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Mass spectrometry data werePLOS Biology | www.plosbiology.orgSupporting InformationFigure S1 Protease networks in mouse and human. Networks ofall proteases (environmentally friendly circles), protease inhibitors (pink diamonds), and protease substrates (grey squares), which take part in any cleavage or inhibition response annotated in MEROPS/TopFIND. Networks are proven for human (A) and mouse (B). To resolve particular person nodes and edges, click to zoom. Proteins are specified by their UniProt gene names. (EPS)Determine S2 Annotation biases in protease substrate identification.Out-degree of protease and inhibitor proteins by having an out-degree of one or bigger within the human and mouse knowledge. Out-degree would be the sum of cleavages catalyzed by a protease or inhibitions GSK2606414 site prompted by a protease inhibitor. Proteins (nodes) are sorted by their out-degree. Human values are in red; mouse values are in blue. (EPS)Determine SHuman proteases are overrepresented as substrates. Proportion of proteases and inhibitors that happen to be known substrates. The chances of all UniProt/Swiss-Prot proteins having an annotated MEROPS ID indicating these are proteases or inhibitors PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/10999558 are demonstrated as ``theoretical. ``TopFIND refers to the proportion of all substrates which can be proteases or inhibitors identified inside the TopFIND database. The percentage of proteases or inhibitors (proteins having a MEROPS ID) among all internal neo-N termini inside of a current TAILS evaluation of murine skin [13] are known as ``murine TAILS facts. (EPS)Figure S4 New connections in recognised proteolytic pathways. (A) Coagulation, (B) enhance method, (C) apoptosis, and (D) kallikreins are proven with connections since they are within the network. Proteases are represented as inexperienced circles and inhibitors as pink diamonds. Edges are cleavages (green, with arrow head) and inhibitions (crimson, with ``T head). Edges of originally described pathways are sound, and extra edges are dotted. (A) Coagulation things XII, XI, X, IX, VII, and V that kind the clot (UniProt gene names: F12, F11, F10, F9, F7, and F2) are connected as initially described [30]. This figure also demonstrates PLG, tissue-type, and urokinase-type PLG activators involved in fibrinolysis (PLG, PLAU, and PLAT) [34] and plenty of connections in between people proteins, which weren't classically described. (B) The key enhance cascade of proteins C1R, C1S, C2, C3, and C5 with the classical pathway, likewise as cofactors within the option pathway enhance things D, B, and that i (UniProt gene names: CFD, CFB, and CFI) [26]. Supplemental connections not initially described are along with the lectin pathway activators mannose-binding lectin serine protease one and a pair of (MASP1 and MASP2) [28] as well as plasma protease C1 inhibitor (SERPING1) [27]. (C) The community contains connections concerning initiator caspases eight, nine, and ten (UniProt gene names: CASP8, CASP9, and CASP10), as well as their cleavage of effector caspases three and 7 (CASP3 and CASP7) and caspase 6 (CASP6) as described in [33]. The Oteseconazole Epigenetics network also consists of caspases 4 (CASP4) and interactions with apoptosis protease inhibitors (BIRC7, BIRC8, and XIAP). (D) Kallikreins on the semen liquefaction cascade are related as explained earlier [31] with the protease network showing lots of added connections. (EPS) Determine S5 The protease web compar.