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/ dejosez-2008-4 Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells. human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. pull down pull down anti tag western anti tag western blot anti tag western Dejosez M., Krumenacker JS., Zitur LJ., Passeri M., Chu LF., Songyang Z., Thomson JA., Zwaka TP. Apoptosis - Interactions involving proteins with a function related to apoptosis tpzwaka@bcm.edu Human embryonic stem cell cDNA Cell (0092-8674) 2008 Only protein-protein interactions 8 imex curation dejosez-2008-2 Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells. mouse-embryonic_stem cell Mus musculus embryonic stem cell es cells embryonic stem cells ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Dejosez M., Krumenacker JS., Zitur LJ., Passeri M., Chu LF., Songyang Z., Thomson JA., Zwaka TP. Apoptosis - Interactions involving proteins with a function related to apoptosis tpzwaka@bcm.edu Human embryonic stem cell cDNA Cell (0092-8674) 2008 Only protein-protein interactions 8 imex curation dejosez-2008-1 Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid nucleotide sequence nucleotide sequence identification sequence cloning sequence cloning nucleotide sequence Dejosez M., Krumenacker JS., Zitur LJ., Passeri M., Chu LF., Songyang Z., Thomson JA., Zwaka TP. Apoptosis - Interactions involving proteins with a function related to apoptosis tpzwaka@bcm.edu Human embryonic stem cell cDNA Cell (0092-8674) 2008 Only protein-protein interactions 8 imex curation dejosez-2008-3 Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Dejosez M., Krumenacker JS., Zitur LJ., Passeri M., Chu LF., Songyang Z., Thomson JA., Zwaka TP. Apoptosis - Interactions involving proteins with a function related to apoptosis tpzwaka@bcm.edu Human embryonic stem cell cDNA Cell (0092-8674) 2008 Only protein-protein interactions 8 imex curation dejosez-2008-5 Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells. in vitro In vitro protease assay protease assay weight by staining molecular weight estimation by staining weight by staining Dejosez M., Krumenacker JS., Zitur LJ., Passeri M., Chu LF., Songyang Z., Thomson JA., Zwaka TP. Apoptosis - Interactions involving proteins with a function related to apoptosis tpzwaka@bcm.edu Human embryonic stem cell cDNA Cell (0092-8674) 2008 Only protein-protein interactions 8 imex curation tha11_human THAP domain-containing protein 11 THAP11 HRIHFB2206 protein protein human Homo sapiens Human MPGFTCCVPGCYNNSHRDKALHFYTFPKDAELRRLWLKNVSRAGVSGCFSTFQPTTGHRLCSVHFQGGRKTYTVRVPTIFPLRGVNERKVARRPAGAAAARRRQQQQQQQQQQQQQQQQQQQQQQQQQQQQQSSPSASTAQTAQLQPNLVSASAAVLLTLQATVDSSQAPGSVQPAPITPTGEDVKPIDLTVQVEFAAAEGAAAAAAASELQAATAGLEAAECPMGPQLVVVGEEGFPDTGSDHSYSLSSGTTEEELLRKLNEQRDILALMEVKMKEMKGSIRHLRLTEAKLREELREKDRLLAMAVIRKKHGM 25235D20CB54D8C2 hcfc1_human Host cell factor 1 HCFC1 HCF1 C1 factor VP16 accessory protein VCAF CFF HFC1 protein protein human Homo sapiens Human MASAVSPANLPAVLLQPRWKRVVGWSGPVPRPRHGHRAVAIKELIVVFGGGNEGIVDELHVYNTATNQWFIPAVRGDIPPGCAAYGFVCDGTRLLVFGGMVEYGKYSNDLYELQASRWEWKRLKAKTPKNGPPPCPRLGHSFSLVGNKCYLFGGLANDSEDPKNNIPRYLNDLYILELRPGSGVVAWDIPITYGVLPPPRESHTAVVYTEKDNKKSKLVIYGGMSGCRLGDLWTLDIDTLTWNKPSLSGVAPLPRSLHSATTIGNKMYVFGGWVPLVMDDVKVATHEKEWKCTNTLACLNLDTMAWETILMDTLEDNIPRARAGHCAVAINTRLYIWSGRDGYRKAWNNQVCCKDLWYLETEKPPPPARVQLVRANTNSLEVSWGAVATADSYLLQLQKYDIPATAATATSPTPNPVPSVPANPPKSPAPAAAAPAVQPLTQVGITLLPQAAPAPPTTTTIQVLPTVPGSSISVPTAARTQGVPAVLKVTGPQATTGTPLVTMRPASQAGKAPVTVTSLPAGVRMVVPTQSAQGTVIGSSPQMSGMAALAAAAAATQKIPPSSAPTVLSVPAGTTIVKTMAVTPGTTTLPATVKVASSPVMVSNPATRMLKTAAAQVGTSVSSATNTSTRPIITVHKSGTVTVAQQAQVVTTVVGGVTKTITLVKSPISVPGGSALISNLGKVMSVVQTKPVQTSAVTGQASTGPVTQIIQTKGPLPAGTILKLVTSADGKPTTIITTTQASGAGTKPTILGISSVSPSTTKPGTTTIIKTIPMSAIITQAGATGVTSSPGIKSPITIITTKVMTSGTGAPAKIITAVPKIATGHGQQGVTQVVLKGAPGQPGTILRTVPMGGVRLVTPVTVSAVKPAVTTLVVKGTTGVTTLGTVTGTVSTSLAGAGGHSTSASLATPITTLGTIATLSSQVINPTAITVSAAQTTLTAAGGLTTPTITMQPVSQPTQVTLITAPSGVEAQPVHDLPVSILASPTTEQPTATVTIADSGQGDVQPGTVTLVCSNPPCETHETGTTNTATTTVVANLGGHPQPTQVQFVCDRQEAAASLVTSTVGQQNGSVVRVCSNPPCETHETGTTNTATTATSNMAGQHGCSNPPCETHETGTTNTATTAMSSVGANHQRDARRACAAGTPAVIRISVATGALEAAQGSKSQCQTRQTSATSTTMTVMATGAPCSAGPLLGPSMAREPGGRSPAFVQLAPLSSKVRLSSPSIKDLPAGRHSHAVSTAAMTRSSVGAGEPRMAPVCESLQGGSPSTTVTVTALEALLCPSATVTQVCSNPPCETHETGTTNTATTSNAGSAQRVCSNPPCETHETGTTHTATTATSNGGTGQPEGGQQPPAGRPCETHQTTSTGTTMSVSVGALLPDATSSHRTVESGLEVAAAPSVTPQAGTALLAPFPTQRVCSNPPCETHETGTTHTATTVTSNMSSNQDPPPAASDQGEVESTQGDSVNITSSSAITTTVSSTLTRAVTTVTQSTPVPGPSVPPPEELQVSPGPRQQLPPRQLLQSASTALMGESAEVLSASQTPELPAAVDLSSTGEPSSGQESAGSAVVATVVVQPPPPTQSEVDQLSLPQELMAEAQAGTTTLMVTGLTPEELAVTAAAEAAAQAAATEEAQALAIQAVLQAAQQAVMGTGEPMDTSEAAATVTQAELGHLSAEGQEGQATTIPIVLTQQELAALVQQQQLQEAQAQQQHHHLPTEALAPADSLNDPAIESNCLNELAGTVPSTVALLPSTATESLAPSNTFVAPQPVVVASPAKLQAAATLTEVANGIESLGVKPDLPPPPSKAPMKKENQWFDVGVIKGTNVMVTHYFLPPDDAVPSDDDLGTVPDYNQLKKQELQPGTAYKFRVAGINACGRGPFSEISAFKTCLPGFPGAPCAIKISKSPDGAHLTWEPPSVTSGKIIEYSVYLAIQSSQAGGELKSSTPAQLAFMRVYCGPSPSCLVQSSSLSNAHIDYTTKPAIIFRIAARNEKGYGPATQVRWLQETSKDSSGTKPANKRPMSSPEMKSAPKKSKADGQ sin3a_human Paired amphipathic helix protein Sin3a SIN3A Transcriptional corepressor Sin3a Histone deacetylase complex subunit Sin3a protein protein human Homo sapiens Human MKRRLDDQESPVYAAQQRRIPGSTEAFPHQHRVLAPAPPVYEAVSETMQSATGIQYSVTPSYQVSAMPQSSGSHGPAIAAVHSSHHHPTAVQPHGGQVVQSHAHPAPPVAPVQGQQQFQRLKVEDALSYLDQVKLQFGSQPQVYNDFLDIMKEFKSQSIDTPGVISRVSQLFKGHPDLIMGFNTFLPPGYKIEVQTNDMVNVTTPGQVHQIPTHGIQPQPQPPPQHPSQPSAQSAPAPAQPAPQPPPAKVSKPSQLQAHTPASQQTPPLPPYASPRSPPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQEVYAQVARLFKNQEDLLSEFGQFLPDANSSVLLSKTTAEKVDSVRNDHGGTVKKPQLNNKPQRPSQNGCQIRRHPTGTTPPVKKKPKLLNLKDSSMADASKHGGGTESLFFDKVRKALRSAEAYENFLRCLVIFNQEVISRAELVQLVSPFLGKFPELFNWFKNFLGYKESVHLETYPKERATEGIAMEIDYASCKRLGSSYRALPKSYQQPKCTGRTPLCKEVLNDTWVSFPSWSEDSTFVSSKKTQYEEHIYRCEDERFELDVVLETNLATIRVLEAIQKKLSRLSAEEQAKFRLDNTLGGTSEVIHRKALQRIYADKAADIIDGLRKNPSIAVPIVLKRLKMKEEEWREAQRGFNKVWREQNEKYYLKSLDHQGINFKQNDTKVLRSKSLLNEIESIYDERQEQATEENAGVPVGPHLSLAYEDKQILEDAAALIIHHVKRQTGIQKEDKYKIKQIMHHFIPDLLFAQRGDLSDVEEEEEEEMDVDEATGAVKKHNGVGGSPPKSKLLFSNTAAQKLRGMDEVYNLFYVNNNWYIFMRLHQILCLRLLRICSQAERQIEEENREREWEREVLGIKRDKSDSPAIQLRLKEPMDVDVEDYYPAFLDMVRSLLDGNIDSSQYEDSLREMFTIHAYIAFTMDKLIQSIVRQLQHIVSDEICVQVTDLYLAENNNGATGGQLNTQNSRSLLESTYQRKAEQLMSDENCFKLMFIQSQGQVQLTIELLDTEEENSDDPVEAERWSDYVERYMNSDTTSPELREHLAQKPVFLPRNLRRIRKCQRGREQQEKEGKEGNSKKTMENVDSLDKLECRFKLNSYKMVYVIKSEDYMYRRTALLRAHQSHERVSKRLHQRFQAWVDKWTKEHVPREMAAETSKWLMGEGLEGLVPCTTTCDTETLHFVSINKYRVKYGTVFKAP thap7_human THAP domain-containing protein 7 THAP7 protein protein human Homo sapiens Human MPRHCSAAGCCTRDTRETRNRGISFHRLPKKDNPRRGLWLANCQRLDPSGQGLWDPASEYIYFCSKHFEEDCFELVGISGYHRLKEGAVPTIFESFSKLRRTTKTKGHSYPPGPAEVSRLRRCRKRCSEGRGPTTPFSPPPPADVTCFPVEEASAPATLPASPAGRLEPGLSSPFSDLLGPLGAQADEAGCSAQPSPERQPSPLEPRPVSPSAYMLRLPPPAGAYIQNEHSYQVGSALLWKRRAEAALDALDKAQRQLQACKRREQRLRLRLTKLQQERAREKRAQADARQTLKEHVQDFAMQLSSSMA hdac3_human Histone deacetylase 3 HDAC3 RPD3-2 SMAP45 protein protein human Homo sapiens Human MAKTVAYFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCRFHSEDYIDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYKHLFQPVINQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQTIFENLKMLNHAPSVQIHDVPADLLTYDRTDEADAEERGPEENYSRPEAPNEFYDGDHDNDKESDVEI tha11_mouse THAP domain-containing protein 11 Thap11 MNCb-2032 Ronin protein protein mouse Mus musculus Mouse MPGFTCCVPGCYNNSHRDKALHFYTFPKDAELRRLWLKNVSRAGVSGCFSTFQPTTGHRLCSVHFQGGRKTYTVRVPTIFPLRGVNERKVARRPAGAAAARRRQQQQQQQQQQQQQQQLQQQQPSPSSSTAQTTQLQPNLVSASAAVLLTLQAAVDSNQAPGSVVPVSTTPSGDDVKPIDLTVQVEFAAAEGAAAAAAASELEAATAGLEAAECTLGPQLVVVGEEGFPDTGSDHSYSLSSGTTEEELLRKLNEQRDILALMEVKMKEMKGSIRHLRLTEAKLREELREKDRLLAMAVIRKKHGM gata4_mouse_gene Mouse gata4 gene gene gene mouse Mus musculus Mouse gata6_mouse_gene Mouse Gata6 gene gene gene mouse Mus musculus Mouse oct4_mouse_gene Mouse Oct4 gene gene gene mouse Mus musculus Mouse casp3_mouse Caspase-3 Casp3 Cpp32 Apopain Cysteine protease CPP32 Protein Yama SREBP cleavage activity 1 LICE protein protein mouse Mus musculus Mouse MENNKTSVDSKSINNFEVKTIHGSKSVDSGIYLDSSYKMDYPEMGICIIINNKNFHKSTGMSSRSGTDVDAANLRETFMGLKYQVRNKNDLTREDILELMDSVSKEDHSKRSSFVCVILSHGDEGVIYGTNGPVELKKLTSFFRGDYCRSLTGKPKLFIIQACRGTELDCGIETDSGTDEEMACQKIPVEADFLYAYSTAPGYYSWRNSKDGSWFIQSLCSMLKLYAHKLEFMHILTRVNRKVATEFESFSLDSTFHAKKQIPCIVSMLTKELYFYH thap11-hcp1-2 Interaction between Thap11 and Hsp1 identified by pulldown 745133 N/A 745138 unspecified role unspecified role bait bait c-terminal sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 745139 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 7D P51610; Q96EK4 transfection thap11-thap11-1 Self interaction of Thap11 identified by pulldown 745133 N/A 745138 unspecified role unspecified role bait bait c-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 745138 unspecified role unspecified role prey prey c-terminal sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 745160 745157 physical association physical association false false false Fig. 7D Q96EK4 transfection thap11-sin3a-1 Interaction of Sin3A and Thap11 identified by pulldown 745133 N/A 745140 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 745138 unspecified role unspecified role bait bait c-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 745167 745164 physical association physical association false false false Fig. 7D Q96EK4; Q96ST3 transfection thap11-thap7-1 Interaction of THAP7 and Thap11 identified by pulldown 745133 N/A 745138 unspecified role unspecified role bait bait n-terminal sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 745141 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 7D Q9BT49; Q96EK4 transfection thap11-hdac3-1 Interaction of HDAC3 and Thap11 identified by pulldown 745133 N/A 745138 unspecified role unspecified role bait bait n-terminal sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 745142 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 7D O15379; Q96EK4 transfection trapp11-gata4-1 Binding of TRAP11 to the Gata4 gene 745134 N/A 745143 unspecified role unspecified role bait bait N/A 745144 unspecified role unspecified role prey prey association association false false false Trap11 binds to the 3x promoter region of this gene, Histone H3 is methylated. Fig. 6E trapp11-gata6-1 Binding of TRAP11 to the Gata6 gene 745134 N/A 745145 unspecified role unspecified role prey prey N/A 745143 unspecified role unspecified role bait bait association association false false false Trap11 binds to the 3x promoter region of this gene, Histone H3 is methylated. Fig. 6E trapp11-ot4-1 Binding of TRAP11 to the Oct4 gene 745134 N/A 745146 unspecified role unspecified role prey prey N/A 745143 unspecified role unspecified role bait bait association association false false false Trap11 binds to the 3x promoter region of this gene, but only in differentiated ES cells Fig. 6E casp3-thap11-1 Interaction between Casp3 and THAP11 (Ronin) identified by Y2H 745135 N/A 745138 unspecified role unspecified role prey prey N/A 745147 unspecified role unspecified role bait bait P70677:p.Cys163Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false thap11-hcp1-1 Interaction between Thap11 and Hsp1 identified by Y2H 745136 N/A 745139 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false N/A 745138 unspecified role unspecified role prey prey c-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false 745198 745196 physical association physical association false false false Fig. 7A Human THAP11 is only 313 amino acids long as desribed in UniProtKB, not 315 as given in the paper casp3-thap11-2 Cleavage of THAP11 (Ronin) by Casp3 745137 N/A 745147 enzyme enzyme neutral component neutral component P70677:p.Cys163Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false N/A 745138 enzyme target enzyme target substrate substrate neutral component neutral component protein cleavage protein cleavage false false false Cleavage of THAP11 (Q96EK4) Supp. Fig. 1A