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/ zeng-2013-2 Construction of a novel oligonucleotide array-based transcription factor interaction assay platform and its uses for profiling STAT1 cofactors in mouse fibroblast cells mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Zeng L., Sun Y., Xie L., Wei L., Ren Y., Zhao J., Qin W., Mitchelson K., Cheng J. The authors state thalis3t3 and 3t3-L1 were used in the publication, but no details as to which cell line was used in which experiment were given. 2013-03-01: Y Sun, National Engineering Research Center for Beijing Biochip Technology, Beijing. Interactions detected using Targeted Immuno-Co-precipitation - Oligonucleotide Array-based TF Assay (TIC-OATFA). Similar to OATFA, the TIC-OATFA assay also involves use of a set of various cis-DNA element sequences as probes that can be bound by their corresponding active TFs in a nuclear extract. In detail, the addition of antibody against a specific target TF results in the co-precipitation of other TF proteins associated in a complex with the target. The cis-element DNA sequence probes which are bound by the individual TFs are also precipitated in such complexes, whilst any unbound probes are eliminated. The TF bound DNA probes are then purified, amplified, and analyzed by array hybridization to determine both their identity and abundance. The targeted immuno-co-precipitation step ensures the identity of the principal TF which is under examination, whilst the co-precipitated active TFs are identified by OATFA assay. A nuclear extract from IFN-gamma treated cells was added to a Probe Mix (a set of double-stranded oligonucleotide probes that contain a known library of cis-elements). After immunoprecipitation with anti-STAT1, bound DNA probes were recovered and amplified using a Cy5 labeled primer. Hybridisation to a DNA microarray (TIC-OATFA platform containing 240 consensus TF binding sequences) was carried out. Fluorescent labels were detected using a scanner (LuxScan). Interaction including NFkB and NFAT could not be included, since antibodies cannot ascertain the identity of the proteins within their families. Information about usf1-stat1 interaction was provided by the authors upon email request. ymsun@capitalbio.com Proteomics (1615-9853) 2013 Only protein-protein interactions imex curation zeng-2013-1 Construction of a novel oligonucleotide array-based transcription factor interaction assay platform and its uses for profiling STAT1 cofactors in mouse fibroblast cells mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells anti bait coip anti bait coimmunoprecipitation anti bait coip tag fluorescence tag visualisation by fluorescence tag fluorescence Zeng L., Sun Y., Xie L., Wei L., Ren Y., Zhao J., Qin W., Mitchelson K., Cheng J. The authors state thalis3t3 and 3t3-L1 were used in the publication, but no details as to which cell line was used in which experiment were given. 2013-03-01: Y Sun, National Engineering Research Center for Beijing Biochip Technology, Beijing. Interactions detected using Targeted Immuno-Co-precipitation - Oligonucleotide Array-based TF Assay (TIC-OATFA). Similar to OATFA, the TIC-OATFA assay also involves use of a set of various cis-DNA element sequences as probes that can be bound by their corresponding active TFs in a nuclear extract. In detail, the addition of antibody against a specific target TF results in the co-precipitation of other TF proteins associated in a complex with the target. The cis-element DNA sequence probes which are bound by the individual TFs are also precipitated in such complexes, whilst any unbound probes are eliminated. The TF bound DNA probes are then purified, amplified, and analyzed by array hybridization to determine both their identity and abundance. The targeted immuno-co-precipitation step ensures the identity of the principal TF which is under examination, whilst the co-precipitated active TFs are identified by OATFA assay. A nuclear extract from IFN-gamma treated cells was added to a Probe Mix (a set of double-stranded oligonucleotide probes that contain a known library of cis-elements). After immunoprecipitation with anti-STAT1, bound DNA probes were recovered and amplified using a Cy5 labeled primer. Hybridisation to a DNA microarray (TIC-OATFA platform containing 240 consensus TF binding sequences) was carried out. Fluorescent labels were detected using a scanner (LuxScan). Interaction including NFkB and NFAT could not be included, since antibodies cannot ascertain the identity of the proteins within their families. Information about usf1-stat1 interaction was provided by the authors upon email request. ymsun@capitalbio.com Proteomics (1615-9853) 2013 Only protein-protein interactions imex curation zeng-2013-3 Construction of a novel oligonucleotide array-based transcription factor interaction assay platform and its uses for profiling STAT1 cofactors in mouse fibroblast cells in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Zeng L., Sun Y., Xie L., Wei L., Ren Y., Zhao J., Qin W., Mitchelson K., Cheng J. The authors state thalis3t3 and 3t3-L1 were used in the publication, but no details as to which cell line was used in which experiment were given. 2013-03-01: Y Sun, National Engineering Research Center for Beijing Biochip Technology, Beijing. Interactions detected using Targeted Immuno-Co-precipitation - Oligonucleotide Array-based TF Assay (TIC-OATFA). Similar to OATFA, the TIC-OATFA assay also involves use of a set of various cis-DNA element sequences as probes that can be bound by their corresponding active TFs in a nuclear extract. In detail, the addition of antibody against a specific target TF results in the co-precipitation of other TF proteins associated in a complex with the target. The cis-element DNA sequence probes which are bound by the individual TFs are also precipitated in such complexes, whilst any unbound probes are eliminated. The TF bound DNA probes are then purified, amplified, and analyzed by array hybridization to determine both their identity and abundance. The targeted immuno-co-precipitation step ensures the identity of the principal TF which is under examination, whilst the co-precipitated active TFs are identified by OATFA assay. A nuclear extract from IFN-gamma treated cells was added to a Probe Mix (a set of double-stranded oligonucleotide probes that contain a known library of cis-elements). After immunoprecipitation with anti-STAT1, bound DNA probes were recovered and amplified using a Cy5 labeled primer. Hybridisation to a DNA microarray (TIC-OATFA platform containing 240 consensus TF binding sequences) was carried out. Fluorescent labels were detected using a scanner (LuxScan). Interaction including NFkB and NFAT could not be included, since antibodies cannot ascertain the identity of the proteins within their families. Information about usf1-stat1 interaction was provided by the authors upon email request. ymsun@capitalbio.com Proteomics (1615-9853) 2013 Only protein-protein interactions imex curation usf2_mouse Upstream stimulatory factor 2 Upstream transcription factor 2 Major late transcription factor 2 Usf2 protein protein mouse Mus musculus Mouse MDMLDPGLDPASSATAAAAASHDKGPEAEEGVELQEGGDGPGAEEQTAVAIASVQQAAFGDHNIQYQFRTESNGGQVTYRVVQVTDGQLDGQGDAAGAVSVVSTAAFAGGQQAVTQVGVDGAAQRPGPAAASVPTGPAAPFPLAVIQNPFSNGGSPAAEAVSGEARFAYFPASSVGDTTAVSVQTTDQSLQAGGQFYVMMTPQDVLQTGTQRTIAPRTHPYSPKIDGTRTPRDERRRAQHNEVERRRRDKINNWIVQLSKIIPDCHADNSKTGASKGGILSKACDYIRELRQTNQRMQETFKEAERLQMDNELLRQQIEELKNENALLRAQLQQHNLEMVGESTRQ stat1_mouse Signal transducer and activator of transcription 1 Stat1 protein protein mouse Mus musculus Mouse MSQWFELQQLDSKFLEQVHQLYDDSFPMEIRQYLAQWLEKQDWEHAAYDVSFATIRFHDLLSQLDDQYSRFSLENNFLLQHNIRKSKRNLQDNFQEDPVQMSMIIYNCLKEERKILENAQRFNQAQEGNIQNTVMLDKQKELDSKVRNVKDQVMCIEQEIKTLEELQDEYDFKCKTSQNREGEANGVAKSDQKQEQLLLHKMFLMLDNKRKEIIHKIRELLNSIELTQNTLINDELVEWKRRQQSACIGGPPNACLDQLQTWFTIVAETLQQIRQQLKKLEELEQKFTYEPDPITKNKQVLSDRTFLLFQQLIQSSFVVERQPCMPTHPQRPLVLKTGVQFTVKSRLLVKLQESNLLTKVKCHFDKDVNEKNTVKGFRKFNILGTHTKVMNMEESTNGSLAAELRHLQLKEQKNAGNRTNEGPLIVTEELHSLSFETQLCQPGLVIDLETTSLPVVVISNVSQLPSGWASILWYNMLVTEPRNLSFFLNPPCAWWSQLSEVLSWQFSSVTKRGLNADQLSMLGEKLLGPNAGPDGLIPWTRFCKENINDKNFSFWPWIDTILELIKNDLLCLWNDGCIMGFISKERERALLKDQQPGTFLLRFSESSREGAITFTWVERSQNGGEPDFHAVEPYTKKELSAVTFPDIIRNYKVMAAENIPENPLKYLYPNIDKDHAFGKYYSRPKEAPEPMELDDPKRTGYIKTELISVSEVHPSRLQTTDNLLPMSPEEFDEMSRIVGPEFDSMMSTV usf1_mouse Upstream stimulatory factor 1 Usf1 Usf Major late transcription factor 1 protein protein mouse Mus musculus Mouse MKGQQKTAETEEGTVQIQEGAVATGEDPTSVAIASIQSAATFPDPNVKYVFRTENGGQVMYRVIQVSEGQLDGQTEGSGAISGYPATQSMTQAVIQGAFTSDDAVDTEGAAAETHYTYFPSTAVGDGSGGTTSGSTTAVVTTQGSEALLGQATPPSTGQFFVMMSPQEVLQGGSQRSIAPRTHPYSPKSEAPRTTRDEKRRAQHNEVERRRRDKINNWIVQLSKIIPDCSMESTKSGQSKGGILSKACDYIQELRQSNHRLSEELQGLDQLQLDNDVLRQQVEDLKNKNLLLRAQLRHHGLEVVIKNDSN nfe2_mouse Transcription factor NF-E2 45 kDa subunit Nfe2 Leucine zipper protein NF-E2 Nuclear factor, erythroid-derived 2 45 kDa subunit p45 NF-E2 protein protein mouse Mus musculus Mouse MPPCPPQQNRNRLSQLPVGELGEMELTWQEIMSITELQGLNVPSETSFEPQAPTPYPGPLPPPTYCPCSIHPDAGFSLPPPSYELPASTPHVPELPYSYGNVAIPVSKPLTLSGLLNEPLPDHLALLDIGLPVGQPKPQEDPESDSGLSLNYSDAESLELEGMEAGRRRSEYVDMYPVEYPYSLMPNSLAHPNYTLPPTETPLALESSSGPVRAKPAVRGEAGSRDERRALAMKIPFPTDKIVNLPVDDFNELLAQYPLTESQLALVRDIRRRGKNKVAAQNCRKRKLETIVQLERELERLSSERERLLRARGEADRTLEVMRQQLAELYHDIFQHLRDESGNSYSPEEYVLQQAADGAIFLVPRGTKMEATD nf1_mouse Neurofibromin Nf1 Neurofibromatosis-related protein NF-1 protein protein mouse Mus musculus Mouse MAAHRPVEWVQAVVSRFDEQLPIKTGQQNTHTKVSTEHNKECLINISKYKFSLVISGLTTILKNVNNMRIFGEAAEKNLYLSQLIILDTLEKCLAGQPKDTMRLDETMLVKQLLPEICHFLHTCREGNQHAAELRNSASGVLFSLSCNNFNAVFSRISTRLQELTVCSEDNVDVHDIELLQYINVDCAKLKRLLKETAFKFKALKKVAQLAVINSLEKAFWNWVENYPDEFTKLYQIPQTDMAECAEKLFDLVDGFAESTKRKAAVWPLQIILLILCPEIIQDISKDVVDESNINKKLFLDSLRKALAGHGGSRQLTESAAIACVKLCKASTYINWEDNSVIFLLVQSMVVDLKNLLFNPSKPFSRGSQPADVDLMIDCLVSCFRISPHNNQHFKICLAQNSPSTFHYVLVNSLHRIITNSALDWWPKIDAVYCHSVELRNMFGETLHKAVQGCGAHPAIRMAPSLTFKEKVTSLKFKEKPTDLETRSYKCLLLSMVKLIHADPKLLLCNPRKQGPETQSSTAELITGLVQLVPQSHMPEVAQEAMEALLVLHQLDSIDLWNPDAPVETFWEISSQMLFYICKKLTSHQMLSSTEILKWLREILICRNKFLLKNKQADRSSCHSLYLYGVGCEMSATGNTTQMSVDHDEFLRACTPGASLRKGRGNSSMDSTAGCSGTPPICRQAQTKLEVALYMFLWNPDTEAVLVAMSCFRHLCEEADIRCGVDEVSVHNFLPNYNTFMEFASVSNMMSTGRAALQKRVMALLRRIEHPTAGNIEAWEDTHAKWEQATKLILNYPKAKMEDGQAAESLHKTIVKRRMSHVSGGGSIDLSDTDSLQEWINMTGFLCALGGVCLQQRSSSGLATYSPPMGAVSERKGSMISVMSSEGNIDSPVSRFMDRLLSLMVCNHEKVGLQIRTNVKDLVGLELSPALYPMLFNKLKNTISKFFDSQGQVLLSDSNTQFVEQTIAIMKNLLDNHTEGSSEHLGQASIETMMLNLVRYVRVLGNMVHAIQIKTKLCQLVEVMMARRDDLSFCQEMKFRNKMVEYLTDWVMGTSNQAADDDIKCLTRDLDQASMEAVVSLLAGLPLQPEEGDGVELMEAKSQLFLKYFTLFMNLLNDCSEVEDENAQTGGRKRGMSRRLASLRHCTVLAMSNLLNANVDSGLMHSIGLGYHKDLQTRATFMEVLTKILQQGTEFDTLAETVLADRFERLVELVTMMGDQGELPIAMALANVVPCSQWDELARVLVTLFDSRHLLYQLLWNMFSKEVELADSMQTLFRGNSLASKIMTFCFKVYGATYLQKLLDPLLRVIITSSDWQHVSFEVDPTRLEPSESLEENQRNLLQMTEKFFHAIISSSSEFPSQLRSVCHCLYQATCHSLLNKATVKERKENKKSVVSQRFPQNSIGAVGSAMFLRFINPAIVSPYEAGILDKKPPPRIERGLKLMSKVLQSIANHVLFTKEEHMRPFNDFVKSNFDLARRFFLDIASDCPTSDAVNHSLSFISDGNVLALHRLLWNNQEKIGQYLSSNRDHKAVGRRPFDKMATLLAYLGPPEHKPVADTHWSSLNLTSSKFEEFMTRHQVHEKEEFKALKTLSIFYQAGTSKAGNPIFYYVARRFKTGQINGDLLIYHVLLTLKPYYAKPYEIVVDLTHTGPSNRFKTDFLSKWFVVFPGFAYDNVSAVYIYNCNSWVREYTKYHERLLTGLKGSKRLIFIDCPGKLAEHIEHEQQKLPAATLALEEDLKVFHNALKLAHKDTKVSIKVGSTAVQVTSAERTKVLGQSVFLNDIYYASEIEEICLVDENQFTLTIANQGTPLTFMHQECEAIVQSIIHIRTRWELSQPDSIPQHTKIRPKDVPGTLLNIALLNLGSSDPSLRSAAYNLLCALTCTFNLKIEGQLLETSGLCIPANNTLFIVSISKTLAANEPHLTLEFLEECISGFSKSSIELKHLCLEYMTPWLSNLVRFCKHNDDAKRQRVTAILDKLITMTINEKQMYPSIQAKIWGSLGQITDLLDVVLDSFIKTSATGGLGSIKAEVMADTAVALASGNVKLVSSKVIGRMCKIIDKTCLSPTPTLEQHLMWDDIAILARYMLMLSFNNSLDVAAHLPYLFHVVTFLVATGPLSLRASTHGLLINIIHSLCTCSQLHFSEETKQVLRLSLTEFSLPKFYLLFGISKVKSAAVIAFRSSYRDRSFSPGSYERETFALTSLETVTEALLEIMEACMRDIPTCKWLDQWTELAQRFAFQYNPSLQPRALVVFGCISKRVSHGQIKQIIRILSKALESCLKGPDTYNSQVLIESTVIALTKLQPLLNKDSPLHKALFWVAVAVLQLDEVNLYSAGTALLEQNLHTLDSLRIFNDKSPEEVFMAIRNPLEWHCKQMDHFVGLNFNSNFNFALVGHLLKGYRHPSPAIVARTVRILHTLLTLVNKHRNCDKFEVNTQSVAYLAALLTVSEEVRSRCSLKHRKSLLLTDISMENVPMDTYPIHHGDPSYRTLKETQPWSSPKGSEGYLAATYPAVGQTSPRARKSMSLDMGQPSQANTKKLLGTRKSFDHLISDTKAPKRQEMESGITTPPKMRRVAETDYEMETQRIPSSQQHPHLRKVSVSESNVLLDEEVLTDPKIQALLLTVLATLVKYTTDEFDQRILYEYLAEASVVFPKVFPVVHNLLDSKINTLLSLCQDPNLLNPIHGIVQSVVYHEESPPQYQTSYLQSFGFNGLWRFAGPFSKQTQIPDYAELIVKFLDALIDTYLPGIDEETSEESLLTPTSPYPPALQSQLSITANLNLSNSMTSLATSQHSPGLDKENVELSPTAGHCNSGRTRHGSASQVQKQRSAGSFKRNSIKKIV tbp_mouse TATA-box-binding protein Tbp Tfiid TATA sequence-binding protein TATA-binding factor TATA-box factor Transcription initiation factor TFIID TBP subunit protein protein mouse Mus musculus Mouse MDQNNSLPPYAQGLASPQGAMTPGIPIFSPMMPYGTGLTPQPIQNTNSLSILEEQQRQQQQQQQQQQQQQAVATAAASVQQSTSQQPTQGASGQTPQLFHSQTLTTAPLPGTTPLYPSPMTPMTPITPATPASESSGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRKTT usf2-stat1 1372359 n/a 1372362 unspecified role unspecified role bait bait n/a 1372363 unspecified role unspecified role prey prey physical association physical association false false false 3c IFN-gamma usf1-stat1-2 1372359 n/a 1372363 unspecified role unspecified role prey prey n/a 1372364 unspecified role unspecified role bait bait physical association physical association false false false 3c IFN-gamma stat1-nf1 1372360 n/a 1372365 unspecified role unspecified role prey prey n/a 1372366 unspecified role unspecified role prey prey n/a 1372367 unspecified role unspecified role prey prey n/a 1372362 unspecified role unspecified role prey prey n/a 1372364 unspecified role unspecified role prey prey n/a 1372363 unspecified role unspecified role bait bait association association false false false 2a and 2b usf2-stat1-1 1372361 n/a 1372362 unspecified role unspecified role bait bait purified purified n-terminal gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) n/a 1372363 unspecified role unspecified role prey prey subcellular prep subcellular preparation subcellular prep mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells physical association physical association false false false 3d