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Network analysis: Case study 1 - The given list contains 21 substrate proteins, wherein 4 E3 ligases, 14 Ubi-substrate proteins, and 3 interacting proteins.
(In this case study, the regulatory network, which contains interactions between all E3 ligases and Ubi-subtrate/interacting proteins, will be constructed for the investigation)
The details of the list as described in the table below:
No. ID AC Gene Name Anotation E3: group-type/
UbiSubstrate: Ubi-SitesPubMed Reference 1 SMUF2_HUMAN Q9HAU4 SMURF2 E3 ligase E3: HECT-type 16950122; 18927080; 19583833; 19255252; 20819168; 14562029; 20073064; 11389444; 11163210; 18671942; 14755250; 20858899 2 ITCH_HUMAN Q96J02 ITCH E3 ligase E3: HECT-type 20650893; 18310276; 15013426; 19592251; 19580544; 19478092; 19433584; 19352540; 16387660; 19340001; 20300110; 19339247; 18278048; 17110928; 16087662; 16055720; 15946939; 20068034; 20818436; 18334649; 18922894; 15703212; 15082780; 21383157; 21212414; 21107885 3 MDM2_HUMAN Q00987 MDM2 E3 ligase E3: RING-type 17545634; 16866370; 18802403; 18981217; 19032150; 14642282; 19713960; 19703557; 19128510; 19683495; 18451149; 18665269; 18948082; 19372219; 19369353; 19363159; 18784257; 19448429; 19345326; 19176998; 19321440; 19247369; 19219073; 17377491; 11927554; 15975924; 15242646; 15456867; 14769800; 20592017; 16678796; 16170383; 17301054; 15577944; 21460856; 21093410; 20453884 4 VHL_HUMAN P40337 VHL E3 ligase E3: Other-type 20300531; 19228690; 12912922; 19695223; 19305426; 20026589; 11574546; 11739384; 12604794; 17350623; 15777842 5 CPSF6_HUMAN Q16630 CPSF6 Ubiquitinated substrate 79;161;185 79:21890473; 161:21890473; 185:21906983 6 PIM1_HUMAN P11309 PIM1 Ubiquitinated substrate 96;158;274;285 96:21890473; 158:21906983; 274:21906983; 285:21906983 7 SPG20_HUMAN Q8N0X7 SPG20 Ubiquitinated substrate 29;47;62;82;362;362; 362;370;377;440;465;475;578 29:21890473; 47:21890473; 62:21890473; 82:21890473; 362:18781797; 362:18781797; 20972266; 21890473; 21906983; 362:18781797; 370:21890473; 377:21890473; 440:21906983; 465:21890473; 475:21890473; 578:21890473 8 ACOX3_HUMAN O15254 ACOX3 Ubiquitinated substrate 73;291;484 73:21906983; 291:21906983; 484:21906983 9 ARRB2_HUMAN P32121 ARRB2 Ubiquitinated substrate 78;178 78:21890473; 178:21906983 10 DDX58_HUMAN O95786 DDX58 Ubiquitinated substrate 99;154; 164;169;172; 181;190; 193;644 99:17392790; 154:19484123; 164:19484123; 169:17392790; 172:17392790; 19484123; 20071582; 20403326; 181:17392790; 190:17392790; 193:17392790; 644:21906983 11 JUN_HUMAN P05412 JUN Ubiquitinated substrate 50 50:21890473 12 SKIL_HUMAN P12757 SKIL Ubiquitinated substrate 249;423;440;446;449 249:21890473; 423:21890473;440:11691834; 446:11691834; 449:11691834 13 ATF4_HUMAN P18848 ATF4 Ubiquitinated substrate 45;55;75;88;335 45:21906983; 55:21906983; 75:21906983; 88:21906983; 335:21906983 14 CTBP1_HUMAN Q13363 CTBP1 Ubiquitinated substrate 273;280 273:21906983; 280:21890473; 21906983 15 PPM1D_HUMAN O15297 PPM1D Ubiquitinated substrate 19;238 19:21906983;238:21890473;21906983 16 MAVS_HUMAN Q7Z434 MAVS Ubiquitinated substrate 362;461;500 362:20483786;461:20483786;500:19380491 17 HIF1A_HUMAN Q16665 HIF1A Ubiquitinated substrate 32;71;185;289; 297;377;389; 391;477; 532;532;538;538;547;674;709 32:21906983; 71:21906983; 185:21906983; 289:21906983; 297:21906983; 377:21906983; 389:21906983; 391:21906983; 477:21906983; 532:10944113; 16500650; 16862177; 532:10944113; 538:16862177; 18781797; 21890473; 21906983; 538:18781797; 547:16862177; 674:21906983; 709:21906983 18 P53_HUMAN P04637 TP53 Ubiquitinated substrate 101; 120; 132; 139; 164; 291; 292; 305; 319; 320; 321; 351; 357; 370; 372; 373; 381; 382; 386 101:17371868; 21890473; 21906983; 120:17371868; 21906983; 132:17371868; 21890473; 139:17371868; 164:17371868; 21890473; 291:19536131; 292:19536131; 21890473; 305:19857530; 21890473; 21906983; 319:19927155; 17110336; 320:19857530; 19927155; 21890473; 17110336; 321:19857530; 19927155; 21890473; ; 17110336; 351:11046142; 357:21906983; 11046142; 370:11046142; 12426395; 17371868; 19619542; 19927155; 21731648; 17110336; 372:11046142; 11094089; 11971195; 12426395; 17371868; 19619542; 19927155; 21731648; 372:17110336; 373:11046142; 11094089; 11971195; 12426395; 17371868; 19619542; 19927155; 21731648; 17110330; 381:11046142; 11094089; 11971195; 12426395; 17371868; 19619542; 19927155; 21731648; 17110336; 382:11046142; 11094089; 11971195; 12426395; 17371868; 19619542; 19927155; 21731648; 386:10562557; 11046142; 17371868; 19927155; 21731648; 17110330; 17110336 19 AKAP5_HUMAN P24588 AKAP5 Interacting protein - Predicted as Ubiquitinated protein at positions: 50, 119 20 FOXO3_HUMAN O43524 FOXO3 Interacting protein - Predicted as Ubiquitinated protein at positions: 176, 271, 569 21 PHOCN_HUMAN Q9Y3A3 MOB4 Interacting protein - Predicted as Non-Ubiquitinated protein
Case Study 1: The given list contains 21 substrate proteins, wherein 4 E3 ligases, 14 Ubi-substrate proteins, and 3 interacting proteins. Case Study 2: The given list contains only 3 E3 ligases (no Ubi-substrate proteins; no interacting proteins).