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/ jeon-2011-2 in vitro In vitro pull down pull down qrt-pcr quantitative reverse transcription pcr QRT-PCR Jeon Y., Lee JT. lee@molbio.mgh.harvard.edu Cell 2011 Only protein-protein interactions imex curation imex curation jeon-2011-4 mouse-embryonic_fibroblast Mus musculus embryonic fibroblasts embryonic_fibroblast Embryonic fibroblast Fibroblasts taken from an embryonic as opposed to a foetal or adult source. Foetus is defined as the stage at which tissue diferentiation is initiated. Tissue taken from an embryonic as opposed to a foetal or adult source. Embryo is defined as the development stage prior to organ formation. ch-ip chromatin immunoprecipitation assay ch-ip q-pcr quantitative pcr q-pcr Jeon Y., Lee JT. lee@molbio.mgh.harvard.edu Cell 2011 Only protein-protein interactions imex curation imex curation jeon-2011-3 mouse-embryonic_fibroblast Mus musculus embryonic fibroblasts embryonic_fibroblast Embryonic fibroblast Fibroblasts taken from an embryonic as opposed to a foetal or adult source. Foetus is defined as the stage at which tissue diferentiation is initiated. Tissue taken from an embryonic as opposed to a foetal or adult source. Embryo is defined as the development stage prior to organ formation. rna-ip rna immunoprecipitation rna-ip qrt-pcr quantitative reverse transcription pcr QRT-PCR Jeon Y., Lee JT. UV crosslinking was used in this experiment. lee@molbio.mgh.harvard.edu Cell 2011 Only protein-protein interactions imex curation imex curation tyy1_mouse Transcriptional repressor protein YY1 Yy1 Ucrbp Delta transcription factor NF-E1 UCR-motif DNA-binding protein Yin and yang 1 protein protein mouse Mus musculus Mouse MASGDTLYIATDGSEMPAEIVELHEIEVETIPVETIETTVVGEEEEEDDDDEDGGGGDHGGGGGGHGHAGHHHHHHHHHHHHPPMIALQPLVTDDPTQVHHHQEVILVQTREEVVGGDDSDGLRAEDGFEDQILIPVPAPAGGDDDYIEQTLVTVAAAGKSGGGASSGGGRVKKGGGKKSGKKSYLGGGAGAAGGGGADPGNKKWEQKQVQIKTLEGEFSVTMWSSDEKKDIDHETVVEEQIIGENSPPDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPRTIACPHKGCTKMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTHAKAKNNQ lncrna_xist Mus musculus inactive X specific transcripts (Xist) lncrna long non-coding ribonucleic acid lncRNA long non coding RNA long non coding ribonucleic acid long non-coding RNA lncrna mouse Mus musculus Mouse 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xist_mouse_gene XIST gene gene gene mouse Mus musculus Mouse peg3_mouse_gene Paternally-expressed gene 3 protein Peg3 Kiaa0287 Pw1 gene gene mouse Mus musculus Mouse yy1-lncrna_xist-1 3544019 N/A 3544022 predetermined predetermined participant predetermined unspecified role unspecified role bait bait purified purified tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 3544023 unspecified role unspecified role prey prey purified purified physical association physical association false false false Fig 6C D yy1-lncrna_xist-2 3544019 N/A 3544022 predetermined predetermined participant predetermined unspecified role unspecified role bait bait purified purified tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 3544023 unspecified role unspecified role prey prey in vitro translated in vitro translated protein in vitro translated physical association physical association false false false Fig 6E yy1-xist_mouse_gene-1 3544020 N/A 3544024 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level N/A 3544022 antibody detection identification by antibody antibody detection unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association false false false Fig 5B This interaction occurs only in female cells not in male The interaction occurs in a region of the xist gene comprised between the "repeat A" and "repeat F" regions yy1-peg3-1 3544020 N/A 3544025 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level N/A 3544022 antibody detection identification by antibody antibody detection unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association false false false Fig 5B lncrna_xist-yy1-1 3544021 N/A 3544022 antibody detection identification by antibody antibody detection unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level N/A 3544023 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association false false false Fig 6B Female MEF cells were used for this experiment