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/ liu-2015-15 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from Table S1 state that mir-1974 shows a decrease in expression after FOXP3 binding, however miRBase and the HGNC have withdrawn the entry for Mir-1974: it maps to the Mt genome, and overlaps a Mt tRNA sequence, so has been removed. 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 Cancer research 2015 Only protein-protein interactions imex curation imex curation IBD - Inflammatory bowel disease liu-2015-17 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 Cancer research 2015 Only protein-protein interactions imex curation imex curation IBD - Inflammatory bowel disease liu-2015-16 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 Cancer research 2015 Only protein-protein interactions imex curation imex curation IBD - Inflammatory bowel disease liu-2015-18 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 Cancer research 2015 Only protein-protein interactions imex curation imex curation IBD - Inflammatory bowel disease mir663b_human_gene gene gene human Homo sapiens Human foxp3_human Forkhead box protein P3 Scurfin FOXP3 IPEX JM2 protein protein human Homo sapiens Human MPNPRPGKPSAPSLALGPSPGASPSWRAAPKASDLLGARGPGGTFQGRDLRGGAHASSSSLNPMPPSQLQLPTLPLVMVAPSGARLGPLPHLQALLQDRPHFMHQLSTVDAHARTPVLQVHPLESPAMISLTPPTTATGVFSLKARPGLPPGINVASLEWVSREPALLCTFPNPSAPRKDSTLSAVPQSSYPLLANGVCKWPGCEKVFEEPEDFLKHCQADHLLDEKGRAQCLLQREMVQSLEQQLVLEKEKLSAMQAHLAGKMALTKASSVASSDKGSCCIVAAGSQGPVVPAWSGPREAPDSLFAVRRHLWGSHGNSTFPEFLHNMDYFKFHNMRPPFTYATLIRWAILEAPEKQRTLNEIYHWFTRMFAFFRNHPATWKNAIRHNLSLHKCFVRVESEKGAVWTVDELEFRKKRSQRPSRCSNPTPGP mir993_human_gene gene gene human Homo sapiens Human mir-9-2_human_gene gene gene human Homo sapiens Human mir-584_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-1204_human_gene gene gene human Homo sapiens Human mir-1206_human_gene gene gene human Homo sapiens Human mir-1299_human_gene gene gene human Homo sapiens Human mir-1915_human_gene gene gene human Homo sapiens Human mir-21_human_gene gene gene human Homo sapiens Human mir-1539_human_gene gene gene human Homo sapiens Human mir-181d_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 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 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 foxp3-mir663b_human_gene-1 1876249 N/A 1876253 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false Supp table 1 Q9BZS1 decreases the expression at RNA level of ENSG00000221288 foxp3-mir993_human_gene-1 1876249 N/A 1876255 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false Supp table 1-2 Q9BZS1 increases the expression at RNA level of ENSG00000215973 foxp3-mir993_human_gene-2 1876249 N/A 1876256 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false Supp table 1-3 Q9BZS1 increases the expression at RNA level of ENSG00000273878 foxp3-mir_584_human_gene-1 1876249 N/A 1876257 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false Supp table 1-4 Q9BZS1 decreases the expression at RNA level of ENSG00000207714 foxp3-mir_146a_human_gene-1 1876249 N/A 1876258 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false Supp table 1-5 Q9BZS1 increases the expression at RNA level of ENSG00000277727 foxp3-mir_1204_human_gene-1 1876249 N/A 1876259 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false Supp table 1-6 Q9BZS1 increases the expression at RNA level of ENSG00000275264 foxp3-mir_1206_human_gene-1 1876249 N/A 1876260 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false 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 1876249 N/A 1876261 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false Supp table 1-8 Q9BZS1 increases the expression at RNA level of ENSG00000275377 foxp3-mir_1915_human_gene-1 1876249 N/A 1876262 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false Supp table 1-9 Q9BZS1 increases the expression at RNA level of ENSG00000222071 foxp3-mir_21_human_gene-1 1876249 N/A 1876263 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false Supp table 1-10 Q9BZS1 decreases the expression at RNA level of ENSG00000199004 foxp3-mir_1539_human_gene-1 1876249 N/A 1876264 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false Supp table 1-11 Q9BZS1 increases the expression at RNA level of ENSG00000278544 foxp3-mir_181d_human_gene-1 1876249 N/A 1876265 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false Supp table 1-12 Q9BZS1 increases the expression at RNA level of ENSG00000207585 mir146a_first_probe-foxp3-1 1876250 N/A 1876254 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 false in vitro In vitro N/A 1876266 unspecified role unspecified role bait bait 5-prime biotin tag biotin tag certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false 5F mir146a_first_probe-foxp3-2 1876250 N/A 1876266 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 false N/A 1876254 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 false in vitro In vitro N/A 1876266 unspecified role unspecified role bait bait 5-prime biotin tag biotin tag certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false 5Fi foxp3-mir_146a_human_gene-2 1876251 N/A 1876258 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 false N/A 1876254 unspecified role unspecified role bait bait association association false false false 5B Q9BZS1 increased the expression at RNA level of ENSG00000277727 P01375 increased the expression at RNA level of ENSG00000277727 CHEBI:85928 decreased the expression at RNA level of ENSG00000277727 w7s4y-1 1876252 N/A 1876267 unspecified role unspecified role ancillary ancillary N/A 1876268 unspecified role unspecified role prey prey N/A 1876254 unspecified role unspecified role bait bait physical association physical association false false false 5G miR-146a/b mimics miR-146a/b inhibitors did not affect the interaction.