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/ kim-2008a-1 Arabidopsis WRKY38 and WRKY62 Transcription Factors Interact with Histone Deacetylase 19 in Basal Defense. nicbe Nicotiana benthamiana bifc bimolecular fluorescence complementation bifc tag fluorescence tag visualisation by fluorescence tag fluorescence Kim KC., Lai Z., Fan B., Chen Z. zhixiang@purdue.edu Plant Cell (1040-4651) 2008 Only protein-protein interactions imex curation kim-2008a-3 Arabidopsis WRKY38 and WRKY62 Transcription Factors Interact with Histone Deacetylase 19 in Basal Defense. in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Kim KC., Lai Z., Fan B., Chen Z. zhixiang@purdue.edu Plant Cell (1040-4651) 2008 Only protein-protein interactions imex curation kim-2008a-5 Arabidopsis WRKY38 and WRKY62 Transcription Factors Interact with Histone Deacetylase 19 in Basal Defense. nicbe Nicotiana benthamiana anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Kim KC., Lai Z., Fan B., Chen Z. Transgenic Arabidopsis plants expressing epitope tagged proteins of interest were used in this study. zhixiang@purdue.edu Plant Cell (1040-4651) 2008 Only protein-protein interactions imex curation kim-2008a-2 Arabidopsis WRKY38 and WRKY62 Transcription Factors Interact with Histone Deacetylase 19 in Basal Defense. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid nucleotide sequence nucleotide sequence identification sequence cloning sequence cloning nucleotide sequence Kim KC., Lai Z., Fan B., Chen Z. The yeast CytoTrap system based on interactiondependent activation of the Ras signaling pathway and cell growth in a temperature-sensitive yeast mutant. zhixiang@purdue.edu Arabidopsis plants sprayed with 2mM salicyclic acid 4 hours before harvesting and cDNA library construction. Plant Cell (1040-4651) 2008 Only protein-protein interactions imex curation kim-2008a-4 Arabidopsis WRKY38 and WRKY62 Transcription Factors Interact with Histone Deacetylase 19 in Basal Defense. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Kim KC., Lai Z., Fan B., Chen Z. The yeast CytoTrap system based on interactiondependent activation of the Ras signaling pathway and cell growth in a temperature-sensitive yeast mutant. zhixiang@purdue.edu Plant Cell (1040-4651) 2008 Only protein-protein interactions imex curation hda19_arath Histone deacetylase 19 HDA19 At4g38130 F20D10.250 HD1 HDA1 RPD3A protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MDTGGNSLASGPDGVKRKVCYFYDPEVGNYYYGQGHPMKPHRIRMTHALLAHYGLLQHMQVLKPFPARDRDLCRFHADDYVSFLRSITPETQQDQIRQLKRFNVGEDCPVFDGLYSFCQTYAGGSVGGSVKLNHGLCDIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKQHERVLYVDIDIHHGDGVEEAFYATDRVMTVSFHKFGDYFPGTGHIQDIGYGSGKYYSLNVPLDDGIDDESYHLLFKPIMGKVMEIFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVKFMRSFNVPLLLLGGGGYTIRNVARCWCYETGVALGVEVEDKMPEHEYYEYFGPDYTLHVAPSNMENKNSRQMLEEIRNDLLHNLSKLQHAPSVPFQERPPDTETPEVDEDQEDGDKRWDPDSDMDVDDDRKPIPSRVKREAVEPDTKDKDGLKGIMERGKGCEVEVDESGSTKVTGVNPVGVEEASVKMEEEGTNKGGAEQAFPPKT wrk62_arath Probable WRKY transcription factor 62 WRKY62 WRKY DNA-binding protein 62 T20L15.170 At5g01900 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MNSCQQKAMEKLLHGHGCANQLLIMDQTESDSSMEREDLAKSVLHCFSDALSILIDTNDHQDDQSNNSSPQDSSPVLESSRKPLHKRGRKTSMAESSDYHRHESSTPIYHDGFLWRKYGQKQIKESEYQRSYYKCAYTKDQNCEAKKQVQKIQHNPPLYSTTYFGQHICQLHQAYATFPIDTSDFEEHEGSHMIRFGHPNISFSSSTSNLRQHQNHQDRIKDEYMKPVIAEDWSPSQWMSSEVALAVEAFEFNPFWTSHDLSS wrk38_arath Probable WRKY transcription factor 38 WRKY38 WRKY DNA-binding protein 38 MQJ16.11 At5g22570 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MEMNSPHEKAVQAIRYGHSCAMRLKRRLNHPMADGGPLSSYDLAKSIVESFSNAISILSAKPETEDDQFSDLSSRDSSPPPQGSPSKKRKIDSTNSSENWRDDSPDPIYYDGYLWRKYGQKSIKKSNHQRSYYRCSYNKDHNCEARKHEQKIKDNPPVYRTTYFGHHTCKTEHNLDAIFIAGQDPLDDFKSTQMIRFGKDQDQEKESRSNGFSLSVKHEEDIIKEQAIDQYREITSNDQDCQDVIEEYLSSPSGSYPPSSSSGSESADFNSDLLFDNPDSWDRYDQFYF wrk18_arath WRKY transcription factor 18 WRKY18 WRKY DNA-binding protein 18 F28M20.10 At4g31800 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MDGSSFLDISLDLNTNPFSAKLPKKEVSVLASTHLKRKWLEQDESASELREELNRVNSENKKLTEMLARVCESYNELHNHLEKLQSRQSPEIEQTDIPIKKRKQDPDEFLGFPIGLSSGKTENSSSNEDHHHHHQQHEQKNQLLSCKRPVTDSFNKAKVSTVYVPTETSDTSLTVKDGFQWRKYGQKVTRDNPSPRAYFRCSFAPSCPVKKKVQRSAEDPSLLVATYEGTHNHLGPNASEGDATSQGGSSTVTLDLVNGCHRLALEKNERDNTMQEVLIQQMASSLTKDSKFTAALAAAISGRLMEQSRT wrk40_arath Probable WRKY transcription factor 40 WRKY40 WRKY DNA-binding protein 40 F23A5.19 At1g80840 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MDQYSSSLVDTSLDLTIGVTRMRVEEDPPTSALVEELNRVSAENKKLSEMLTLMCDNYNVLRKQLMEYVNKSNITERDQISPPKKRKSPAREDAFSCAVIGGVSESSSTDQDEYLCKKQREETVVKEKVSRVYYKTEASDTTLVVKDGYQWRKYGQKVTRDNPSPRAYFKCACAPSCSVKKKVQRSVEDQSVLVATYEGEHNHPMPSQIDSNNGLNRHISHGGSASTPVAANRRSSLTVPVTTVDMIESKKVTSPTSRIDFPQVQKLLVEQMASSLTKDPNFTAALAAAVTGKLYQQNHTEK wbox-arath-dna ds dna double stranded deoxyribonucleic acid ds DNA ds dna arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress AACTTTGACCAATCTTTCAAGTA The oligonucleotide contains a W box (TTGACC/T). wrky62-hda19-2 WRKY62 interacts with HDA19 765272 n/a 765277 unspecified role unspecified role neutral component neutral component region C-terminal region YFP protein yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 765278 unspecified role unspecified role neutral component neutral component region N-terminal region YFP protein yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false direct interaction direct interaction false false false Figure 5 wrky38-hda19-3 WRKY38 interacts with HDA19 765272 n/a 765279 unspecified role unspecified role neutral component neutral component region N-terminal region YFP protein yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 765277 unspecified role unspecified role neutral component neutral component region C-terminal region YFP protein yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false direct interaction direct interaction false false false Figure 5 wrky18-wrky40 WRKY18 interacts with WRKY40 765272 n/a 765280 unspecified role unspecified role neutral component neutral component n/a 765281 unspecified role unspecified role neutral component neutral component direct interaction direct interaction false false false Supplementary Figure 5 wrky62-dna WRKY62 interacts with W box oligonucleotide 765273 n/a 765282 unspecified role unspecified role bait bait n/a 765278 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Figure 1B The authors noted that "binding of the WRKY proteins to a mutant probe (mP12a) in which the TTGACC sequence was changed to TTGAAC was not detectable". The authors conclude "binding of WRKY38 and WRKY62 to the TTGACC W-box sequence is highly specific". wrky38-dna WRKY38 interacts with W box oligonucleotide 765273 n/a 765279 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 765282 unspecified role unspecified role bait bait direct interaction direct interaction false false false Supplementary Figure 1B The authors noted that "binding of the WRKY proteins to a mutant probe (mP12a) in which the TTGACC sequence was changed to TTGAAC was not detectable". The authors conclude "binding of WRKY38 and WRKY62 to the TTGACC W-box sequence is highly specific". wrky38-hda19-4 WRKY38 interacts with HDA19 765274 n/a 765277 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 765279 unspecified role unspecified role prey prey 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 false physical association physical association false false false Supplementary Figure 4B wrky62-hda19-4 WRKY62 interacts with HDA19 765274 n/a 765277 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 765278 unspecified role unspecified role prey prey 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 false direct interaction direct interaction false false false Supplementary Figure 4B wrky62-hda19 WRKY62 interacts with HDA19 765275 n/a 765278 unspecified role unspecified role bait bait n/a 765277 unspecified role unspecified role prey prey physical association physical association false false false wrky62-hda19-1 WRKY62 interacts with HDA19 765276 n/a 765278 unspecified role unspecified role bait bait n/a 765277 unspecified role unspecified role prey prey physical association physical association false false false Supplementary Figure 4A