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/ NEMO and RIP1 control cell fate in response to extensive DNA damage via TNF-α feedforward signaling. NEMO and RIP1 control cell fate in response to extensive DNA damage via TNF-α feedforward signaling. Cell (0092-8674) 2011 imex curation Biton S., Ashkenazi A. Apoptosis - Interactions involving proteins with a function related to apoptosis aa@gene.com 26-Sep-2011: Contacted by JYOTI. mgt Only protein-protein interactions human-rko Homo sapiens colorectal carcinoma cell line rko Human colorectal carcinoma cell line anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Biton S., Ashkenazi A. Apoptosis - Interactions involving proteins with a function related to apoptosis Rejected 2011-JUL-06 by MGT. Could not the Caspase-8 assays have been included? - (Caspase/enzyme Assay) - according to supplier the assay is specific(ish) for Caspase 8...There are several of these assays. Fig 1E appears to have been omitted from EBI-3955536, also figs 1G, 3D, 3H, S5N EBI-3955381:- omitted figs = Fig 1H, 2I, S2A, 3E, 3I, (S4H - but there is no label for IP-ing antibody), S5H, S5J, EBI-3955376:- has Fig1I entered here - but bait and prey are the wrong way round, though correct for fig S1D. Fig S2C- has an interaction using (2) extra cell line (s) other than HeLa- not added, same for S2F, S5F aa@gene.com Accepted 2011-JUL-20 by MGT 26-Sep-2011: Contacted by JYOTI. Cell (0092-8674) 2011 mgt Only protein-protein interactions imex curation NEMO and RIP1 control cell fate in response to extensive DNA damage via TNF-α feedforward signaling. NEMO and RIP1 control cell fate in response to extensive DNA damage via TNF-α feedforward signaling. Cell (0092-8674) 2011 imex curation Biton S., Ashkenazi A. Apoptosis - Interactions involving proteins with a function related to apoptosis aa@gene.com 26-Sep-2011: Contacted by JYOTI. mgt Only protein-protein interactions human-mda_mb_435 Human cell line derived from the M14 melanoma cell line mda_mb_435 Human cell line derived from the M14 melanoma cell line This cell line is now thought to be derived from the M14 melanoma cell line. This cell line was originally thought to be a Human epithelial breast cancer cell line. see pmid: 17004106 anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Biton S., Ashkenazi A. Apoptosis - Interactions involving proteins with a function related to apoptosis aa@gene.com Accepted 2011-JUL-20 by MGT 26-Sep-2011: Contacted by JYOTI. Cell (0092-8674) 2011 mgt Only protein-protein interactions imex curation NEMO and RIP1 control cell fate in response to extensive DNA damage via TNF-α feedforward signaling. NEMO and RIP1 control cell fate in response to extensive DNA damage via TNF-α feedforward signaling. Cell (0092-8674) 2011 imex curation Biton S., Ashkenazi A. Apoptosis - Interactions involving proteins with a function related to apoptosis aa@gene.com 26-Sep-2011: Contacted by JYOTI. mgt Only protein-protein interactions human-hela Homo sapiens epitheloid cervix carcinoma cells Human hela Human epitheloid cervix carcinoma HeLa cells derivation: cervix; epithelial; adenocarcinoma ATCC no:CCL-2 anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Biton S., Ashkenazi A. Apoptosis - Interactions involving proteins with a function related to apoptosis Rejected 2011-JUL-06 by MGT. Could not the Caspase-8 assays have been included? - (Caspase/enzyme Assay) - according to supplier the assay is specific(ish) for Caspase 8...There are several of these assays. Fig 1E appears to have been omitted from EBI-3955536, also figs 1G, 3D, 3H, S5N EBI-3955381:- omitted figs = Fig 1H, 2I, S2A, 3E, 3I, (S4H - but there is no label for IP-ing antibody), S5H, S5J, EBI-3955376:- has Fig1I entered here - but bait and prey are the wrong way round, though correct for fig S1D. Fig S2C- has an interaction using (2) extra cell line (s) other than HeLa- not added, same for S2F, S5F aa@gene.com Accepted 2011-JUL-20 by MGT 26-Sep-2011: Contacted by JYOTI. Cell (0092-8674) 2011 mgt Only protein-protein interactions imex curation NEMO and RIP1 control cell fate in response to extensive DNA damage via TNF-α feedforward signaling. NEMO and RIP1 control cell fate in response to extensive DNA damage via TNF-α feedforward signaling. Cell (0092-8674) 2011 imex curation Biton S., Ashkenazi A. Apoptosis - Interactions involving proteins with a function related to apoptosis aa@gene.com 26-Sep-2011: Contacted by JYOTI. mgt Only protein-protein interactions human-mda_mb_231 Homo sapiens Caucasian breast adenocarcinoma mda_mb_231 Human Caucasian breast adenocarcinoma anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Biton S., Ashkenazi A. Apoptosis - Interactions involving proteins with a function related to apoptosis aa@gene.com Accepted 2011-JUL-20 by MGT 26-Sep-2011: Contacted by JYOTI. Cell (0092-8674) 2011 mgt Only protein-protein interactions imex curation fadd_human FAS-associated death domain protein FAS-associating death domain-containing protein Mediator of receptor induced toxicity FADD MORT1 GIG3 Growth-inhibiting gene 3 protein protein protein human Homo sapiens Human MDPFLVLLHSVSSSLSSSELTELKFLCLGRVGKRKLERVQSGLDLFSMLLEQNDLEPGHTELLRELLASLRRHDLLRRVDDFEAGAAAGAAPGEEDLCAAFNVICDNVGKDWRRLARQLKVSDTKIDSIEDRYPRNLTERVRESLRIWKNTEKENATVAHLVGALRSCQMNLVADLVQEVQQARDLQNRSGAMSPMSWNSDASTSEAS DIP protein Q13158 original sequence version: 155 DIP protein Q13158 original sequence version: 130 DIP protein Q13158 original sequence version: 110 DIP protein Q13158 original sequence version: 118 DIP protein Q13158 original sequence version: 141 DIP protein Q13158 original sequence version: 166 0E65E2F852E83507 nemo_human NF-kappa-B essential modulator IKBKG FIP3 NEMO NF-kappa-B essential modifier Inhibitor of nuclear factor kappa-B kinase subunit gamma IkB kinase-associated protein 1 FIP-3 protein protein human Homo sapiens Human MNRHLWKSQLCEMVQPSGGPAADQDVLGEESPLGKPAMLHLPSEQGAPETLQRCLEENQELRDAIRQSNQILRERCEELLHFQASQREEKEFLMCKFQEARKLVERLGLEKLDLKRQKEQALREVEHLKRCQQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEGRARAASEQARQLESEREALQQQHSVQVDQLRMQGQSVEAALRMERQAASEEKRKLAQLQVAYHQLFQEYDNHIKSSVVGSERKRGMQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQREYSKLKASCQESARIEDMRKRHVEVSQAPLPPAPAYLSSPLALPSQRRSPPEEPPDFCCPKCQYQAPDMDTLQIHVMECIE DIP protein Q9Y6K9 original sequence version: 85 DIP protein Q9Y6K9 original sequence version: 118 DIP protein Q9Y6K9 original sequence version: 123 DIP protein Q9Y6K9 original sequence version: 141 DIP protein Q9Y6K9 original sequence version: 125 DIP protein Q9Y6K9 original sequence version: 156 DIP protein Q9Y6K9 original sequence version: 83 DIP protein Q9Y6K9 original sequence version: 132 DIP protein Q9Y6K9 original sequence version: 124 DIP protein Q9Y6K9 original sequence version: 90 322D1037881447FF ripk1_human Receptor-interacting serine/threonine-protein kinase 1 RIPK1 RIP Cell death protein RIP RIP1 Receptor-interacting protein 1 protein protein human Homo sapiens Human MQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLCFHRTQGLMIMKTVYKGPNCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIILEIIEGMCYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELREVDGTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAICEQQLIMCIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLEESVEEDVKSLKKEYSNENAVVKRMQSLQLDCVAVPSSRSNSATEQPGSLHSSQGLGMGPVEESWFAPSLEHPQEENEPSLQSKLQDEANYHLYGSRMDRQTKQQPRQNVAYNREEERRRRVSHDPFAQQRPYENFQNTEGKGTAYSSAASHGNAVHQPSGLTSQPQVLYQNNGLYSSHGFGTRPLDPGTAGPRVWYRPIPSHMPSLHNIPVPETNYLGNTPTMPFSSLPPTDESIKYTIYNSTGIQIGAYNYMEIGGTSSSLLDSTNTNFKEEPAAKYQAIFDNTTSLTDKHLDPIRENLGKHWKNCARKLGFTQSQIDEIDHDYERDGLKEKVYQMLQKWVMREGIKGATVGKLAQALHQCSRIDLLSSLIYVSQN DIP protein Q13546 original sequence version: 158 DIP protein Q13546-1 original sequence version: 140 DIP protein Q13546 original sequence version: 146 DIP protein Q13546-1 original sequence version: 146 DIP protein Q13546 original sequence version: 134 DIP protein Q13546 original sequence version: 109 976E2428D525A9B2 casp8_human Caspase-8 CASP8 MCH5 ICE-like apoptotic protease 5 MORT1-associated ced-3 homolog FADD-homologous ICE/ced-3-like protease FADD-like ICE Apoptotic cysteine protease Apoptotic protease Mch-5 CAP4 protein protein human Homo sapiens Human MDFSRNLYDIGEQLDSEDLASLKFLSLDYIPQRKQEPIKDALMLFQRLQEKRMLEESNLSFLKELLFRINRLDLLITYLNTRKEEMERELQTPGRAQISAYRVMLYQISEEVSRSELRSFKFLLQEEISKCKLDDDMNLLDIFIEMEKRVILGEGKLDILKRVCAQINKSLLKIINDYEEFSKERSSSLEGSPDEFSNGEELCGVMTISDSPREQDSESQTLDKVYQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHDDCTVEQIYEILKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVFFIQACQGDNYQKGIPVETDSEEQPYLEMDLSSPQTRYIPDEADFLLGMATVNNCVSYRNPAEGTWYIQSLCQSLRERCPRGDDILTILTEVNYEVSNKDDKKNMGKQMPQPTFTLRKKLVFPSD DIP protein Q14790 original sequence version: 184 DIP protein Q14790 original sequence version: 135 DIP protein Q14790 original sequence version: 136 DIP protein Q14790 original sequence version: 147 DIP protein Q14790 original sequence version: 146 DIP protein Q14790 original sequence version: 170 DIP protein Q14790 original sequence version: 198 DIP protein Q14790-1 original sequence version: 197 DIP protein Q14790 original sequence version: 158 7A5FEAA6B39B582F ripk1-fadd-2 3 5 unspecified role unspecified role prey prey 7 unspecified role unspecified role bait bait physical association physical association Supp. Fig. 1D Cells were treated for 20 hr with 100 uM etoposide. zVAD-fmk pan-caspase inhibitor etoposide casp8-fadd-5 3 8 unspecified role unspecified role bait bait 5 unspecified role unspecified role prey prey 7 unspecified role unspecified role prey prey association association Figs. 1D, 1F, 1H, 2F, 2I, 3E, 3I, 4D, 4I, 5F, 6J, 6O Supp. Figs. 1H, 2A, 4C, 4H, 5H, 5J, 6F 50-100 uM etoposide. BMS-345541, IKK inhibitor Ku-55933, ATM inhibitor Necrostatin1 , RIP1-specific inhibitor BV6, bivalent IAP antagonist A soluble TNFR1-Fc decoy receptor Interaction inhibited by siRNA depletion of TNFR1 or by anti-TNF-α neutralizing antibody zVAD, pan-Capsase inhibitor ikbkg-ripk1-3 3 6 unspecified role unspecified role bait bait 7 unspecified role unspecified role prey prey physical association physical association Fig. 1C, 1E, 5E Etoposide (0-25um) ikbkg-fadd 3 7 unspecified role unspecified role prey prey 6 unspecified role unspecified role bait bait 5 unspecified role unspecified role prey prey association association Fig. 1E, 1G, 2E, 3D, 3H, 4C, 4H, 6I, 6N, Supp Fig. 5N Etoposide (50-100um) zVAD-fmk (pan-Caspase inhibitor) Ku-55933, ATM inhibitor BMS-345541, IKK inhibitor Interaction inhibited by siRNA depletion of TNFR1 or by anti-TNF-α neutralizing antibody. The RIP1-specific inhibitor Necrostatin1 did not block RIPK1 association with IKBKG but did prevent association of FADD with IKBKG and RIPK1. A soluble TNFR1-Fc decoy receptor fadd-ripk1-4 3 7 unspecified role unspecified role prey prey 5 unspecified role unspecified role bait bait physical association physical association Fig. 1I Cells were treated for 20 hr with 100 uM etoposide. zVAD-fmk pan-caspase inhibitor etoposide casp8-ripk1-4 4 8 unspecified role unspecified role bait bait 7 unspecified role unspecified role prey prey physical association physical association Supp. Fig. 2C casp8-ripk1-5 2 8 unspecified role unspecified role bait bait 7 unspecified role unspecified role prey prey physical association physical association Supp. Fig. 2C casp8-fadd-6 1 7 unspecified role unspecified role prey prey 5 unspecified role unspecified role prey prey 8 unspecified role unspecified role bait bait association association Fig S2F 50-100 uM etoposide. casp8-fadd-7 4 5 unspecified role unspecified role prey prey 8 unspecified role unspecified role bait bait 7 unspecified role unspecified role prey prey association association Fig S5F 50-100 uM etoposide. Necrostatin1 , RIP1-specific inhibitor