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/ Silencing of the transforming growth factor-beta (TGFbeta) receptor II by Kruppel-like factor 14 underscores the importance of a negative feedback mechanism in TGFbeta signaling. Silencing of the transforming growth factor-beta (TGFbeta) receptor II by Kruppel-like factor 14 underscores the importance of a negative feedback mechanism in TGFbeta signaling. The Journal of biological chemistry 2009 imex curation Truty MJ., Lomberk G., Fernandez-Zapico ME., Urrutia R. IBD - Inflammatory bowel disease No Species of TGF-beta given. KLF14 is of Human origin - as taken from the sequence in figure 6A. urrutia.raul@mayo.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro emsa supershift electrophoretic mobility supershift assay emsa supershift autoradiography autoradiography Truty MJ., Lomberk G., Fernandez-Zapico ME., Urrutia R. IBD - Inflammatory bowel disease No Species of TGF-beta given. KLF14 is of Human origin - as taken from the sequence in figure 6A. urrutia.raul@mayo.edu Accepted 2015-OCT-07 AT 15:48 BST AT 15:48 BST by ORCHARD The Journal of biological chemistry 2009 Only protein-protein interactions imex curation imex curation I dont think the fact you dont see a band is relevant;I was arguing this point with Kim- he convinced me that either a supershift OR a reduction/absence in binding shows the antibody is binding to the complex - presumably the binding site of the antibody in this instance stops the radiolabeled probe binding as well (or similar).. To back this position I found a comment from a website 'BioTechniques Molecular Biology Techniques Forums":- " By that I mean that you will see your band running higher (supershift) OR your band will disappear (because sometime your antibody interfere with the binding to the probe). " From a "Cell Death Website"- "Supershift--In order to determine which NF-kB subunits are responsible for the observed shifted bands, the EMSA signals can be "supershifted" by adding different NF-kB subunit-specific antibodies to the binding reactions. The antibodies will bind to the corresponding NF-kB subunit what results in a NF-kB/probe/antibody ternary complex: the electrophoretic mobility of this complex is even lower than that of the NF-kB/probe complex so that a supershifted band can be observed. Sometimes an antibody does not result in a shifted band even if its corresponding NF-kB subunit is present: instead, by binding to its NF-kB subunit the antibody prevents the association of the NF-kB subunit and the labeled probe so that the intensity of the primary shifted signal decreases. " Silencing of the transforming growth factor-beta (TGFbeta) receptor II by Kruppel-like factor 14 underscores the importance of a negative feedback mechanism in TGFbeta signaling. Silencing of the transforming growth factor-beta (TGFbeta) receptor II by Kruppel-like factor 14 underscores the importance of a negative feedback mechanism in TGFbeta signaling. The Journal of biological chemistry 2009 imex curation Truty MJ., Lomberk G., Fernandez-Zapico ME., Urrutia R. IBD - Inflammatory bowel disease No Species of TGF-beta given. KLF14 is of Human origin - as taken from the sequence in figure 6A. urrutia.raul@mayo.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-panc1 Homo sapiens pancreatic carcinoma cell line PANC-1 panc1 Human pancreatic carcinoma cell line PANC-1 Established from a pancreatic carcinoma of ductal origin from a 56-year-old Caucasian male. Cells possess the type B phenotype for G6PD. anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Truty MJ., Lomberk G., Fernandez-Zapico ME., Urrutia R. IBD - Inflammatory bowel disease No Species of TGF-beta given. KLF14 is of Human origin - as taken from the sequence in figure 6A. urrutia.raul@mayo.edu Accepted 2015-OCT-07 AT 15:48 BST AT 15:48 BST by ORCHARD The Journal of biological chemistry 2009 Only protein-protein interactions imex curation imex curation I dont think the fact you dont see a band is relevant;I was arguing this point with Kim- he convinced me that either a supershift OR a reduction/absence in binding shows the antibody is binding to the complex - presumably the binding site of the antibody in this instance stops the radiolabeled probe binding as well (or similar).. To back this position I found a comment from a website 'BioTechniques Molecular Biology Techniques Forums":- " By that I mean that you will see your band running higher (supershift) OR your band will disappear (because sometime your antibody interfere with the binding to the probe). " From a "Cell Death Website"- "Supershift--In order to determine which NF-kB subunits are responsible for the observed shifted bands, the EMSA signals can be "supershifted" by adding different NF-kB subunit-specific antibodies to the binding reactions. The antibodies will bind to the corresponding NF-kB subunit what results in a NF-kB/probe/antibody ternary complex: the electrophoretic mobility of this complex is even lower than that of the NF-kB/probe complex so that a supershifted band can be observed. Sometimes an antibody does not result in a shifted band even if its corresponding NF-kB subunit is present: instead, by binding to its NF-kB subunit the antibody prevents the association of the NF-kB subunit and the labeled probe so that the intensity of the primary shifted signal decreases. " Silencing of the transforming growth factor-beta (TGFbeta) receptor II by Kruppel-like factor 14 underscores the importance of a negative feedback mechanism in TGFbeta signaling. Silencing of the transforming growth factor-beta (TGFbeta) receptor II by Kruppel-like factor 14 underscores the importance of a negative feedback mechanism in TGFbeta signaling. The Journal of biological chemistry 2009 imex curation Truty MJ., Lomberk G., Fernandez-Zapico ME., Urrutia R. IBD - Inflammatory bowel disease No Species of TGF-beta given. KLF14 is of Human origin - as taken from the sequence in figure 6A. urrutia.raul@mayo.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa autoradiography autoradiography Truty MJ., Lomberk G., Fernandez-Zapico ME., Urrutia R. IBD - Inflammatory bowel disease The supplier -Promega- no longer stocks "rhSp1 protein" so the expression system for this protein is not known, nor is the presence/absence of any tag(s). No Species of TGF-beta given. KLF14 is of Human origin - as taken from the sequence in figure 6A. urrutia.raul@mayo.edu Accepted 2015-OCT-07 AT 15:48 BST AT 15:48 BST by ORCHARD The Journal of biological chemistry 2009 Only protein-protein interactions imex curation imex curation I dont think the fact you dont see a band is relevant;I was arguing this point with Kim- he convinced me that either a supershift OR a reduction/absence in binding shows the antibody is binding to the complex - presumably the binding site of the antibody in this instance stops the radiolabeled probe binding as well (or similar).. To back this position I found a comment from a website 'BioTechniques Molecular Biology Techniques Forums":- " By that I mean that you will see your band running higher (supershift) OR your band will disappear (because sometime your antibody interfere with the binding to the probe). " From a "Cell Death Website"- "Supershift--In order to determine which NF-kB subunits are responsible for the observed shifted bands, the EMSA signals can be "supershifted" by adding different NF-kB subunit-specific antibodies to the binding reactions. The antibodies will bind to the corresponding NF-kB subunit what results in a NF-kB/probe/antibody ternary complex: the electrophoretic mobility of this complex is even lower than that of the NF-kB/probe complex so that a supershifted band can be observed. Sometimes an antibody does not result in a shifted band even if its corresponding NF-kB subunit is present: instead, by binding to its NF-kB subunit the antibody prevents the association of the NF-kB subunit and the labeled probe so that the intensity of the primary shifted signal decreases. " Silencing of the transforming growth factor-beta (TGFbeta) receptor II by Kruppel-like factor 14 underscores the importance of a negative feedback mechanism in TGFbeta signaling. Silencing of the transforming growth factor-beta (TGFbeta) receptor II by Kruppel-like factor 14 underscores the importance of a negative feedback mechanism in TGFbeta signaling. The Journal of biological chemistry 2009 imex curation Truty MJ., Lomberk G., Fernandez-Zapico ME., Urrutia R. IBD - Inflammatory bowel disease No Species of TGF-beta given. KLF14 is of Human origin - as taken from the sequence in figure 6A. urrutia.raul@mayo.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-panc1 Homo sapiens pancreatic carcinoma cell line PANC-1 panc1 Human pancreatic carcinoma cell line PANC-1 Established from a pancreatic carcinoma of ductal origin from a 56-year-old Caucasian male. Cells possess the type B phenotype for G6PD. ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Truty MJ., Lomberk G., Fernandez-Zapico ME., Urrutia R. IBD - Inflammatory bowel disease No Species of TGF-beta given. KLF14 is of Human origin - as taken from the sequence in figure 6A. urrutia.raul@mayo.edu Accepted 2015-OCT-07 AT 15:48 BST AT 15:48 BST by ORCHARD The Journal of biological chemistry 2009 Only protein-protein interactions imex curation imex curation I dont think the fact you dont see a band is relevant;I was arguing this point with Kim- he convinced me that either a supershift OR a reduction/absence in binding shows the antibody is binding to the complex - presumably the binding site of the antibody in this instance stops the radiolabeled probe binding as well (or similar).. To back this position I found a comment from a website 'BioTechniques Molecular Biology Techniques Forums":- " By that I mean that you will see your band running higher (supershift) OR your band will disappear (because sometime your antibody interfere with the binding to the probe). " From a "Cell Death Website"- "Supershift--In order to determine which NF-kB subunits are responsible for the observed shifted bands, the EMSA signals can be "supershifted" by adding different NF-kB subunit-specific antibodies to the binding reactions. The antibodies will bind to the corresponding NF-kB subunit what results in a NF-kB/probe/antibody ternary complex: the electrophoretic mobility of this complex is even lower than that of the NF-kB/probe complex so that a supershifted band can be observed. Sometimes an antibody does not result in a shifted band even if its corresponding NF-kB subunit is present: instead, by binding to its NF-kB subunit the antibody prevents the association of the NF-kB subunit and the labeled probe so that the intensity of the primary shifted signal decreases. " tgfbrii_promoter_sp1_probe_no_4 ds dna double stranded deoxyribonucleic acid ds DNA ds dna human Homo sapiens Human GGGCGG tgfbrii_promoter_sp1_probe_no_2 ds dna double stranded deoxyribonucleic acid ds DNA ds dna human Homo sapiens Human GGGGCTGG tgfbrii_promoter_sp1_probe_no_1 ds dna double stranded deoxyribonucleic acid ds DNA ds dna human Homo sapiens Human GGGCGGT tgfbrii_promoter_sp1_probe_no_5 ds dna double stranded deoxyribonucleic acid ds DNA ds dna human Homo sapiens Human CCTGCCC tgfr2_human_gene TGF-beta receptor type-2 TGFBR2 gene gene human Homo sapiens Human h4_human Histone H4 H4-16 H4C1 H4C11 H4C12 H4C13 H4C14 H4C15 H4C2 H4C3 H4C4 H4C5 H4C6 H4C8 H4C9 H4/A H4/B H4/C H4/D H4/E H4/G H4/H H4/I H4/J H4/K H4/M H4/N H4/O H4F2 H4FA H4FB H4FC H4FD H4FE H4FG H4FH H4FI H4FJ H4FK H4FM H4FN H4FO HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4 HIST2H4A HIST2H4B HIST4H4 protein protein human Homo sapiens Human MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG DIP protein P62805 original sequence version: 68 DIP protein P62805 original sequence version: 111 DIP protein P62805 original sequence version: 94 DIP protein P62805 original sequence version: 97 DIP protein P62805 original sequence version: 116 DIP protein P62805 original sequence version: 105 DIP protein P62805 original sequence version: 120 DIP protein P62805 original sequence version: 144 DIP protein P62805 original sequence version: 150 DIP protein P62805 original sequence version: 154 DIP protein P62805 original sequence version: 156 DIP protein P62805 original sequence version: 112 DIP protein P62805 original sequence version: 121 DIP protein P62805 original sequence version: 123 DIP protein P62805 original sequence version: 126 DIP protein P62805 original sequence version: 132 DIP protein P62805 original sequence version: 136 DIP protein P62805 original sequence version: 119 A9E5DFD3F8B97598 sp1_human Transcription factor Sp1 SP1 TSFP1 protein protein human Homo sapiens Human MSDQDHSMDEMTAVVKIEKGVGGNNGGNGNGGGAFSQARSSSTGSSSSTGGGGQESQPSPLALLAATCSRIESPNENSNNSQGPSQSGGTGELDLTATQLSQGANGWQIISSSSGATPTSKEQSGSSTNGSNGSESSKNRTVSGGQYVVAAAPNLQNQQVLTGLPGVMPNIQYQVIPQFQTVDGQQLQFAATGAQVQQDGSGQIQIIPGANQQIITNRGSGGNIIAAMPNLLQQAVPLQGLANNVLSGQTQYVTNVPVALNGNITLLPVNSVSAATLTPSSQAVTISSSGSQESGSQPVTSGTTISSASLVSSQASSSSFFTNANSYSTTTTTSNMGIMNFTTSGSSGTNSQGQTPQRVSGLQGSDALNIQQNQTSGGSLQAGQQKEGEQNQQTQQQQILIQPQLVQGGQALQALQAAPLSGQTFTTQAISQETLQNLQLQAVPNSGPIIIRTPTVGPNGQVSWQTLQLQNLQVQNPQAQTITLAPMQGVSLGQTSSSNTTLTPIASAASIPAGTVTVNAAQLSSMPGLQTINLSALGTSGIQVHPIQGLPLAIANAPGDHGAQLGLHGAGGDGIHDDTAGGEEGENSPDAQPQAGRRTRREACTCPYCKDSEGRGSGDPGKKKQHICHIQGCGKVYGKTSHLRAHLRWHTGERPFMCTWSYCGKRFTRSDELQRHKRTHTGEKKFACPECPKRFMRSDHLSKHIKTHQNKKGGPGVALSVGTLPLDSGAGSEGSGTATPSALITTNMVAMEAICPEGIARLANSGINVMQVADLQSINISGNGF DIP protein P08047 original sequence version: 185 DIP protein P08047 original sequence version: 187 DIP protein P08047 original sequence version: 181 DIP protein P08047 original sequence version: 162 DIP protein P08047 original sequence version: 161 43893DBF6518B9EA tgfbrii_promoter_sp1_consensus_probe ds dna double stranded deoxyribonucleic acid ds DNA ds dna human Homo sapiens Human ATTCGATCGGGGCGGGGCGAGC sp6_human Transcription factor Sp6 SP6 KLF14 Krueppel-like factor 14 protein protein human Homo sapiens Human MLTAVCGSLGSQHTEAPHASPPRLDLQPLQTYQGHTSPEAGDYPSPLQPGELQSLPLGPEVDFSQGYELPGASSRVTCEDLESDSPLAPGPFSKLLQPDMSHHYESWFRPTHPGAEDGSWWDLHPGTSWMDLPHTQGALTSPGHPGALQAGLGGYVGDHQLCAPPPHPHAHHLLPAAGGQHLLGPPDGAKALEVAAPESQGLDSSLDGAARPKGSRRSVPRSSGQTVCRCPNCLEAERLGAPCGPDGGKKKHLHNCHIPGCGKAYAKTSHLKAHLRWHSGDRPFVCNWLFCGKRFTRSDELQRHLQTHTGTKKFPCAVCSRVFMRSDHLAKHMKTHEGAKEEAAGAASGEGKAGGAVEPPGGKGKREAEGSVAPSN 1F4355CFB75206E8 sin3a_human Paired amphipathic helix protein Sin3a SIN3A Transcriptional corepressor Sin3a Histone deacetylase complex subunit Sin3a protein protein human Homo sapiens Human MKRRLDDQESPVYAAQQRRIPGSTEAFPHQHRVLAPAPPVYEAVSETMQSATGIQYSVTPSYQVSAMPQSSGSHGPAIAAVHSSHHHPTAVQPHGGQVVQSHAHPAPPVAPVQGQQQFQRLKVEDALSYLDQVKLQFGSQPQVYNDFLDIMKEFKSQSIDTPGVISRVSQLFKGHPDLIMGFNTFLPPGYKIEVQTNDMVNVTTPGQVHQIPTHGIQPQPQPPPQHPSQPSAQSAPAPAQPAPQPPPAKVSKPSQLQAHTPASQQTPPLPPYASPRSPPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQEVYAQVARLFKNQEDLLSEFGQFLPDANSSVLLSKTTAEKVDSVRNDHGGTVKKPQLNNKPQRPSQNGCQIRRHPTGTTPPVKKKPKLLNLKDSSMADASKHGGGTESLFFDKVRKALRSAEAYENFLRCLVIFNQEVISRAELVQLVSPFLGKFPELFNWFKNFLGYKESVHLETYPKERATEGIAMEIDYASCKRLGSSYRALPKSYQQPKCTGRTPLCKEVLNDTWVSFPSWSEDSTFVSSKKTQYEEHIYRCEDERFELDVVLETNLATIRVLEAIQKKLSRLSAEEQAKFRLDNTLGGTSEVIHRKALQRIYADKAADIIDGLRKNPSIAVPIVLKRLKMKEEEWREAQRGFNKVWREQNEKYYLKSLDHQGINFKQNDTKVLRSKSLLNEIESIYDERQEQATEENAGVPVGPHLSLAYEDKQILEDAAALIIHHVKRQTGIQKEDKYKIKQIMHHFIPDLLFAQRGDLSDVEEEEEEEMDVDEATGAVKKHNGVGGSPPKSKLLFSNTAAQKLRGMDEVYNLFYVNNNWYIFMRLHQILCLRLLRICSQAERQIEEENREREWEREVLGIKRDKSDSPAIQLRLKEPMDVDVEDYYPAFLDMVRSLLDGNIDSSQYEDSLREMFTIHAYIAFTMDKLIQSIVRQLQHIVSDEICVQVTDLYLAENNNGATGGQLNTQNSRSLLESTYQRKAEQLMSDENCFKLMFIQSQGQVQLTIELLDTEEENSDDPVEAERWSDYVERYMNSDTTSPELREHLAQKPVFLPRNLRRIRKCQRGREQQEKEGKEGNSKKTMENVDSLDKLECRFKLNSYKMVYVIKSEDYMYRRTALLRAHQSHERVSKRLHQRFQAWVDKWTKEHVPREMAAETSKWLMGEGLEGLVPCTTTCDTETLHFVSINKYRVKYGTVFKAP DIP protein Q96ST3 original sequence version: 128 DIP protein Q96ST3 original sequence version: 147 E6A329BE0EAD84CD hdac2_human Histone deacetylase 2 HDAC2 protein protein human Homo sapiens Human MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEEFSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGTKSEQLSNP DIP protein Q92769 original sequence version: 161 DIP protein Q92769 original sequence version: 154 DIP protein Q92769 original sequence version: 117 DIP protein Q92769 original sequence version: 113 DIP protein Q92769 original sequence version: 139 DIP protein Q92769 original sequence version: 163 DIP protein Q92769 original sequence version: 179 DIP protein Q92769 original sequence version: 153 DIP protein Q92769 original sequence version: 112 775419CCCDAE07FA tgfbrii_promoter_sp1_probe_no_3 ds dna double stranded deoxyribonucleic acid ds DNA ds dna human Homo sapiens Human GGGGCTGG tgfbrii_promoter_sp1_consensus_probe-sp6-1 3 12 unspecified role unspecified role bait bait G_G11-12T_T mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain GG TT region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction 5B (lane1+2) tgfbrii_promoter_sp1_consensus_probe-sp6-2 3 11 competitor competitor competitor prey prey 12 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined G_G11-12T_T mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain GG TT chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction 5B (lane 3) tgfbrii_promoter_sp1_probe_no_1-sp6-1 3 7 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction 5B (lane 4) Lanes 5+6 show competition from mutated versions of the probe; but no sequence/mutations are stated. tgfbrii_promoter_sp1_probe_no_1-sp6-2 3 7 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) 7 competitor competitor competitor prey prey direct interaction direct interaction 5B (lane 7+8) tgfbrii_promoter_sp1_probe_no_1-sp6-3 1 7 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) physical association physical association 5B (lane 9) tgfbrii_promoter_sp1_probe_no_1-sp1-1 3 11 competitor competitor competitor prey prey 7 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction 5B (lane 10+11) tgfbrii_promoter_sp1_probe_no_2-sp1-1 3 11 competitor competitor competitor prey prey 6 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction 5B (lane 10+11) tgfbrii_promoter_sp1_probe_no_2-sp6-1 3 6 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction 5B (lane 4) Lanes 5+6 show competition from mutated versions of the probe; but no sequence/mutations are stated. tgfbrii_promoter_sp1_probe_no_2-sp6-2 3 6 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) 6 competitor competitor competitor prey prey direct interaction direct interaction 5B (lane 7+8) tgfbrii_promoter_sp1_probe_no_2-sp6-3 1 6 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) physical association physical association 5B (lane 9) tgfbrii_promoter_sp1_probe_no_3-sp6-1 3 16 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction 5B (lane 4) Lanes 5+6 show competition from mutated versions of the probe; but no sequence/mutations are stated. tgfbrii_promoter_sp1_probe_no_3-sp6-2 3 16 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) 16 competitor competitor competitor prey prey direct interaction direct interaction 5B (lane 7+8) tgfbrii_promoter_sp1_probe_no_3-sp1-1 3 11 competitor competitor competitor prey prey 16 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction 5B (lane 10+11) tgfbrii_promoter_sp1_probe_no_4-sp1-1 3 11 competitor competitor competitor prey prey 5 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction 5B (lane 10+11) Weak binding only, was seen using probe #4 tgfbrii_promoter_sp1_probe_no_4-sp6-1 3 5 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction 5B (lane 4) Lanes 5+6 show competition from mutated versions of the probe; but no sequence/mutations are stated. Weak binding only, was seen using probe #4 tgfbrii_promoter_sp1_probe_no_4-sp6-2 3 5 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) 5 competitor competitor competitor prey prey direct interaction direct interaction 5B (lane 7+8) Weak binding only, was seen using probe #4 tgfbrii_promoter_sp1_probe_no_5-sp6-1 3 8 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) 8 competitor competitor competitor prey prey direct interaction direct interaction 5B (lane 7+8) tgfbrii_promoter_sp1_probe_no_5-sp1-1 3 11 competitor competitor competitor prey prey 8 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction 5B (lane 10+11) tgfbrii_promoter_sp1_probe_no_5-sp6-2 3 8 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction 5B (lane 4) Lanes 5+6 show competition from mutated versions of the probe; but no sequence/mutations are stated. tgfbrii_promoter_sp1_probe_no_5-sp6-3 1 8 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) physical association physical association 5B (lane 9) tgfbrii_promoter_sp1_probe_no_3-sp6-3 1 16 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) physical association physical association 5B (lane 9) tgfbrii_promoter_sp1_probe_no_4-sp6-3 1 5 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 13 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 n_terminus 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 ecoli Escherichia coli (strain K12) physical association physical association 5B (lane 9) sp6-hdac2-1 2 14 unspecified role unspecified role prey prey 15 unspecified role unspecified role prey prey 13 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 6B sp6-tgfbr2-1 4 9 unspecified role unspecified role prey prey promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 13 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 6 C/D TGF-beta Q3SY56 decreases expression at RNA level of ENSG00000163513 causality from Fig 3 + elsewhere sin3a-tgfbr2-1 4 9 unspecified role unspecified role prey prey promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 14 unspecified role unspecified role bait bait association association 6 D TGF-beta Sin3A only binds in the presence of TGF-beta. hist1h4a-tgfbr2-1 4 9 unspecified role unspecified role prey prey promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 10 unspecified role unspecified role bait bait association association 6 Di TGF-beta Histone H4 only binds in the absence of TGF-beta sin3a-tgfbr2-2 4 9 unspecified role unspecified role prey prey promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 10 unspecified role unspecified role bait bait lys21 n6me3+lys N6,N6,N6-trimethyl-L-lysine (5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminium 2-amino-6-(trimethylammonio)hexanoic acid 5-azanyl-5-carboxy-N,N,N-trimethylpentanazanium MOD_RES N6,N6,N6-trimethyllysine N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine N6,N6,N6-trimethylated L-lysine N6,N6,N6-trimethyllysin-N6-ium N6,N6,N6-trimethyllysine cation epsilon-trimethyllysine N-trimethylation (of lysine) N6Me3+Lys Trimethyl tri-Methylation certain certain sequence position certain certain certain sequence position certain observed-ptm observed-ptm observed ptm observed-ptm association association 6 Dii TGF-beta Tri-methylated (K21) Histone H4 only binds in the presence of TGF-beta.