For the negative set, protein variants that were never found (693 variants) or found only once( 323 variants) in human cancer have been selected (no_cancer p53 variants)
[TP53_PROF:a machine learning model to predict impact of missense mutations inTP53]
[TP53_PROF:a machine learning model to predict impact of missense mutations inTP53]
A diagram of the calculated values for each set of p53 protein mutations, which we will further analyze.
Cancer-related Mutations
TP53 mutation data was aggregated from multiple studies
Effects of Common Cancer Mutations on Stability
Silent and oncological mutations in p53
Heat map of reliable electrostatic interaction energy between pairwise amino acid residues of the p53 monomer
The difference in the calculations obtained for the Positive and Negative set of p53 mutations
Interplay between physical quantities
on the affinity of the complex
on the affinity of the complex
The best way to improve your professional skills and increase your value
- 45%Free energy1 year
- 67%Entropy change3 years
- 15%Entalpy change2 years
- 20%Hydrophobicity
- 30%Solvatation
- 55%Stability
Fechner Correlation
The FECHNER CORRELATION command calculates the Fechner signs correlation coefficient between all the pairs of variables. Fechner correlation coefficient is used to check relationship for small samples.
How To
Run: STATISTICS->NONPARAMETRIC STATISTICS-> FECHNER CORRELATION...
Select the variables you want to correlate.
Pairwise deletion is default for missing values removal (use the MISSING VALUES option in the PREFERENCES window to force casewise deletion).
Results:
Matrix with Fechner correlation coefficients between each pair of variables is calculated.
Fechner correlation coefficient is defined by
Run: STATISTICS->NONPARAMETRIC STATISTICS-> FECHNER CORRELATION...
Select the variables you want to correlate.
Pairwise deletion is default for missing values removal (use the MISSING VALUES option in the PREFERENCES window to force casewise deletion).
Results:
Matrix with Fechner correlation coefficients between each pair of variables is calculated.
Fechner correlation coefficient is defined by
Negative Set of p53 mutations
p.A119P,p.A119S, p.A129G, p.A129P, p.A129S, p.A138G, p.A189S, p.C124F, p.C124W, p.C182F, p.C229G, p.C229W, p.D148A, p.D148V, p.D184A, p.D184E, p.D184V, p.D186A, p.D186E, p.D186Y p.D207A, p.D207V p.E171A, p.E171V, p.E180A, p.E180V, p.E198A, p.E198V, p.E224Q, p.E287A, ,p.F109Y, p.F113Y, p.F134Y, p.F212C, p.G108A, p.G108C, p.G112A, p.G112C, p.G112R, p.G112V, p.G117A, p.G117V, p.G117W, p.G154A, p.G154R, p.G187A, p.G226C, p.G262A, p.G262C p.G262R, p.G279A, p.H115D, p.H115L, p.H115N, p.H115P, p.H115Q, p.H115R p.H168Q, p.H178L, p.H214N, p.H233N, p.I162L, p.I195L, p.I195V, p.I255L, p.K101I, p.K101N, p.K101Q, p.K101T, p.K120T, p.L111V, p.L114F, p.L114M, p.L114S, p.L114V, p.L114W, p.L137R, p.L188Q, p.L188R, p.L201M, p.L201W, p.L206F, p.L206M, p.L206V, p.L206W, p.L252R, p.L257M, p.L264P, p.L264Q p.L264V, p.L265V, p.M169L, p.S106T, p.S116A, p.S116T, p.S116Y, p.S121A, p.S121C, p.S121T, p.S121Y, p.S127A, p.S149A, p.S149C, p.S183A, p.S183T, p.S185C, p.S185T, p.S227A, p.S227Y, p.S261I, p.T102N, p.T102P, p.T118K, p.T118P, p.T118R, p.T118S, p.T123N p.T123P, p.T123S, p.T125S, p.T140N, p.T150S, p.T170K, p.T256R, p.T284R, p.V122E, p.V122G, p.V122M, p.V147L, p.V203G, p.V225L, p.Y103C, p.Y103D, p.Y103F, p.Y103H, p.Y103N, p.Y103S, p.Y107F, p.Y107N, p.Y107S
p.A119P,p.A119S, p.A129G, p.A129P, p.A129S, p.A138G, p.A189S, p.C124F, p.C124W, p.C182F, p.C229G, p.C229W, p.D148A, p.D148V, p.D184A, p.D184E, p.D184V, p.D186A, p.D186E, p.D186Y p.D207A, p.D207V p.E171A, p.E171V, p.E180A, p.E180V, p.E198A, p.E198V, p.E224Q, p.E287A, ,p.F109Y, p.F113Y, p.F134Y, p.F212C, p.G108A, p.G108C, p.G112A, p.G112C, p.G112R, p.G112V, p.G117A, p.G117V, p.G117W, p.G154A, p.G154R, p.G187A, p.G226C, p.G262A, p.G262C p.G262R, p.G279A, p.H115D, p.H115L, p.H115N, p.H115P, p.H115Q, p.H115R p.H168Q, p.H178L, p.H214N, p.H233N, p.I162L, p.I195L, p.I195V, p.I255L, p.K101I, p.K101N, p.K101Q, p.K101T, p.K120T, p.L111V, p.L114F, p.L114M, p.L114S, p.L114V, p.L114W, p.L137R, p.L188Q, p.L188R, p.L201M, p.L201W, p.L206F, p.L206M, p.L206V, p.L206W, p.L252R, p.L257M, p.L264P, p.L264Q p.L264V, p.L265V, p.M169L, p.S106T, p.S116A, p.S116T, p.S116Y, p.S121A, p.S121C, p.S121T, p.S121Y, p.S127A, p.S149A, p.S149C, p.S183A, p.S183T, p.S185C, p.S185T, p.S227A, p.S227Y, p.S261I, p.T102N, p.T102P, p.T118K, p.T118P, p.T118R, p.T118S, p.T123N p.T123P, p.T123S, p.T125S, p.T140N, p.T150S, p.T170K, p.T256R, p.T284R, p.V122E, p.V122G, p.V122M, p.V147L, p.V203G, p.V225L, p.Y103C, p.Y103D, p.Y103F, p.Y103H, p.Y103N, p.Y103S, p.Y107F, p.Y107N, p.Y107S
Positive Set of p53 mutations
p.A138V, p.A159P, p.A159V, p.A161S, p.A161T, p.A276D, p.A276G, p.A276P, p.C124G, p.C135F, p.C135R, pC135S, p.C135W, p.C135Y, p.C141G, p.C141R, p.C141W, p.C141Y, p.C176F, p.C176G, p.C176R, p.C176W, p.C176Y, p.C238F, p.C238R, p.C238Y, p.C242F, p.C242G, p.C242S, p.C242Y, p.C275F, p.C275G, p.C275R, p.C275W, p.C275Y, p.C277F, p.C277Y, p.D259V, p.D259Y, p.D281E, p.D281H, p.D281N, p.D281V, p.D281Y, p.E180K, p.E224D, p.E258A, p.E258K, p.E258Q, p.E271K, p.E271V, p.E285K,p.E285V, p.E286A, p.E286G, p.E286K, p.E286Q, p.E286V, p.E287D, p.F109C, p.F109V, p.F113C, p.F113V, p.F134C, p.F134L, p.F134V, p.F270C, p.F270L, p.F270S, p.G105C, p.G105D, p.G105V, p.G154V, p.G199V, p.G244C, p.G244D, p.G244S, p.G244V, p.G245C, p.G245D, p.G245R, p.G245S, p.G245V, p.G262V, p.G266E, .G266R, p.G266V, p.G279E
p.A138V, p.A159P, p.A159V, p.A161S, p.A161T, p.A276D, p.A276G, p.A276P, p.C124G, p.C135F, p.C135R, pC135S, p.C135W, p.C135Y, p.C141G, p.C141R, p.C141W, p.C141Y, p.C176F, p.C176G, p.C176R, p.C176W, p.C176Y, p.C238F, p.C238R, p.C238Y, p.C242F, p.C242G, p.C242S, p.C242Y, p.C275F, p.C275G, p.C275R, p.C275W, p.C275Y, p.C277F, p.C277Y, p.D259V, p.D259Y, p.D281E, p.D281H, p.D281N, p.D281V, p.D281Y, p.E180K, p.E224D, p.E258A, p.E258K, p.E258Q, p.E271K, p.E271V, p.E285K,p.E285V, p.E286A, p.E286G, p.E286K, p.E286Q, p.E286V, p.E287D, p.F109C, p.F109V, p.F113C, p.F113V, p.F134C, p.F134L, p.F134V, p.F270C, p.F270L, p.F270S, p.G105C, p.G105D, p.G105V, p.G154V, p.G199V, p.G244C, p.G244D, p.G244S, p.G244V, p.G245C, p.G245D, p.G245R, p.G245S, p.G245V, p.G262V, p.G266E, .G266R, p.G266V, p.G279E
The fact is that the yi values for Negative Set practically coincide with the obtained average value; as a result of the difference between the average and yi values, we get a very small value tending to zero.
Neutral Mutations
Oncological mutations
WOW! affect
Difference in calculated characteristics for Positive and Negative sets of P53 protein mutations.
To determine the correlation coefficient, we use Boolean variables and the Fechner coefficient.
rb(integr) is a Fechner coefficient
rb(integr) is a Fechner coefficient
enthalpy change
N1-N60
N1-N60
Negative set
Negative set
Positive set
Positive set
Positive set
Negative set
N53-N140
N2-N89
p.A119P
p.A119S
p.A129G
p.A129P
p.A129S
p.A138G
p.A189S
p.C124F
p.C124W
p.C182F
p.C229G
p.C229W
p.D148A
p.D148V
p.D184A
p.D184E
p.D184V
p.D186A
p.D186E
p.D186Y
p.D207A
p.D207V
p.E171A
p.E171V
p.E180A
p.E180V
p.E198A
p.E198V
p.E224Q
p.E287A
p.F109Y
p.F113Y
p.F134Y
p.F212C
p.G108A
p.G108C
p.G112A
p.G112C
p.G112R
p.G112V
p.G117A
p.G117V
p.G117W
p.G154A
p.G154R
p.G187A
p.G226C
p.G262A
p.G262C
p.G262R
p.G279A
p.H115D
p.H115L
p.H115N
p.H115P
p.H115Q
p.H115R
p.H168Q
p.H178L
p.H214N
p.A119S
p.A129G
p.A129P
p.A129S
p.A138G
p.A189S
p.C124F
p.C124W
p.C182F
p.C229G
p.C229W
p.D148A
p.D148V
p.D184A
p.D184E
p.D184V
p.D186A
p.D186E
p.D186Y
p.D207A
p.D207V
p.E171A
p.E171V
p.E180A
p.E180V
p.E198A
p.E198V
p.E224Q
p.E287A
p.F109Y
p.F113Y
p.F134Y
p.F212C
p.G108A
p.G108C
p.G112A
p.G112C
p.G112R
p.G112V
p.G117A
p.G117V
p.G117W
p.G154A
p.G154R
p.G187A
p.G226C
p.G262A
p.G262C
p.G262R
p.G279A
p.H115D
p.H115L
p.H115N
p.H115P
p.H115Q
p.H115R
p.H168Q
p.H178L
p.H214N
0.73993787
0.73993397
0.7399646
0.73995984
0.73995537
0.73985441
0.7399354
0.7375981
0.73758668
0.73957824
0.73991268
0.73990698
0.73998011
0.73997562
0.74010023
0.74000325
0.73998995
0.74002283
0.74000103
0.73997485
0.74000402
0.73997575
0.74002357
0.73997244
0.74015927
0.73999621
0.74005368
0.73997331
0.74003208
0.73998698
0.73999584
0.73997822
0.7399458
0.74006543
0.73999537
0.74001586
0.74005163
0.74015792
0.74014309
0.73999474
0.74011601
0.74000749
0.74000731
0.74000035
0.74007487
0.74001805
0.74003
0.74
0.74002
0.74008
0.74007
0.74
0.73998
0.73999
0.73998
0.74007
0.74013
0.74006
0.74008
0.73999
0.73993397
0.7399646
0.73995984
0.73995537
0.73985441
0.7399354
0.7375981
0.73758668
0.73957824
0.73991268
0.73990698
0.73998011
0.73997562
0.74010023
0.74000325
0.73998995
0.74002283
0.74000103
0.73997485
0.74000402
0.73997575
0.74002357
0.73997244
0.74015927
0.73999621
0.74005368
0.73997331
0.74003208
0.73998698
0.73999584
0.73997822
0.7399458
0.74006543
0.73999537
0.74001586
0.74005163
0.74015792
0.74014309
0.73999474
0.74011601
0.74000749
0.74000731
0.74000035
0.74007487
0.74001805
0.74003
0.74
0.74002
0.74008
0.74007
0.74
0.73998
0.73999
0.73998
0.74007
0.74013
0.74006
0.74008
0.73999
p.A138V
p.A159P
p.A159V
p.A161S
p.A161T
p.A276D
p.A276G
p.A276P
p.C124G
p.C135F
p.C135R
p.C135S
p.C135W
p.C135Y
p.C141G
p.C141R
p.C141W
p.C141Y
p.C176F
p.C176G
p.C176R
p.C176W
p.C176Y
p.C238F
p.C238R
p.C238Y
p.C242F
p.C242G
p.C242S
p.C242Y
p.C275F
p.C275G
p.C275R
p.C275W
p.C275Y
p.C277F
p.C277Y
p.D259V
p.D259Y
p.D281E
p.D281H
p.D281N
p.D281V
p.D281Y
p.E180K
p.E224D
p.E258A
p.E258K
p.E258Q
p.E271K
p.E271V
p.E285K
p.E285V
p.E286A
p.E286G
p.E286K
p.E286Q
p.E286V
p.E287D
p.F109C
p.A159P
p.A159V
p.A161S
p.A161T
p.A276D
p.A276G
p.A276P
p.C124G
p.C135F
p.C135R
p.C135S
p.C135W
p.C135Y
p.C141G
p.C141R
p.C141W
p.C141Y
p.C176F
p.C176G
p.C176R
p.C176W
p.C176Y
p.C238F
p.C238R
p.C238Y
p.C242F
p.C242G
p.C242S
p.C242Y
p.C275F
p.C275G
p.C275R
p.C275W
p.C275Y
p.C277F
p.C277Y
p.D259V
p.D259Y
p.D281E
p.D281H
p.D281N
p.D281V
p.D281Y
p.E180K
p.E224D
p.E258A
p.E258K
p.E258Q
p.E271K
p.E271V
p.E285K
p.E285V
p.E286A
p.E286G
p.E286K
p.E286Q
p.E286V
p.E287D
p.F109C
0.73979859
0.73992935
0.73992999
0.73990309
0.73991134
0.739866
0.73989952
0.7398477
0.73790811
0.73676158
0.73993565
0.73758584
0.73644711
0.73674552
0.73650341
0.73801977
0.73835483
0.73771861
0.73755947
0.73683127
0.73725951
0.73756511
0.73681525
0.73657199
0.73682142
0.73757876
0.73656484
0.73762472
0.73793314
0.73740206
0.73744179
0.73944582
0.73950486
0.73972086
0.73944381
0.73941679
0.73973285
0.73972298
0.73997548
0.73997854
0.73998977
0.73998112
0.73998263
0.73997477
0.73997529
0.73999009
0.7399824
0.74008994
0.74003253
0.7402447
0.73997668
0.74017278
0.73997055
0.74000908
0.73997871
0.74014231
0.74005099
0.73996981
0.73998965
0.74006329
0.73992935
0.73992999
0.73990309
0.73991134
0.739866
0.73989952
0.7398477
0.73790811
0.73676158
0.73993565
0.73758584
0.73644711
0.73674552
0.73650341
0.73801977
0.73835483
0.73771861
0.73755947
0.73683127
0.73725951
0.73756511
0.73681525
0.73657199
0.73682142
0.73757876
0.73656484
0.73762472
0.73793314
0.73740206
0.73744179
0.73944582
0.73950486
0.73972086
0.73944381
0.73941679
0.73973285
0.73972298
0.73997548
0.73997854
0.73998977
0.73998112
0.73998263
0.73997477
0.73997529
0.73999009
0.7399824
0.74008994
0.74003253
0.7402447
0.73997668
0.74017278
0.73997055
0.74000908
0.73997871
0.74014231
0.74005099
0.73996981
0.73998965
0.74006329
Negative set
Positive set
Histogram of values distribution for the magnitude of enthalpy change
Сalculated data obtained for two sets of mutations. Plot of differential entropy changes for two data sets. The graphs show Boolean variables and the final Fechner coefficient.
Positive set
N1-N60
Positive set
Negative set
Negative set
Negativ set
p.A119P
p.A119S
p.A129G
p.A129P
p.A129S
p.A138G
p.A189S
p.C124F
p.C124W
p.C182F
p.C229G
p.C229W
p.D148A
p.D148V
p.D184A
p.D184E
p.D184V
p.D186A
p.D186E
p.D186Y
p.D207A
p.D207V
p.E171A
p.E171V
p.E180A
p.E180V
p.E198A
p.E198V
p.E224Q
p.E287A
p.F109Y
p.F113Y
p.F134Y
p.F212C
p.G108A
p.G108C
p.G112A
p.G112C
p.G112R
p.G112V
p.G117A
p.G117V
p.G117W
p.G154A
p.G154R
p.G187A
p.G226C
p.G262A
p.G262C
p.G262R
p.G279A
p.H115D
p.H115L
p.H115N
p.H115P
p.H115Q
p.H115R
p.H168Q
p.H178L
p.A119P
p.A119S
p.A129G
p.A129P
p.A129S
p.A138G
p.A189S
p.C124F
p.C124W
p.C182F
p.C229G
p.C229W
p.D148A
p.D148V
p.D184A
p.D184E
p.D184V
p.D186A
p.D186E
p.D186Y
p.D207A
p.D207V
p.E171A
p.E171V
p.E180A
p.E180V
p.E198A
p.E198V
p.E224Q
p.E287A
p.F109Y
p.F113Y
p.F134Y
p.F212C
p.G108A
p.G108C
p.G112A
p.G112C
p.G112R
p.G112V
p.G117A
p.G117V
p.G117W
p.G154A
p.G154R
p.G187A
p.G226C
p.G262A
p.G262C
p.G262R
p.G279A
p.H115D
p.H115L
p.H115N
p.H115P
p.H115Q
p.H115R
p.H168Q
p.H178L
lg[Kd],Mol/L
-0.614253
-0.61426091
-0.61419881
-0.61420846
-0.61421752
-0.6144222
-0.61425801
-0.61899628
-0.61901944
-0.61498207
-0.61430407
-0.61431562
-0.61416737
-0.61417648
-0.61392386
-0.61412046
-0.61414743
-0.61408077
-0.61412496
-0.61417803
-0.6141189
-0.61417621
-0.61407927
-0.61418292
-0.61380418
-0.61413473
-0.61401822
-0.61418116
-0.61406201
-0.61415345
-0.61413549
-0.61417121
-0.61423694
-0.6139944
-0.61413644
-0.61409489
-0.61402239
-0.61380691
-0.61383698
-0.61413771
-0.61389187
-0.61411186
-0.61411223
-0.61412633
-0.61397528
-0.61409047
-0.61407
-0.61413
-0.61408
-0.61397
-0.61399
-0.61413
-0.61416
-0.61415
-0.61416
-0.61398
-0.61385
-0.61401
-0.61397
-0.614253
-0.61426091
-0.61419881
-0.61420846
-0.61421752
-0.6144222
-0.61425801
-0.61899628
-0.61901944
-0.61498207
-0.61430407
-0.61431562
-0.61416737
-0.61417648
-0.61392386
-0.61412046
-0.61414743
-0.61408077
-0.61412496
-0.61417803
-0.6141189
-0.61417621
-0.61407927
-0.61418292
-0.61380418
-0.61413473
-0.61401822
-0.61418116
-0.61406201
-0.61415345
-0.61413549
-0.61417121
-0.61423694
-0.6139944
-0.61413644
-0.61409489
-0.61402239
-0.61380691
-0.61383698
-0.61413771
-0.61389187
-0.61411186
-0.61411223
-0.61412633
-0.61397528
-0.61409047
-0.61407
-0.61413
-0.61408
-0.61397
-0.61399
-0.61413
-0.61416
-0.61415
-0.61416
-0.61398
-0.61385
-0.61401
-0.61397
Positiv set
p.A138V
p.A159P
p.A159V
p.A161S
p.A161T
p.A276D
p.A276G
p.A276P
p.C124G
p.C135F
p.C135R
p.C135S
p.C135W
p.C135Y
p.C141G
p.C141R
p.C141W
p.C141Y
p.C176F
p.C176G
p.C176R
p.C176W
p.C176Y
p.C238F
p.C238R
p.C238Y
p.C242F
p.C242G
p.C242S
p.C242Y
p.C275F
p.C275G
p.C275R
p.C275W
p.C275Y
p.C277F
p.C277Y
p.D259V
p.D259Y
p.D281E
p.D281H
p.D281N
p.D281V
p.D281Y
p.E180K
p.E224D
p.E258A
p.E258K
p.E258Q
p.E271K
p.E271V
p.E285K
p.E285V
p.E286A
p.E286G
p.E286K
p.E286Q
p.E286V
p.E287D
p.A138V
p.A159P
p.A159V
p.A161S
p.A161T
p.A276D
p.A276G
p.A276P
p.C124G
p.C135F
p.C135R
p.C135S
p.C135W
p.C135Y
p.C141G
p.C141R
p.C141W
p.C141Y
p.C176F
p.C176G
p.C176R
p.C176W
p.C176Y
p.C238F
p.C238R
p.C238Y
p.C242F
p.C242G
p.C242S
p.C242Y
p.C275F
p.C275G
p.C275R
p.C275W
p.C275Y
p.C277F
p.C277Y
p.D259V
p.D259Y
p.D281E
p.D281H
p.D281N
p.D281V
p.D281Y
p.E180K
p.E224D
p.E258A
p.E258K
p.E258Q
p.E271K
p.E271V
p.E285K
p.E285V
p.E286A
p.E286G
p.E286K
p.E286Q
p.E286V
p.E287D
lg[Kd],Mol/L
-0.614535352
-0.614270272
-0.614268987
-0.614323517
-0.614306795
-0.614398712
-0.614330745
-0.61443581
-0.618367833
-0.620692116
-0.614257509
-0.619021144
-0.62132964
-0.620724674
-0.621215486
-0.618141465
-0.617462206
-0.618751991
-0.619074608
-0.620550837
-0.619682692
-0.619063178
-0.620583317
-0.621076466
-0.620570816
-0.619035497
-0.621090966
-0.618942322
-0.618317076
-0.619393704
-0.619313177
-0.615250519
-0.615130812
-0.614692929
-0.615254583
-0.615309361
-0.614668627
-0.614688648
-0.614176768
-0.614170555
-0.614147785
-0.614165335
-0.614162272
-0.614178203
-0.61417715
-0.61414715
-0.614162733
-0.613944716
-0.614061115
-0.613630991
-0.614174336
-0.613776781
-0.614186748
-0.614108647
-0.614170203
-0.613838552
-0.614023677
-0.614188258
-0.614148036
-0.614535352
-0.614270272
-0.614268987
-0.614323517
-0.614306795
-0.614398712
-0.614330745
-0.61443581
-0.618367833
-0.620692116
-0.614257509
-0.619021144
-0.62132964
-0.620724674
-0.621215486
-0.618141465
-0.617462206
-0.618751991
-0.619074608
-0.620550837
-0.619682692
-0.619063178
-0.620583317
-0.621076466
-0.620570816
-0.619035497
-0.621090966
-0.618942322
-0.618317076
-0.619393704
-0.619313177
-0.615250519
-0.615130812
-0.614692929
-0.615254583
-0.615309361
-0.614668627
-0.614688648
-0.614176768
-0.614170555
-0.614147785
-0.614165335
-0.614162272
-0.614178203
-0.61417715
-0.61414715
-0.614162733
-0.613944716
-0.614061115
-0.613630991
-0.614174336
-0.613776781
-0.614186748
-0.614108647
-0.614170203
-0.613838552
-0.614023677
-0.614188258
-0.614148036
N1-N60
Positive set
Negative set
