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/ soleimanpour-2014-1 The diabetes susceptibility gene Clec16a regulates mitophagy. mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells anti tag coip anti tag coimmunoprecipitation anti tag coip sequence tag sequence tag identification sequence tag Soleimanpour S.A., Gupta A., Bakay M., Ferrari A.M., Groff D.N., Fadista J., Spruce L.A., Kushner J.A., Groop L., Seeholzer S.H., Kaufman B.A., Hakonarson H., Stoffers D.A. Diabetes - Interactions investigated in the context of Diabetes NIH 3T3 fibroblasts containing Flag-tagged Clec16a were grown in heavy isotopic abundance medium (13C6,15N2-lysine and 13C6,15N4-arginine), whereas wild-type cells were grown in light (12C, 14N), natural isotope abundance medium. Equal quantities of the two cell preparations were mixed, and the epitope-tagged protein complex was isolated. Specific protein interactions are identified by mass spectrometry as isotopically heavy, whereas non-specific interactions appear as a mixture of isotopically light and heavy. stoffers@mail.med.upenn.edu Cell (0092-8674) 2014 Only protein-protein interactions imex curation soleimanpour-2014-2 The diabetes susceptibility gene Clec16a regulates mitophagy. mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Soleimanpour S.A., Gupta A., Bakay M., Ferrari A.M., Groff D.N., Fadista J., Spruce L.A., Kushner J.A., Groop L., Seeholzer S.H., Kaufman B.A., Hakonarson H., Stoffers D.A. Diabetes - Interactions investigated in the context of Diabetes NIH 3T3 fibroblasts containing Flag-tagged Clec16a were grown in heavy isotopic abundance medium (13C6,15N2-lysine and 13C6,15N4-arginine), whereas wild-type cells were grown in light (12C, 14N), natural isotope abundance medium. Equal quantities of the two cell preparations were mixed, and the epitope-tagged protein complex was isolated. Specific protein interactions are identified by mass spectrometry as isotopically heavy, whereas non-specific interactions appear as a mixture of isotopically light and heavy. stoffers@mail.med.upenn.edu Cell (0092-8674) 2014 Only protein-protein interactions imex curation soleimanpour-2014-3 The diabetes susceptibility gene Clec16a regulates mitophagy. mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells anti bait coip anti bait coimmunoprecipitation anti bait coip anti tag western anti tag western blot anti tag western Soleimanpour S.A., Gupta A., Bakay M., Ferrari A.M., Groff D.N., Fadista J., Spruce L.A., Kushner J.A., Groop L., Seeholzer S.H., Kaufman B.A., Hakonarson H., Stoffers D.A. Diabetes - Interactions investigated in the context of Diabetes NIH 3T3 fibroblasts containing Flag-tagged Clec16a were grown in heavy isotopic abundance medium (13C6,15N2-lysine and 13C6,15N4-arginine), whereas wild-type cells were grown in light (12C, 14N), natural isotope abundance medium. Equal quantities of the two cell preparations were mixed, and the epitope-tagged protein complex was isolated. Specific protein interactions are identified by mass spectrometry as isotopically heavy, whereas non-specific interactions appear as a mixture of isotopically light and heavy. stoffers@mail.med.upenn.edu Cell (0092-8674) 2014 Only protein-protein interactions imex curation rnf41_mouse E3 ubiquitin-protein ligase NRDP1 Rnf41 Flrf Nrdp1 RING finger protein 41 RING-type E3 ubiquitin transferase NRDP1 protein protein mouse Mus musculus Mouse MGYDVTRFQGDVDEDLICPICSGVLEEPVQAPHCEHAFCNACITQWFSQQQTCPVDRSVVTVAHLRPVPRIMRNMLSKLQIACDNAVFGCSAVVRLDNLMSHLSDCEHNPKRPVTCEQGCGLEMPKDELPNHNCIKHLRSVVQQQQSRIAELEKTSAEHKHQLAEQKRDIQLLKAYMRAIRSVNPNLQNLEETIEYNEILEWVNSLQPARVTRWGGMISTPDAVLQAVIKRSLVESGCPASIVNELIENAHERSWPQGLATLETRQMNRRYYENYVAKRIPGKQAVVVMACENQHMGDDMVQEPGLVMIFAHGVEEI mint q80u30-2 Protein CLEC16A Clec16a Kiaa0350 protein protein mouse Mus musculus Mouse MFGRSRSWVGGGHSKSSRNIHSLDHLKYLYHVLTKNTTVTEQNRNLLVETIRSITEILIWGDQNDSSVFDFFLEKNMFVFFLNILRQKSGRYVCVQLLQTLNILFENISHETSLYYLLSNNYVNSIIVHKFDFSDEEIMAYYISFLKTLSLKLNNHTVHFFYNEHTNDFALYTEAIKFFNHPESMVRIAVRTITLNVYKVDNQAMLHYIRDKTAVPYFSNLVWFIGSHVIELDNCVQTDEEHRNRGKLSDLVAEHLDHLHYLNDILIINCEFLNDVLTDHLLNRLFLPLYVYSLENPDKGGERPKISLPVSLYLLSQVFLIIHHAPLVNSLAEVILNGDLSETYTKPAQDVPRSSAKPSIRCFIKPTETLERSLEMNKHKGKKRMQKRPNYKNVGEEEDEERGSAEDAQEDAEKTKEIEMVIMKLGKLSEVAAAGTSVQEQNTTDEEKSAATNSENAQWSRPFLDMVYHALDSPDDDYHALFVLCLLYAMSHNKGMDPEKLKRIQLPVPSEAEKTTYNHLLAERLIRIMNNAAQPDGRIRLATLELSCLLLKQQVLTSSGCVIKDVHLACLEGAREESVHLVRHFYKGEEIFLDMFEDEYRSMTIKPMNVEYLMMDASILLPPTGTPLTGIDFVKRLPCGDVEKTRRAIRVFFMLRSLSLQLRGEPETQLPLTREEDLIKTDDVLDLNNSDLIACTVITKDGGMVQRFLAVDIYQMSLVEPDVSRLGWGVVKFAGLLQDMQVTGVEDDSRALNITIHKPASSPHSKPFPILQATFVFSDHIRCIIAKQRLAKGRIQARRMKMQRIAALLDLPIQPTTEVLGFGLCSSSSSSQHLPFRFYEQCRRGSSDPTVQRSVFASVDKVPGFAVAQCINQHSSPSLSSPSPPFASGSPGGSGSTSHCDSGGSSSAPSATQSPADAPTTPEQPQPHLDQSVIGNEMDVNSKPSKNSSARSSEGETMHLSPSLLPAQQPTISLLYEDTADTLSVESLTIVPPVDPHSLRALSGISQLPTLPAADTETPAEGAVNPEPAEPTEH clec16a-rnf41 1566357 n/a 1566360 unspecified role unspecified role prey prey region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain false region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain false region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain false region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain false region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain false region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain false region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain false region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain false region identified peptide identified peptide certain certain sequence position certain certain certain sequence position certain false region 13c label 13c label C13 13C C13 13C undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region 15n label 15n label 15N N15 15N N15 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1566361 unspecified role unspecified role bait bait c_terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false region 13c label 13c label C13 13C C13 13C undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region 15n label 15n label 15N N15 15N N15 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Figs 1A-E clec16a-rnf41-2 1566358 n/a 1566360 unspecified role unspecified role prey prey n/a 1566361 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 false physical association physical association false false false Fig 1F rnf41-clec16a 1566359 n/a 1566360 unspecified role unspecified role bait bait n/a 1566361 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 Fig 1F