhibition of de novo NAD(+) synthesis by oncogenic URI causes liver tumorigenesis through DNA damage. Cancer cell 2014 imex curation Tummala KS., Gomes AL., Yilmaz M., Graña O., Bakiri L., Ruppen I., Ximénez-Embún P., Sheshappanavar V., Rodriguez-Justo M., Pisano DG., Wagner EF., Djouder N. Cancer - Interactions investigated in the context of cancer Supp fig 6G is meant to show a reduction in co-loc of AHR/URI and ER/URI in mouse liver in the "mutant". But the "control" is not meant to express any URI (See Fig 1A, S1 + others) so how can you have a reduction of a non-reaction? -( not annotated) email sent 18/5/15 - regarding the fact a human cell line was used for ChIp, but BLAT results only found for Murine genome.-author replied - added a caution statement. ndjouder@cnio.es Only protein-protein interactions imex curation mouse-liver Mus musculus liver liver anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Tummala KS., Gomes AL., Yilmaz M., Graña O., Bakiri L., Ruppen I., Ximénez-Embún P., Sheshappanavar V., Rodriguez-Justo M., Pisano DG., Wagner EF., Djouder N. Cancer - Interactions investigated in the context of cancer Interactions of HSP90 cannot be entered due to lack of antibody specificity. Supp fig 6G is meant to show a reduction in co-loc of AHR/URI and ER/URI in mouse liver in the "mutant". But the "control" is not meant to express any URI (See Fig 1A, S1 + others) so how can you have a reduction of a non-reaction? -( not annotated) email sent 18/5/15 - regarding the fact a human cell line was used for ChIp, but BLAT results only found for Murine genome.-author replied - added a caution statement. ndjouder@cnio.es Accepted 2015-JUN-15 by ORCHARD Cancer cell 2014 Only protein-protein interactions imex curation imex curation I think the Bait/Prey relationships are stable Inhibition of de novo NAD(+) synthesis by oncogenic URI causes liver tumorigenesis through DNA damage. Inhibition of de novo NAD(+) synthesis by oncogenic URI causes liver tumorigenesis through DNA damage. Cancer cell 2014 imex curation Tummala KS., Gomes AL., Yilmaz M., Graña O., Bakiri L., Ruppen I., Ximénez-Embún P., Sheshappanavar V., Rodriguez-Justo M., Pisano DG., Wagner EF., Djouder N. Cancer - Interactions investigated in the context of cancer Supp fig 6G is meant to show a reduction in co-loc of AHR/URI and ER/URI in mouse liver in the "mutant". But the "control" is not meant to express any URI (See Fig 1A, S1 + others) so how can you have a reduction of a non-reaction? -( not annotated) email sent 18/5/15 - regarding the fact a human cell line was used for ChIp, but BLAT results only found for Murine genome.-author replied - added a caution statement. ndjouder@cnio.es Only protein-protein interactions imex curation mouse-aml12 MOUSE AML12- alpha mouse liver 12, hepatocyte cell line transgenic for human TGF alpha. aml12 AML 12- alpha mouse liver 12, hepatocyte cell line transgenic for human TGF alpha. http://www.lgcstandards-atcc.org/products/all/CRL-2254.aspx?geo_country=gb#generalinformation ch-ip chromatin immunoprecipitation assay ch-ip q-pcr quantitative pcr q-pcr Tummala KS., Gomes AL., Yilmaz M., Graña O., Bakiri L., Ruppen I., Ximénez-Embún P., Sheshappanavar V., Rodriguez-Justo M., Pisano DG., Wagner EF., Djouder N. Cancer - Interactions investigated in the context of cancer The cell line used is stated to be SNU-449 - a high grade Human hepatocellular carcinoma cell line. However blatting the stated primers only gives matches to Murine sequences. The authors have confirmed that the cell line used was the mouse liver cell line aml-12. Supp fig 6G is meant to show a reduction in co-loc of AHR/URI and ER/URI in mouse liver in the "mutant". But the "control" is not meant to express any URI (See Fig 1A, S1 + others) so how can you have a reduction of a non-reaction? -( not annotated) email sent 18/5/15 - regarding the fact a human cell line was used for ChIp, but BLAT results only found for Murine genome.-author replied - added a caution statement. ndjouder@cnio.es Accepted 2015-JUN-15 by ORCHARD Cancer cell 2014 Only protein-protein interactions imex curation imex curation I think the Bait/Prey relationships are stable pp1g_mouse Serine/threonine-protein phosphatase PP1-gamma catalytic subunit Ppp1cc Protein phosphatase 1C catalytic subunit protein protein mouse Mus musculus Mouse MADIDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAEKKKPNATRPVTPPRGMITKQAKK 4E28412C16898615 ahr_mouse Aryl hydrocarbon receptor Ahr protein protein mouse Mus musculus Mouse MSSGANITYASRKRRKPVQKTVKPIPAEGIKSNPSKRHRDRLNTELDRLASLLPFPQDVINKLDKLSVLRLSVSYLRAKSFFDVALKSTPADRNGGQDQCRAQIRDWQDLQEGEFLLQALNGFVLVVTADALVFYASSTIQDYLGFQQSDVIHQSVYELIHTEDRAEFQRQLHWALNPDSAQGVDEAHGPPQAAVYYTPDQLPPENASFMERCFRCRLRCLLDNSSGFLAMNFQGRLKYLHGQNKKGKDGALLPPQLALFAIATPLQPPSILEIRTKNFIFRTKHKLDFTPIGCDAKGQLILGYTEVELCTRGSGYQFIHAADMLHCAESHIRMIKTGESGMTVFRLFAKHSRWRWVQSNARLIYRNGRPDYIIATQRPLTDEEGREHLQKRSTSLPFMFATGEAVLYEISSPFSPIMDPLPIRTKSNTSRKDWAPQSTPSKDSFHPSSLMSALIQQDESIYLCPPSSPAPLDSHFLMGSVSKCGSWQDSFAAAGSEAALKHEQIGHAQDVNLALSGGPSELFPDNKNNDLYNIMRNLGIDFEDIRSMQNEEFFRTDSTAAGEVDFKDIDITDEILTYVQDSLNNSTLMNSACQQQPVTQHLSCMLQERLQLEQQQQLQQPPPQALEPQQQLCQMVCPQQDLGPKHTQINGTFASWNPTPPVSFNCPQQELKHYQLFSSLQGTAQEFPYKPEVDSVPYTQNFAPCNQPLLPEHSKSVQLDFPGRDFEPSLHPTTSNLDFVSCLQVPENQSHGINSQSTMVSPQAYYAGAMSMYQCQPGPQRTPVDQTQYSSEIPGSQAFLSKVQSRGIFNETYSSDLSSIGHAAQTTGHLHHLAEARPLPDITPGGFL DIP protein P30561 original sequence version: 90 DIP protein P30561 original sequence version: 94 AA1560FA83DDD03C rmp_human Unconventional prefoldin RPB5 interactor 1 URI1 C19orf2 NNX3 PPP1R19 Protein NNX3 Protein phosphatase 1 regulatory subunit 19 RMP RNA polymerase II subunit 5-mediating protein URI protein protein human Homo sapiens Human MEAPTVETPPDPSPPSAPAPALVPLRAPDVARLREEQEKVVTNCQERIQHWKKVDNDYNALRERLSTLPDKLSYNIMVPFGPFAFMPGKLVHTNEVTVLLGDNWFAKCSAKQAVGLVEHRKEHVRKTIDDLKKVMKNFESRVEFTEDLQKMSDAAGDIVDIREEIKCDFEFKAKHRIAHKPHSKPKTSDIFEADIANDVKSKDLLADKELWARLEELERQEELLGELDSKPDTVIANGEDTTSSEEEKEDRNTNVNAMHQVTDSHTPCHKDVASSEPFSGQVNSQLNCSVNGSSSYHSDDDDDDDDDDDDDNIDDDDGDNDHEALGVGDNSIPTIYFSHTVEPKRVRINTGKNTTLKFSEKKEEAKRKRKNSTGSGHSAQELPTIRTPADIYRAFVDVVNGEYVPRKSILKSRSRENSVCSDTSESSAAEFDDRRGVLRSISCEEATCSDTSESILEEEPQENQKKLLPLSVTPEAFSGTVIEKEFVSPSLTPPPAIAHPALPTIPERKEVLLEASEETGKRVSKFKAARLQQKD DBB046A392E3C752 esr1_mouse Estrogen receptor Esr1 Esr Estr Estra Nr3a1 Estradiol receptor ER-alpha Nuclear receptor subfamily 3 group A member 1 protein protein mouse Mus musculus Mouse MTMTLHTKASGMALLHQIQGNELEPLNRPQLKMPMERALGEVYVDNSKPTVFNYPEGAAYEFNAAAAAAAAASAPVYGQSGIAYGPGSEAAAFSANSLGAFPQLNSVSPSPLMLLHPPPQLSPFLHPHGQQVPYYLENEPSAYAVRDTGPPAFYRSNSDNRRQNGRERLSSSNEKGNMIMESAKETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRRGGRMLKHKRQRDDLEGRNEMGASGDMRAANLWPSPLVIKHTKKNSPALSLTADQMVSALLDAEPPMIYSEYDPSRPFSEASMMGLLTNLADRELVHMINWAKRVPGFGDLNLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHRRLAQLLLILSHIRHMSNKGMEHLYNMKCKNVVPLYDLLLEMLDAHRLHAPASRMGVPPEEPSQTQLATTSSTSAHSLQTYYIPPEAEGFPNTI 05F5E2FC21CC0A8B t23o_mouse_gene Tryptophan 2,3-dioxygenase Tdo2 Tdo gene gene mouse Mus musculus Mouse kfa_mouse_gene Kynurenine formamidase Afmid gene gene mouse Mus musculus Mouse uri1-ahr-2 1 4 unspecified role unspecified role prey prey 5 unspecified role unspecified role bait bait N/A flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range 6 unspecified role unspecified role prey prey association association 6C uri1-ahr-3 1 4 unspecified role unspecified role bait bait 5 unspecified role unspecified role prey prey N/A flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range physical association physical association 6Cii uri1-esr1-1 1 6 unspecified role unspecified role bait bait 5 unspecified role unspecified role prey prey N/A flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range physical association physical association 6Ciii ppp1cc-uri1-1 1 3 unspecified role unspecified role bait bait 5 unspecified role unspecified role prey prey N/A flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range physical association physical association Supp 4B ahr-tdo2-1 2 4 unspecified role unspecified role bait bait 7 unspecified role unspecified role prey prey N/A sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Supp 6C binding was observed at the proximal promoter region. afmid-tdo2-1 2 4 unspecified role unspecified role bait bait 8 unspecified role unspecified role prey prey N/A sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Supp 6Ci Binding was observed at promoter regions -2kb and -1.3 kb from the TSS. ahr-tdo2-2 2 6 unspecified role unspecified role bait bait 7 unspecified role unspecified role prey prey N/A sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Supp 6D Binding was observed at a promoter region -2.4kb from the TSS. ahr-afmid-1 2 6 unspecified role unspecified role bait bait 8 unspecified role unspecified role prey prey N/A sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Supp 6D Binding was observed at a region -4.8 kb from the TSS.