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Data update #31

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Feb 3, 2025
Merged

Data update #31

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b984c16
Fixing processing error in PDHK1 and PDHK4 - Y column should be repla…
yaront Feb 3, 2025
ce22169
Data update
yaront Feb 3, 2025
59151b2
Update README
yaront Feb 3, 2025
5a538cb
Updating version
yaront Feb 3, 2025
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -115,7 +115,7 @@ This is the expected output from using the PhosphoProteomics.predict() function.

| Release | Date | New | Updated | Removed | Total Ser/Thr | Total Tyrosine | Total Non-Canonicals (Tyrosine) | Notes |
|:-------:|:----:|:---:|:-------:|:-------:|:-------------:|:--------------:|:-------------------------------:|:-----:|
| **v1.0.4** | Jan 28, 2025 | CDKL2 | CK1D, GRK7, SRPK2 | _None_ | 310 | 78 | 15 | Fixed processing error for PDHK1 and PDHK4 |
| **v1.1.0** | Feb 2, 2025 | CDKL2 | CK1D, GRK7, SRPK2 | _None_ | 310 | 78 | 15 | Fixed processing error for PDHK1 and PDHK4 |
| **v1.0.0** | Dec 5, 2024 | ALK1, ALK7, TSSK3, TSSK4, ULK3, WNK2 | CAMKK2, CDK3, CDK5, CDK13, CHAK1, CLK3, GRK1, GRK4, GRK5, ICK, IKKA, LATS1, MEKK6, MLK3, MNK2, MST1, NIM1, PASK, PBK, PKN3, SKMLCK, SMG1, VRK2, WNK3 | _None_ | 309 | 78 | 15 | |
| **v0.1.0** | Oct 30, 2024 | _None_ | _None_ | _None_ | 303 | 78 | 15 | Legacy version - data as described in papers |

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2 changes: 1 addition & 1 deletion src/kinase_library/__init__.py
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Expand Up @@ -23,7 +23,7 @@

#%%

__version__ = "1.0.5"
__version__ = "1.1.0"

#%% Loading scored phosphoproteome one time per session

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1 change: 1 addition & 0 deletions src/kinase_library/databases/kinase_data/kinome_information.tsv
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Expand Up @@ -59,6 +59,7 @@ CDK7 CDK7 CDK7 ser_thr STK CMGC P50613 CDK7_HUMAN 1LG3 ser_thr FALSE CDK7
CDK8 CDK8 CDK8 ser_thr STK CMGC P49336 CDK8_HUMAN 3RGF ser_thr FALSE CDK8
CDK9 CDK9 CDK9 ser_thr STK CMGC P50750 CDK9_HUMAN 1PF6 ser_thr FALSE CDK9
CDKL1 CDKL1 CDKL1 ser_thr STK CMGC Q00532 CDKL1_HUMAN 4AGU ser_thr FALSE CDKL1
CDKL2 CDKL2 CDKL2 ser_thr STK CMGC Q92772 CDKL2_HUMAN 4AAA ser_thr FALSE CDKL2
CDKL5 CDKL5 CDKL5 ser_thr STK CMGC O76039 CDKL5_HUMAN 4BGQ ser_thr FALSE CDKL5
CHAK1 CHAK1 TRPM7 ser_thr STK Alpha Q96QT4 TRPM7_HUMAN nan ser_thr FALSE TRPM7
CHAK2 CHAK2 TRPM6 ser_thr STK Alpha Q9BX84 TRPM6_HUMAN nan ser_thr FALSE TRPM6
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25 changes: 25 additions & 0 deletions src/kinase_library/databases/matrices/ser_thr/densitometry/CDKL2_densitometry.txt
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1 2 3 4 5 6 7 8 9 10 11 12
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M 598231.52 444422.53 233116.92 330807.96 484003.23 483777.55 466056.24 494880.01 440764.17 672681.05 655677.17 536602.18
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O 508234.13 481859.52 209025.71 275233.93 614166.24 331369.02 365793.07 473462.92 495907.2 546018.84 915191.36 577467.45
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S 468440.02 448496.74 232548.93 393890.39 433507.12 396400.29 452266.53 340065.64 548446.06 760206.59 383722.69 270137.99
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U 571193.92 527635.37 486637.55 549307.7 469337.1 470405.94 593298.9 673613.16 578020.21 695808.97 328780.46 225699.37
V 450076.94 429552.47 348412.3 309440.57 453623.85 1528314.58 376064.66 465538.42 403858.24 653823.43 468095.6 218911.74
W 460575.56 379302.29 252435.69 379040.31 507294.16 581437.92 372318.97 452731.71 467368.08 617040.53 744960.27 471515.13
X 378427.78 417631.52 381752.6 1943036.99 430909.88 1100199.38 341941.68 532738.96 481627.04 839518.36 813609.67 494318.95
48 changes: 24 additions & 24 deletions src/kinase_library/databases/matrices/ser_thr/densitometry/CK1D_densitometry.txt
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1 2 3 4 5 6 7 8 9 10 11 12
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E 8179652.61 10360685.11 19087320.68 10660480.01 9368459.49 9607297.72 7109292.49 8200208.38 7524234.02 8586544.14 8368450.47 11234239.75
F 8765219.23 9067197.42 12838688.04 7891935.83 7502789.73 7177401.25 7023921.95 7954763.40 7680014.10 8894761.59 8144128.15 12256549.92
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M 9129642.65 9884108.27 9098575.59 7223375.65 7769101.05 7197943.40 9484477.40 8797712.15 9485765.51 10184272.82 9506921.28 9644503.15
N 9282709.26 9954282.89 7572697.51 7889420.93 7958996.93 7566060.42 8794322.45 9574259.53 8987158.66 10106698.28 10896048.84 10049126.65
O 8742757.61 9318472.84 7731120.98 7858303.08 9074581.91 8546261.95 8813490.31 9626537.87 8662054.40 9648429.62 10806496.99 8396395.92
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Q 9429775.71 10115248.14 9968108.02 8859354.04 8258680.16 9969715.52 9755457.91 8785609.36 8397700.20 8960577.19 9859695.60 8053047.50
R 8789050.46 8989899.26 7872947.95 7824627.88 7520821.29 10373460.72 8537255.10 7984147.33 7399760.82 8379404.11 8880957.02 7515397.16
S 8926071.52 17731273.51 9426734.30 8656852.49 7248303.75 7644202.68 8467719.60 6948986.67 7307189.14 8931702.57 8259550.31 7420207.16
T 10504318.28 39572714.57 11264504.24 9377751.79 9156388.41 8483777.34 13369261.64 9114010.25 7498121.28 12024766.00 10299363.01 8333049.56
U 10175779.75 10810241.60 11895671.77 12233170.93 10722391.64 10287348.63 10489173.89 10103441.41 9442786.46 10865086.06 8730328.40 6966289.88
V 8226460.83 8711796.55 9386539.68 12042207.65 8601745.73 8146880.73 7880728.71 7927292.27 7888726.99 9123588.51 9705550.21 7392680.21
W 8613506.36 9385170.74 8943451.31 8581611.36 9284896.19 7651472.37 7653635.32 10370324.74 8577466.82 9645862.68 10334409.77 8103955.02
X 8926441.25 9962542.90 10107234.84 10162005.13 10699438.33 8553887.43 8309156.96 9441911.07 10098375.76 13085567.15 10202852.99 9791344.74
A 6434827.33 2777019.28 6234703.51 757217.30 1896303.11 11118079.90 7899783.44 24339544.26 1482558.88 8734379.91 831129.17 2876396.87
B 1075697.15 1257814.02 1128177.31 935558.70 1168075.92 1381609.23 3092791.31 3581735.32 1610593.00 5449265.60 821057.35 2747673.70
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E 6782082.25 10413660.24 10446600.20 6687383.33 6998806.21 11030743.47 3125140.06 13269577.50 7799696.25 7062399.78 2989006.90 6734417.84
F 8128309.44 11522842.38 24096626.02 6461752.07 4128266.82 4741108.09 4445113.03 11960178.63 6717374.92 7790432.88 2161707.30 4789560.45
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I 4014119.11 3778983.46 3711562.78 2650283.17 4561530.98 1493930.38 2044499.59 2014665.58 1865681.05 4075196.40 1073953.77 662739.44
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K 5410883.58 5158519.82 2751266.10 3294073.22 3708670.54 2350226.02 4795199.29 4127968.16 3889671.46 4607379.92 2164858.12 6736773.32
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M 5007616.56 4700366.99 6035728.61 2272443.81 3970614.56 2329428.07 7291315.98 3887813.82 5983916.00 5075423.83 2836295.39 6835941.20
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P 4008989.45 4055871.80 1920851.44 2185536.42 3423345.39 4736319.40 3962891.17 4076300.59 4138927.55 4413243.40 3218177.20 3480829.75
Q 4930813.63 4409970.81 2758018.61 2597879.74 2579761.60 8046053.32 6975320.46 3979006.37 4421613.63 4454432.26 2684891.92 4142116.49
R 4352425.84 4272516.15 2995446.45 3090123.72 3753190.68 12951476.71 5968435.97 3477281.79 4252536.34 5304785.32 3711766.66 5474359.62
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T 8401875.49 43097870.13 9828190.75 9395970.20 6579217.05 5285486.83 19487794.69 9180767.49 4322538.84 13090511.81 5777778.75 5599272.45
U 7631412.36 7515715.17 7755384.64 8509371.34 5177805.80 5138039.27 7042116.83 6702699.45 5987760.66 5426040.11 3354314.21 2106301.80
V 5592375.79 5087828.75 5182068.84 15220252.85 5133557.77 2541372.03 4096290.31 4934360.67 4691285.03 5956215.21 5167626.32 2445847.93
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X 3848136.75 4309131.21 3943642.17 4340129.08 5924218.23 816433.81 1647068.42 2525678.89 4171411.49 10511880.75 5039953.58 3796199.31
50 changes: 25 additions & 25 deletions src/kinase_library/databases/matrices/ser_thr/densitometry/GRK7_densitometry.txt
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1 2 3 4 5 6 7 8 9 10
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O 2008578.61 1918020.67 1772600.62 1840996.39 2211875.01 2686752.18 1927603.36 1620440.97 2084266.78 1344114.51
P 1743996.07 1785636.47 1919300.24 1762386.71 2592980.1 2711333.5 2578224.85 2347375.85 2590309.13 1421908.1
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U 4402949.29 3701189.98 3739114.06 3919325.38 3923233.3 3932222.65 5531764.57 4004897.43 4926264.36 1424336.83
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1 2 3 4 5 6 7 8 9 10 11 12
A 635378.09 148498.79 575911.32 61346.72 39998.35 44111.4 46733.27 42553.94 61967.3 834348.64 109387.74 386361.42
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I 366012.28 334559.32 367756.67 310706.48 312348.09 177745.16 175183.31 163711.65 238557.5 312545.76 144103.97 75719.57
J 357916.89 347521.67 280026.25 326405.25 349398.95 161707.28 159641.87 162556.15 274659.68 312294.58 293373.24 112633.84
K 431075.47 407585.33 377315.25 366912.54 531301.22 415762.39 234151.52 283216.18 417423.79 445085.4 252786.23 434519.01
L 415951.74 383664.83 338290.8 325834.48 294151.82 1124071.41 341060.72 295073.38 417703.06 357723 302419.24 1578747.2
M 361161.3 345186.83 331748.46 306283.55 487445.63 849985.26 398723.85 277542.52 369584.67 391280.1 350662.82 1593501.91
N 296898.77 296529.81 268248.23 278819.47 284954.67 928465.49 286307.14 225050.2 301717.23 334078.89 345044.56 1083383.08
O 315658.05 376055.69 299512.21 250713.62 309159.15 498363.69 299947.47 254554.73 414768.17 398852.83 377989.49 424828.06
P 285975.81 318379.8 258985.18 231251.87 290592.91 207111.6 389050.83 198725.09 313586.72 386135.24 432629.54 393772.81
Q 343274.79 332940.85 267684.07 261415.08 276514.36 290506.3 731584.57 231961.91 362358.82 360911.25 209414.92 229735.34
R 354053.39 367884.25 283255.87 276477.64 453439.91 301918.98 698728.87 238533.54 329908.95 396357.78 286206.19 269651.59
S 377446.99 375879.66 371451.58 499529.24 468376.74 327355.19 250017.65 200669.81 337944.81 480642.44 282535.68 199562.48
T 794938.79 820155.69 606866.9 684473.04 504724.55 468480.7 490166.44 433056.07 312420.31 666842.65 399074.97 283152.44
U 645027.67 614200.55 543442.94 593223.86 494651.31 319672.76 641746.37 458039.82 495745.66 524039.73 294328.57 237248.71
V 485057.94 410030.24 321596.06 371712.59 288092.5 184346.26 313008.96 282808.37 338050.74 514672.33 338684.01 308857.08
W 426219.67 405241.73 381111.41 421528.78 261333.6 173955.31 99523.58 373932.5 311099.17 474171.49 377474.16 301722.64
X 291204.97 388346.36 280482.37 270034.63 282593.23 80786 75581.67 117314.18 541596.32 644954.54 413179.15 356217.74
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