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/ leali-2012-1 in vitro In vitro elisa enzyme linked immunosorbent assay ELISA ELISA elisa antibody detection identification by antibody antibody detection Leali D., Inforzato A., Ronca R., Bianchi R., Belleri M., Coltrini D., Di Salle E., Sironi M., Norata GD., Bottazzi B., Garlanda C., Day AJ., Presta M. The expression system for the PTX3 N terminal construct has been taken from Ref 13; HEK-293F cells -also with C-terminal His/V5 tag. anthony.day@manchester.ac.uk,presta@med.unibs.it Arteriosclerosis, thrombosis, and vascular biology 2012 Only protein-protein interactions imex curation imex curation leali-2012-3 in vitro In vitro solid phase assay solid phase assay tag visualisation tag visualisation Leali D., Inforzato A., Ronca R., Bianchi R., Belleri M., Coltrini D., Di Salle E., Sironi M., Norata GD., Bottazzi B., Garlanda C., Day AJ., Presta M. anthony.day@manchester.ac.uk,presta@med.unibs.it Arteriosclerosis, thrombosis, and vascular biology 2012 Only protein-protein interactions imex curation imex curation leali-2012-2 in vitro In vitro spr surface plasmon resonance Optical biosensor BIAcore(r) BIAcore(r) Optical biosensor spr predetermined predetermined participant predetermined Leali D., Inforzato A., Ronca R., Bianchi R., Belleri M., Coltrini D., Di Salle E., Sironi M., Norata GD., Bottazzi B., Garlanda C., Day AJ., Presta M. anthony.day@manchester.ac.uk,presta@med.unibs.it Arteriosclerosis, thrombosis, and vascular biology 2012 Only protein-protein interactions imex curation imex curation leali-2012-4 in vitro In vitro crosslink cross-linking study crosslink western blot western blot Immuno blot Immuno blot Leali D., Inforzato A., Ronca R., Bianchi R., Belleri M., Coltrini D., Di Salle E., Sironi M., Norata GD., Bottazzi B., Garlanda C., Day AJ., Presta M. Cross-linking agent is BS -Bis[sulfosuccinimidyl]suberate anthony.day@manchester.ac.uk,presta@med.unibs.it Arteriosclerosis, thrombosis, and vascular biology 2012 Only protein-protein interactions imex curation imex curation ptx3_human Pentraxin-related protein PTX3 Pentaxin-related protein PTX3 TNFAIP5 TSG14 Tumor necrosis factor alpha-induced protein 5 Tumor necrosis factor-inducible gene 14 protein PTX3 protein protein human Homo sapiens Human MHLLAILFCALWSAVLAENSDDYDLMYVNLDNEIDNGLHPTEDPTPCACGQEHSEWDKLFIMLENSQMRERMLLQATDDVLRGELQRLREELGRLAESLARPCAPGAPAEARLTSALDELLQATRDAGRRLARMEGAEAQRPEEAGRALAAVLEELRQTRADLHAVQGWAARSWLPAGCETAILFPMRSKKIFGSVHPVRPMRLESFSACIWVKATDVLNKTILFSYGTKRNPYEIQLYLSYQSIVFVVGGEENKLVAEAMVSLGRWTHLCGTWNSEEGLTSLWVNGELAATTVEMATGHIVPEGGILQIGQEKNGCCVGGGFDETLAFSGRLTGFNIWDSVLSNEEIRETGGAESCHIRGNIVGWGVTEIQPHGGAQYVS tsg6_human Tumor necrosis factor-inducible gene 6 protein TSG6 TNFAIP6 Hyaluronate-binding protein TNF-stimulated gene 6 protein Tumor necrosis factor alpha-induced protein 6 protein protein human Homo sapiens Human MIILIYLFLLLWEDTQGWGFKDGIFHNSIWLERAAGVYHREARSGKYKLTYAEAKAVCEFEGGHLATYKQLEAARKIGFHVCAAGWMAKGRVGYPIVKPGPNCGFGKTGIIDYGIRLNRSERWDAYCYNPHAKECGGVFTDPKQIFKSPGFPNEYEDNQICYWHIRLKYGQRIHLSFLDFDLEDDPGCLADYVEIYDSYDDVHGFVGRYCGDELPDDIISTGNVMTLKFLSDASVTAGGFQIKYVAMDPVSKSSQGKNTSTTSTGNKNFLAGRFSHL fgf2_human Fibroblast growth factor 2 Basic fibroblast growth factor FGF2 FGFB Heparin-binding growth factor 2 protein protein human Homo sapiens Human MVGVGGGDVEDVTPRPGGCQISGRGARGCNGIPGAAAWEAALPRRRPRRHPSVNPRSRAAGSPRTRGRRTEERPSGSRLGDRGRGRALPGGRLGGRGRGRAPERVGGRGRGRGTAAPRAAPAARGSRPGPAGTMAAGSITTLPALPEDGGSGAFPPGHFKDPKRLYCKNGGFFLRIHPDGRVDGVREKSDPHIKLQLQAEERGVVSIKGVCANRYLAMKEDGRLLASKCVTDECFFFERLESNNYNTYRSRKYTSWYVALKRTGQYKLGSKTGPGQKAILFLPMSAKS 23424-1 1936183 N/A 1936187 unspecified role unspecified role prey prey human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f N/A 1936188 unspecified role unspecified role bait bait c_terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false c_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false drome-schneider_2 Drosophila melanogaster late embryo cells Fruit fly schneider_2 Established from the late embryo of Drosophila melanogaster Mixture of diploid and tetraploid. Originally had some XY cells now predominantly XX. direct interaction direct interaction false false false 1A tnfaip6-ptx3-1 1936183 N/A 1936187 unspecified role unspecified role prey prey human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f N/A 1936188 unspecified role unspecified role bait bait link_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1Ai tnfaip6-ptx3-2 1936183 N/A 1936187 unspecified role unspecified role bait bait c_terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false c_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f N/A 1936188 unspecified role unspecified role prey prey c_terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false c_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false drome-schneider_2 Drosophila melanogaster late embryo cells Fruit fly schneider_2 Established from the late embryo of Drosophila melanogaster Mixture of diploid and tetraploid. Originally had some XY cells now predominantly XX. direct interaction direct interaction false false false 2 tnfaip6-ptx3-3 1936183 N/A 1936187 unspecified role unspecified role bait bait human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f N/A 1936188 unspecified role unspecified role prey prey c_terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false c_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false drome-schneider_2 Drosophila melanogaster late embryo cells Fruit fly schneider_2 Established from the late embryo of Drosophila melanogaster Mixture of diploid and tetraploid. Originally had some XY cells now predominantly XX. direct interaction direct interaction false false false 2i tnfaip6-ptx3-6 1936183 N/A 1936187 unspecified role unspecified role bait bait human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f N/A 1936188 unspecified role unspecified role prey prey link_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 2B ptx3-tnfaip6-1 1936183 N/A 1936187 unspecified role unspecified role bait bait c_terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false c_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f N/A 1936188 unspecified role unspecified role prey prey link_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) 1936222 1936220 direct interaction direct interaction false false false 2B fgf2-ptx3-3 1936183 N/A 1936188 competitor competitor competitor prey prey drome-schneider_2 Drosophila melanogaster late embryo cells Fruit fly schneider_2 Established from the late embryo of Drosophila melanogaster Mixture of diploid and tetraploid. Originally had some XY cells now predominantly XX. N/A 1936187 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 false human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f N/A 1936189 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3B fgf2-ptx3-5 1936183 N/A 1936187 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 false human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f N/A 1936189 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3Bi 245w345-1 1936184 N/A 1936187 unspecified role unspecified role prey prey region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1936189 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3A-1 fgf2-ptx3-1 1936184 N/A 1936187 competitor competitor competitor prey prey human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f N/A 1936187 unspecified role unspecified role prey prey region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1936189 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3A-2 fgf2-ptx3-2 1936184 N/A 1936188 competitor competitor competitor prey prey drome-schneider_2 Drosophila melanogaster late embryo cells Fruit fly schneider_2 Established from the late embryo of Drosophila melanogaster Mixture of diploid and tetraploid. Originally had some XY cells now predominantly XX. N/A 1936187 unspecified role unspecified role prey prey region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1936189 unspecified role unspecified role bait bait ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3A-3 tnfaip6-ptx3-4 1936185 N/A 1936187 unspecified role unspecified role bait bait human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f Stoichiometry: 1.0 N/A 1936188 unspecified role unspecified role prey prey P98066:p.Tyr94Phe mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false c_terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false c_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P98066:p.Tyr47Phe mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P98066:p.Glu183Ser mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false drome-schneider_2 Drosophila melanogaster late embryo cells Fruit fly schneider_2 Established from the late embryo of Drosophila melanogaster Mixture of diploid and tetraploid. Originally had some XY cells now predominantly XX. Stoichiometry: 1.0 direct interaction direct interaction false false false 1936185 1B, Supp fig 1 tnfaip6-ptx3-5 1936185 N/A 1936187 unspecified role unspecified role bait bait human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f Stoichiometry: 1.0 N/A 1936188 unspecified role unspecified role prey prey link_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false 1936185 1Bi fgf2-ptx3-4 1936186 N/A 1936189 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) N/A 1936187 unspecified role unspecified role neutral component neutral component human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f direct interaction direct interaction false false false Supp fig 2 fgf2-ptx3-6 1936186 N/A 1936188 competitor competitor competitor neutral component neutral component drome-schneider_2 Drosophila melanogaster late embryo cells Fruit fly schneider_2 Established from the late embryo of Drosophila melanogaster Mixture of diploid and tetraploid. Originally had some XY cells now predominantly XX. N/A 1936187 unspecified role unspecified role neutral component neutral component human-293f Homo sapiens HEK293F cell line 293f embryonic kidney cell 293f N/A 1936189 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) physical association physical association false false false 3A-3