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/ FOXP3 Controls an miR-146/NF-κB Negative Feedback Loop That Inhibits Apoptosis in Breast Cancer Cells. FOXP3 Controls an miR-146/NF-κB Negative Feedback Loop That Inhibits Apoptosis in Breast Cancer Cells. Cancer research 2015 imex curation Liu R., Liu C., Chen D., Yang WH., Liu X., Liu CG., Dugas CM., Tang F., Zheng P., Liu Y., Wang L. Cancer - Interactions investigated in the context of cancer IBD - Inflammatory bowel disease lwang12@uab.edu,runhua@uab.edu 21-Mar-2017: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-mcf7 Homo sapiens mammary carcinoma cells mcf7 mammary carcinoma cells ch-ip chromatin immunoprecipitation assay ch-ip nucleotide sequence nucleotide sequence identification sequence cloning sequence cloning nucleotide sequence Liu R., Liu C., Chen D., Yang WH., Liu X., Liu CG., Dugas CM., Tang F., Zheng P., Liu Y., Wang L. Cancer - Interactions investigated in the context of cancer Results from Table S1 state that mir-1974 shows a decrease in expression after FOXP3 binding, however miRBase and the HGNC have withdrawn the entry for Mir-1974: it maps to the Mt genome, and overlaps a Mt tRNA sequence, so has been removed. It is not mentioned but I assume the red/green bands are those miRNAs whose expression relates to :-"a cutoff of at least a 1.5-fold change in miR expression after FOXP3 induction and no significant change (<1.5-fold) in the GFP-Tet-off MCF7 control cells....... to identify potential FOXP3-target miRs. ". (So I have NOT entered any "white" MiRNAs =-?non-specific binding??.) Results show FOXP3 binding to regions within 2 KB of MiRNA transcription start sites for MiRNAs with >1.5 fold change in expression after FOXP3 induction and no significant change in control cells. MiRNA expression was determined by TaqMan assay in the presence and absence of Doxycycline. FOXP3-Tet-off MCF7 cells -doxycycline removal results in FOXP3 expression. lwang12@uab.edu,runhua@uab.edu Accepted 2017-JAN-18 AT 12:56 GMT AT 12:56 GMT by PPORRAS Cancer research 2015 Only protein-protein interactions imex curation imex curation Fig 5F has a recombinant protein - which is annotated here - Supp Fig 6 only has a lysate/extract which we do not annotate as there is no identification of what is binding. In the light of our recent conversation I have added for "Expt Prep" the term "partially purified" to the GST tagged FOXP3 protein - please remove if you dont like this! - especially as I can find no info as to how the protein was purified - though it must be to some extent?? - as a "cell free protein"? FOXP3 Controls an miR-146/NF-κB Negative Feedback Loop That Inhibits Apoptosis in Breast Cancer Cells. FOXP3 Controls an miR-146/NF-κB Negative Feedback Loop That Inhibits Apoptosis in Breast Cancer Cells. Cancer research 2015 imex curation Liu R., Liu C., Chen D., Yang WH., Liu X., Liu CG., Dugas CM., Tang F., Zheng P., Liu Y., Wang L. Cancer - Interactions investigated in the context of cancer IBD - Inflammatory bowel disease lwang12@uab.edu,runhua@uab.edu 21-Mar-2017: 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 tag visualisation tag visualisation Liu R., Liu C., Chen D., Yang WH., Liu X., Liu CG., Dugas CM., Tang F., Zheng P., Liu Y., Wang L. Cancer - Interactions investigated in the context of cancer lwang12@uab.edu,runhua@uab.edu Accepted 2017-JAN-18 AT 12:56 GMT AT 12:56 GMT by PPORRAS Cancer research 2015 Only protein-protein interactions imex curation imex curation Fig 5F has a recombinant protein - which is annotated here - Supp Fig 6 only has a lysate/extract which we do not annotate as there is no identification of what is binding. In the light of our recent conversation I have added for "Expt Prep" the term "partially purified" to the GST tagged FOXP3 protein - please remove if you dont like this! - especially as I can find no info as to how the protein was purified - though it must be to some extent?? - as a "cell free protein"? FOXP3 Controls an miR-146/NF-κB Negative Feedback Loop That Inhibits Apoptosis in Breast Cancer Cells. FOXP3 Controls an miR-146/NF-κB Negative Feedback Loop That Inhibits Apoptosis in Breast Cancer Cells. Cancer research 2015 imex curation Liu R., Liu C., Chen D., Yang WH., Liu X., Liu CG., Dugas CM., Tang F., Zheng P., Liu Y., Wang L. Cancer - Interactions investigated in the context of cancer IBD - Inflammatory bowel disease lwang12@uab.edu,runhua@uab.edu 21-Mar-2017: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-mcf7 Homo sapiens mammary carcinoma cells mcf7 mammary carcinoma cells anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Liu R., Liu C., Chen D., Yang WH., Liu X., Liu CG., Dugas CM., Tang F., Zheng P., Liu Y., Wang L. Cancer - Interactions investigated in the context of cancer lwang12@uab.edu,runhua@uab.edu Accepted 2017-JAN-18 AT 12:56 GMT AT 12:56 GMT by PPORRAS Cancer research 2015 Only protein-protein interactions imex curation imex curation Fig 5F has a recombinant protein - which is annotated here - Supp Fig 6 only has a lysate/extract which we do not annotate as there is no identification of what is binding. In the light of our recent conversation I have added for "Expt Prep" the term "partially purified" to the GST tagged FOXP3 protein - please remove if you dont like this! - especially as I can find no info as to how the protein was purified - though it must be to some extent?? - as a "cell free protein"? FOXP3 Controls an miR-146/NF-κB Negative Feedback Loop That Inhibits Apoptosis in Breast Cancer Cells. FOXP3 Controls an miR-146/NF-κB Negative Feedback Loop That Inhibits Apoptosis in Breast Cancer Cells. Cancer research 2015 imex curation Liu R., Liu C., Chen D., Yang WH., Liu X., Liu CG., Dugas CM., Tang F., Zheng P., Liu Y., Wang L. Cancer - Interactions investigated in the context of cancer IBD - Inflammatory bowel disease lwang12@uab.edu,runhua@uab.edu 21-Mar-2017: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-mcf7 Homo sapiens mammary carcinoma cells mcf7 mammary carcinoma cells ch-ip chromatin immunoprecipitation assay ch-ip q-pcr quantitative pcr q-pcr Liu R., Liu C., Chen D., Yang WH., Liu X., Liu CG., Dugas CM., Tang F., Zheng P., Liu Y., Wang L. Cancer - Interactions investigated in the context of cancer lwang12@uab.edu,runhua@uab.edu Accepted 2017-JAN-18 AT 12:56 GMT AT 12:56 GMT by PPORRAS Cancer research 2015 Only protein-protein interactions imex curation imex curation Fig 5F has a recombinant protein - which is annotated here - Supp Fig 6 only has a lysate/extract which we do not annotate as there is no identification of what is binding. In the light of our recent conversation I have added for "Expt Prep" the term "partially purified" to the GST tagged FOXP3 protein - please remove if you dont like this! - especially as I can find no info as to how the protein was purified - though it must be to some extent?? - as a "cell free protein"? mir-181d_human_gene gene gene human Homo sapiens Human mir663b_human_gene gene gene human Homo sapiens Human mir-584_human_gene gene gene human Homo sapiens Human mir-9-2_human_gene gene gene human Homo sapiens Human tf65_human Transcription factor p65 Nuclear factor NF-kappa-B p65 subunit RELA NFKB3 Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3 protein protein human Homo sapiens Human MDELFPLIFPAEPAQASGPYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLVTKDPPHRPHPHELVGKDCRDGFYEAELCPDRCIHSFQNLGIQCVKKRDLEQAISQRIQTNNNPFQVPIEEQRGDYDLNAVRLCFQVTVRDPSGRPLRLPPVLSHPIFDNRAPNTAELKICRVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPYADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPDTDDRHRIEEKRKRTYETFKSIMKKSPFSGPTDPRPPPRRIAVPSRSSASVPKPAPQPYPFTSSLSTINYDEFPTMVFPSGQISQASALAPAPPQVLPQAPAPAPAPAMVSALAQAPAPVPVLAPGPPQAVAPPAPKPTQAGEGTLSEALLQLQFDDEDLGALLGNSTDPAVFTDLASVDNSEFQQLLNQGIPVAPHTTEPMLMEYPEAITRLVTGAQRPPDPAPAPLGAPGLPNGLLSGDEDFSSIADMDFSALLSQISS DIP protein Q04206 original sequence version: 170 DIP protein Q04206 original sequence version: 173 DIP protein Q04206 original sequence version: 99 DIP protein Q04206-1 original sequence version: 99 DIP protein Q04206 original sequence version: 168 DIP protein Q04206 original sequence version: 128 DIP protein Q04206 original sequence version: 131 DIP protein Q04206 original sequence version: 153 DIP protein Q04206 original sequence version: 185 DIP protein Q04206 original sequence version: 181 DIP protein Q04206 original sequence version: 183 8147A6AF9F2445C6 mir-1299_human_gene gene gene human Homo sapiens Human mir993_human_gene gene gene human Homo sapiens Human mir-1539_human_gene gene gene human Homo sapiens Human mir-1206_human_gene gene gene human Homo sapiens Human mir-21_human_gene gene gene human Homo sapiens Human mir-1204_human_gene gene gene human Homo sapiens Human mir-146a_human_gene microRNA-146a (miR-146a) human gene gene gene human Homo sapiens Human mir-1915_human_gene gene gene human Homo sapiens Human mir146a_first_probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human CACTTGAAAAGCCAACAGGCTCATTGGGCAGCCGATAAAGCTCTCGGGATTTCCCCGCGGGGCTG foxp3_human Forkhead box protein P3 Scurfin FOXP3 IPEX JM2 protein protein human Homo sapiens Human MPNPRPGKPSAPSLALGPSPGASPSWRAAPKASDLLGARGPGGTFQGRDLRGGAHASSSSLNPMPPSQLQLPTLPLVMVAPSGARLGPLPHLQALLQDRPHFMHQLSTVDAHARTPVLQVHPLESPAMISLTPPTTATGVFSLKARPGLPPGINVASLEWVSREPALLCTFPNPSAPRKDSTLSAVPQSSYPLLANGVCKWPGCEKVFEEPEDFLKHCQADHLLDEKGRAQCLLQREMVQSLEQQLVLEKEKLSAMQAHLAGKMALTKASSVASSDKGSCCIVAAGSQGPVVPAWSGPREAPDSLFAVRRHLWGSHGNSTFPEFLHNMDYFKFHNMRPPFTYATLIRWAILEAPEKQRTLNEIYHWFTRMFAFFRNHPATWKNAIRHNLSLHKCFVRVESEKGAVWTVDELEFRKKRSQRPSRCSNPTPGP DIP protein Q9BZS1 original sequence version: 139 DIP protein Q9BZS1 original sequence version: 131 91737C3CEA665A15 tnfa_human Tumor necrosis factor TNF TNFA TNFSF2 TNF-alpha Tumor necrosis factor ligand superfamily member 2 Cachectin protein protein human Homo sapiens Human MSTESMIRDVELAEEALPKKTGGPQGSRRCLFLSLFSFLIVAGATTLFCLLHFGVIGPQREEFPRDLSLISPLAQAVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL DIP protein P01375 original sequence version: 198 DIP protein P01375 original sequence version: 151 DIP protein P01375 original sequence version: 156 DIP protein P01375 original sequence version: 186 DIP protein P01375 original sequence version: 201 DIP protein P01375 original sequence version: 174 DIP protein P01375 original sequence version: 211 3DF90F96C9031FFE foxp3-mir663b_human_gene-1 1 6 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 19 unspecified role unspecified role bait bait association association Supp table 1 Q9BZS1 decreases the expression at RNA level of ENSG00000221288 foxp3-mir993_human_gene-1 1 11 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 19 unspecified role unspecified role bait bait association association Supp table 1-2 Q9BZS1 increases the expression at RNA level of ENSG00000215973 foxp3-mir993_human_gene-2 1 8 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 19 unspecified role unspecified role bait bait association association Supp table 1-3 Q9BZS1 increases the expression at RNA level of ENSG00000273878 foxp3-mir_584_human_gene-1 1 7 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 19 unspecified role unspecified role bait bait association association Supp table 1-4 Q9BZS1 decreases the expression at RNA level of ENSG00000207714 foxp3-mir_146a_human_gene-1 1 16 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 19 unspecified role unspecified role bait bait association association Supp table 1-5 Q9BZS1 increases the expression at RNA level of ENSG00000277727 foxp3-mir_1204_human_gene-1 1 15 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 19 unspecified role unspecified role bait bait association association Supp table 1-6 Q9BZS1 increases the expression at RNA level of ENSG00000275264 foxp3-mir_1206_human_gene-1 1 13 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 19 unspecified role unspecified role bait bait association association Supp table 1-7 Q9BZS1 decreases the expression at RNA level of MI0006339 MIR-1206 does not have an Ensembl entry; the gene was imported into ensembl from NCBI Ref-Seq for the use in a CCDS comparison between NCBI and Ensembl. foxp3-mir_1299_human_gene-1 1 10 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 19 unspecified role unspecified role bait bait association association Supp table 1-8 Q9BZS1 increases the expression at RNA level of ENSG00000275377 foxp3-mir_1915_human_gene-1 1 17 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 19 unspecified role unspecified role bait bait association association Supp table 1-9 Q9BZS1 increases the expression at RNA level of ENSG00000222071 foxp3-mir_21_human_gene-1 1 14 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 19 unspecified role unspecified role bait bait association association Supp table 1-10 Q9BZS1 decreases the expression at RNA level of ENSG00000199004 foxp3-mir_1539_human_gene-1 1 12 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 19 unspecified role unspecified role bait bait association association Supp table 1-11 Q9BZS1 increases the expression at RNA level of ENSG00000278544 foxp3-mir_181d_human_gene-1 1 5 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 19 unspecified role unspecified role bait bait association association Supp table 1-12 Q9BZS1 increases the expression at RNA level of ENSG00000207585 foxp3-mir_146a_human_gene-2 4 16 unspecified role unspecified role prey prey proximal_promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 19 unspecified role unspecified role bait bait association association 5B Q9BZS1 increased the expression at RNA level of ENSG00000277727 P01375 increased the expression at RNA level of ENSG00000277727 caus. from 5C/E CHEBI:85928 decreased the expression at RNA level of ENSG00000277727 mir146a_first_probe-foxp3-1 2 19 unspecified role unspecified role prey prey partially purified partially purified 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 in vitro In vitro 18 unspecified role unspecified role bait bait 5-prime biotin tag biotin tag certain certain sequence position certain certain certain sequence position certain physical association physical association 5F The only competitor i can see any decrease in binding is when using the WT comp. mir146a_first_probe-foxp3-2 2 18 competitor competitor competitor unspecified role unspecified role C12G,C13G,A14T,A15T,C16T,A17C mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain CCAACA GGTTTC 19 unspecified role unspecified role prey prey partially purified partially purified 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 in vitro In vitro 18 unspecified role unspecified role bait bait 5-prime biotin tag biotin tag certain certain sequence position certain certain certain sequence position certain physical association physical association 5Fi The only competitor i can see any decrease in binding is when using the WT comp.-the text does not illuminate. [Strictly speaking maybe the "mutant" sequences should be entered on the competitor as a "mutation increasing" - and the "DL" construct entered as a separate interaction, as it does bind (as the binding site is suppossed to be deleted, I dont think it IS meant to bind!) - but as I have had to hand type in the 60 mer WT sequence I think I can better spend my time elsewhere... w7s4y-1 3 20 unspecified role unspecified role ancillary ancillary 9 unspecified role unspecified role prey prey 19 unspecified role unspecified role bait bait physical association physical association 5G miR-146a/b mimics miR-146a/b inhibitors did not affect the interaction.