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Data update (#27)
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* Fixing processing error in PDHK1 and PDHK4 - Y column should be replaced with F (dual specificity)

* Data update
New: CDKL2
Updated: CK1D, GRK7, SRPK2

* Update README

* Updating version
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yaront authored Jan 29, 2025
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15 changes: 12 additions & 3 deletions README.md
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Expand Up @@ -109,6 +109,18 @@ This is the expected output from using the PhosphoProteomics.predict() function.

</div>

## Data Updates

<div>

| Release | Date | New | Updated | Removed | Total Ser/Thr | Total Tyrosine | Total Non-Canonicals (Tyrosine) | Notes |
|:-------:|:----:|:---:|:-------:|:-------:|:-------------:|:--------------:|:-------------------------------:|:-----:|
| **v0.1.0** | Oct 30, 2024 | _None_ | _None_ | _None_ | 303 | 78 | 15 | Legacy version - data as described in papers |
| **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 | |
| **v1.0.4** | Jan 28, 2025 | CDKL2 | CK1D, GRK7, SRPK2 | _None_ | 310 | 78 | 15 | Fixed processing error for PDHK1 and PDHK4 |

</div>

## Citations

Please cite the following papers when using this package:
Expand All @@ -119,9 +131,6 @@ Please cite the following papers when using this package:
**For the tyrosine kinome:**
> Yaron-Barir, T. M., Joughin, B. A., Huntsman, E. M., Kerelsky, A., Cizin, D. M., Cohen, B. M., ... & Johnson, J. L. (2024). **The intrinsic substrate specificity of the human tyrosine kinome**. _Nature_, 1-8. [https://doi.org/10.1038/s41586-024-07407-y](https://doi.org/10.1038/s41586-024-07407-y)
**If you are using the MEA tool, please also cite:**
> Fang, Z., Liu, X., & Peltz, G. (2023). **GSEApy: a comprehensive package for performing gene set enrichment analysis in Python**. _Bioinformatics_, 39(1), btac757. [https://doi.org/10.1093/bioinformatics/btac757](https://doi.org/10.1093/bioinformatics/btac757)
## License

This package is distributed under the Creative Commons License. See `LICENSE` for more information.
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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__ = "1.0.3"
__version__ = "1.0.4"

#%% Loading scored phosphoproteome one time per session

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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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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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