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/ A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PloS one 2009 imex curation Jung M., Peterson H., Chavez L., Kahlem P., Lehrach H., Vilo J., Adjaye J. adjaye@molgen.mpg.de,jung@molgen.mpg.de 09-May-2019: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Jung M., Peterson H., Chavez L., Kahlem P., Lehrach H., Vilo J., Adjaye J. adjaye@molgen.mpg.de,jung@molgen.mpg.de Accepted 2018-DEC-11 AT 17:24 GMT AT 17:24 GMT by PPORRAS PloS one 2009 imex curation all done; go xrefs removed from interaction A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PloS one 2009 imex curation Jung M., Peterson H., Chavez L., Kahlem P., Lehrach H., Vilo J., Adjaye J. adjaye@molgen.mpg.de,jung@molgen.mpg.de 09-May-2019: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-nccit Human NCCIT-a mediastinal mixed germ cell tumor-pluripotent stem cell line. nccit Human NCCIT pluripotent stem cell line,from a mediastinal mixed germ cell tumor. http://www.lgcstandards-atcc.org/LGCAdvancedCatalogueSearch/ProductDescription/tabid/1068/Default.aspx?ATCCNum=CRL-2073&Template=cellBiology crosslink cross-linking study crosslink rt-pcr reverse transcription pcr RT-PCR Jung M., Peterson H., Chavez L., Kahlem P., Lehrach H., Vilo J., Adjaye J. after cross-linking Chromatine Immunoprecipitation (Ch-ip) was performed Cross-linker: formaldehyde adjaye@molgen.mpg.de,jung@molgen.mpg.de Accepted 2018-DEC-11 AT 17:24 GMT AT 17:24 GMT by PPORRAS PloS one 2009 imex curation all done; go xrefs removed from interaction A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PloS one 2009 imex curation Jung M., Peterson H., Chavez L., Kahlem P., Lehrach H., Vilo J., Adjaye J. adjaye@molgen.mpg.de,jung@molgen.mpg.de 09-May-2019: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro emsa supershift electrophoretic mobility supershift assay emsa supershift weight identificat confirmation by molecular weight weight identificat Jung M., Peterson H., Chavez L., Kahlem P., Lehrach H., Vilo J., Adjaye J. Preys were prepared from nuclear extracts of NCCIT cells. adjaye@molgen.mpg.de,jung@molgen.mpg.de Accepted 2018-DEC-11 AT 17:24 GMT AT 17:24 GMT by PPORRAS PloS one 2009 imex curation all done; go xrefs removed from interaction po5f1_human POU domain, class 5, transcription factor 1 Octamer-binding transcription factor 3 Octamer-binding protein 3 POU5F1 OCT3 OCT4 OTF3 Octamer-binding protein 4 protein protein human Homo sapiens Human MAGHLASDFAFSPPPGGGGDGPGGPEPGWVDPRTWLSFQGPPGGPGIGPGVGPGSEVWGIPPCPPPYEFCGGMAYCGPQVGVGLVPQGGLETSQPEGEAGVGVESNSDGASPEPCTVTPGAVKLEKEKLEQNPEESQDIKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKWVEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLEKDVVRVWFCNRRQKGKRSSSDYAQREDFEAAGSPFSGGPVSFPLAPGPHFGTPGYGSPHFTALYSSVPFPEGEAFPPVSVTTLGSPMHSN DIP protein Q01860 original sequence version: 131 DIP protein Q01860 original sequence version: 150 DIP protein Q01860 original sequence version: 138 934C58DAEA0C535B ubp44_human_gene Ubiquitin carboxyl-terminal hydrolase 44 USP44 gene gene human Homo sapiens Human nanog_human_gene Homeobox protein NANOG NANOG gene gene human Homo sapiens Human ga45g_human_gene Growth arrest and DNA damage-inducible protein GADD45 gamma GADD45G CR6 DDIT2 gene gene human Homo sapiens Human lfty2_human_gene Left-right determination factor 2 LEFTY2 EBAF LEFTA LEFTYA TGFB4 gene gene human Homo sapiens Human sox2_human_gene Transcription factor SOX-2 gene gene gene human Homo sapiens Human oct4-sox2-1 2 9 unspecified role unspecified role prey prey living cell living cell physiological level physiological level endogenous level endogenous endogenous endogenous level promoter region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined GTGAGCAAGAACTGGCGAATGT TTATTCCAGTTCCCAATTCTAAGCAAG 4 unspecified role unspecified role bait bait living cell living cell physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association Fig. 1 pou5f1-nanog-2 2 6 unspecified role unspecified role prey prey living cell living cell physiological level physiological level endogenous level endogenous endogenous endogenous level promoter region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ACCTAGAAGTATTTGTTGCTGGGTTT AATTCTCAGTTAATCCCGTCTACCAG 4 unspecified role unspecified role bait bait living cell living cell physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association Fig. 1 pou5f1-lefty2-1 2 8 unspecified role unspecified role prey prey living cell living cell physiological level physiological level endogenous level endogenous endogenous endogenous level promoter region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined GAGTGGAGAGTCTGGCTGTGG TCCCACCAGGACAGAAGAGG 4 unspecified role unspecified role bait bait living cell living cell physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association Fig. 1 pou5f1-nanog-3 3 6 unspecified role unspecified role bait bait purified purified promoter region OCT4-SOX2 motif sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined TCTGCAGCTACTTTTGCATTACAATGGCCTTGGTGAG CTCACCAAGGCCATTGTAATGCAAAAGTAGCTGCAGA cy5 label cy5 label cy5 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 4 unspecified role unspecified role prey prey subcellular prep subcellular preparation subcellular prep physiological level physiological level endogenous level endogenous endogenous endogenous level human-nccit Human NCCIT-a mediastinal mixed germ cell tumor-pluripotent stem cell line. nccit Human NCCIT pluripotent stem cell line,from a mediastinal mixed germ cell tumor. http://www.lgcstandards-atcc.org/LGCAdvancedCatalogueSearch/ProductDescription/tabid/1068/Default.aspx?ATCCNum=CRL-2073&Template=cellBiology physical association physical association Fig. 4A nanog-pou5f1-1 3 7 unspecified role unspecified role bait bait purified purified promoter region OCT4 motif 1 sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined TTACTTAAATGCGCATATGTAAAAAGCCTTT AAAGGCTTTTTACATATGCGCATTTAAGTAA cy5 label cy5 label cy5 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined promoter region OCT4 motif 2 sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ATGCGCATATGTAAAAAGCCTTTTTTCCGGC GCCGGAAAAAAGGCTTTTTACATATGCGCAT chemical synthesis Chemical synthesis (Chemical synthesis) 4 unspecified role unspecified role prey prey subcellular prep subcellular preparation subcellular prep physiological level physiological level endogenous level endogenous endogenous endogenous level human-nccit Human NCCIT-a mediastinal mixed germ cell tumor-pluripotent stem cell line. nccit Human NCCIT pluripotent stem cell line,from a mediastinal mixed germ cell tumor. http://www.lgcstandards-atcc.org/LGCAdvancedCatalogueSearch/ProductDescription/tabid/1068/Default.aspx?ATCCNum=CRL-2073&Template=cellBiology physical association physical association Fig. 8A For additional independent confirmation of binding, we performed a bandshift assay using two oligos flanking the core OCT4 motif (Fig. 8A). We obtained a supershift with OCT4 antibody for both sets of oligos, thus demonstrating specific binding of OCT4 to this locus. usp44-pou5f1-1 1 5 unspecified role unspecified role bait bait purified purified promoter region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined GGTTTTTTTTTTCTCTCCGACCTGTCGTCACCGGATTTCGCCCCGCCTTCGTTTCTTGGCCCATGCTGTATTCCTTAAATGGACAGATACCATATCGTTGTACCGGCTCTTTTG GGTTTTTTTTTTCCCATCCCCCACCCCCAGCAGTGCATTATTATGCAGTCACTGCTTTTGTTCCGAGTTCTGAGCCTGCTTCTATTTGCATCGTAACCTCTTTGGGGGCCTTTG biotin tag biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 4 unspecified role unspecified role prey prey subcellular prep subcellular preparation subcellular prep physiological level physiological level endogenous level endogenous endogenous endogenous level human-nccit Human NCCIT-a mediastinal mixed germ cell tumor-pluripotent stem cell line. nccit Human NCCIT pluripotent stem cell line,from a mediastinal mixed germ cell tumor. http://www.lgcstandards-atcc.org/LGCAdvancedCatalogueSearch/ProductDescription/tabid/1068/Default.aspx?ATCCNum=CRL-2073&Template=cellBiology physical association physical association Fig. 7D the text says:"The OCT4 antibody shows higher binding intensity to the USP44- specific probe compared to the corresponding scrambled oligo." since pap1 doesn't show the same pattern, I haven't added it.