python-katlas 0.0.1__tar.gz

python-katlas-0.0.1/LICENSE

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python-katlas-0.0.1/MANIFEST.in

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+include settings.ini
+include LICENSE
+include CONTRIBUTING.md
+include README.md
+recursive-exclude * __pycache__

python-katlas-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: python-katlas
+Version: 0.0.1
+Summary: tools for predicting kinome specificities
+Home-page: https://github.com/sky1ove/python-katlas
+Author: lily
+Author-email: lcai888666@gmail.com
+License: Apache Software License 2.0
+Keywords: nbdev jupyter notebook python
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: License :: OSI Approved :: Apache Software License
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+Provides-Extra: dev
+License-File: LICENSE
+
+# KATLAS
+
+
+<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
+
+<a target="_blank" href="https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/index.ipynb">
+<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
+</a>
+
+<img alt="Katlas logo" width="700" caption="Katlas logo" src="https://github.com/sky1ove/katlas/raw/main/dataset/images/logo.png" id="logo"/>
+
+KATLAS is a repository containing python tools to predict kinases given
+a substrate sequence. It also contains datasets of kinase substrate
+specificities and human phosphoproteomics.
+
+***References***: Please cite the appropriate papers if KATLAS is
+helpful to your research.
+
+- KATLAS was described in the paper \[Decoding Human Kinome
+  Specificities through a Computational Data-Driven Approach
+  (manuscript)\]
+
+- The positional scanning peptide array (PSPA) data is from paper [An
+  atlas of substrate specificities for the human serine/threonine
+  kinome](https://www.nature.com/articles/s41586-022-05575-3) and paper
+  [The intrinsic substrate specificity of the human tyrosine
+  kinome](https://www.nature.com/articles/s41586-024-07407-y)
+
+- The kinase substrate datasets used for generating PSSMs are derived
+  from
+  [PhosphoSitePlus](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245126/)
+  and paper [Large-scale Discovery of Substrates of the Human
+  Kinome](https://www.nature.com/articles/s41598-019-46385-4)
+
+- Phosphorylation sites are acquired from
+  [PhosphoSitePlus](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245126/),
+  paper [The functional landscape of the human
+  phosphoproteome](https://www.nature.com/articles/s41587-019-0344-3),
+  and [CPTAC](https://pdc.cancer.gov/pdc/cptac-pancancer) /
+  [LinkedOmics](https://academic.oup.com/nar/article/46/D1/D956/4607804)
+
+## Tutorials on Colab
+
+- 1.  [Substrate scoring on a single substrate
+      sequence](https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/tutorial_01_sinlge_input.ipynb)
+- 2.  [High throughput substrate scoring on phosphoproteomics
+      dataset](https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/tutorial_02_high_throughput.ipynb)
+- 3.  [Query a protein’s phosphorylation sites and predict their
+      upstream
+      kinases](https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/tutorial_03_query_gene.ipynb)
+- 4.  [Kinase enrichment analysis for AKT
+      inhibitor](https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/tutorial_04a_enrichment_AKTi.ipynb)
+      / [Kinase enrichment analysis for EGFR
+      inhibitor](https://colab.research.google.com/github/sky1ove/katlas/blob/main/nbs/tutorial_04b_enrichment_EGFRi.ipynb)
+
+## Install
+
+Install the latest version through git
+
+``` python
+!pip install git+https://github.com/sky1ove/katlas.git -Uqq
+```
+
+## Import
+
+``` python
+from katlas.core import *
+```
+
+# Quick start
+
+We provide two methods to calculate substrate sequence:
+
+- Computational Data-Driven Method (CDDM)
+- Positional Scanning Peptide Array (PSPA)
+
+We consider the input in two formats:
+
+- a single input string (phosphorylation site)
+- a csv/dataframe that contains a column of phosphorylation sites
+
+For input sequences, we also consider it in two conditions:
+
+- all capital
+- contains lower cases indicating phosphorylation status
+
+## Single sequence as input
+
+### CDDM, all capital
+
+``` python
+predict_kinase('AAAAAAASGGAGSDN',**param_CDDM_upper)
+```
+
+    considering string: ['-7A', '-6A', '-5A', '-4A', '-3A', '-2A', '-1A', '0S', '1G', '2G', '3A', '4G', '5S', '6D', '7N']
+
+    kinase
+    PAK6     2.032
+    ULK3     2.032
+    PRKX     2.012
+    ATR      1.991
+    PRKD1    1.988
+             ...  
+    DDR2     0.928
+    EPHA4    0.928
+    TEK      0.921
+    KIT      0.915
+    FGFR3    0.910
+    Length: 289, dtype: float64
+
+### CDDM, with lower case indicating phosphorylation status
+
+``` python
+predict_kinase('AAAAAAAsGGAGsDN',**param_CDDM)
+```
+
+    considering string: ['-7A', '-6A', '-5A', '-4A', '-3A', '-2A', '-1A', '0s', '1G', '2G', '3A', '4G', '5s', '6D', '7N']
+
+    kinase
+    ULK3     1.987
+    PAK6     1.981
+    PRKD1    1.946
+    PIM3     1.944
+    PRKX     1.939
+             ...  
+    EPHA4    0.905
+    EGFR     0.900
+    TEK      0.898
+    FGFR3    0.894
+    KIT      0.882
+    Length: 289, dtype: float64
+
+### PSPA, with lower case indicating phosphorylation status
+
+``` python
+predict_kinase('AEEKEyHsEGG',**param_PSPA).head()
+```
+
+    considering string: ['-5A', '-4E', '-3E', '-2K', '-1E', '0y', '1H', '2s', '3E', '4G', '5G']
+
+    kinase
+    EGFR     4.013
+    FGFR4    3.568
+    ZAP70    3.412
+    CSK      3.241
+    SYK      3.209
+    dtype: float64
+
+### To replicate the results from The Kinase Library (PSPA)
+
+Check this link: [The Kinase
+Library](https://kinase-library.phosphosite.org/site?s=AEEKEy*HsEGG&pp=false&scp=true),
+and use log2(score) to rank, it shows same results with the below (with
+slight differences due to rounding).
+
+``` python
+predict_kinase('AEEKEyHSEGG',**param_PSPA).head(10)
+```
+
+    considering string: ['-5A', '-4E', '-3E', '-2K', '-1E', '0y', '1H', '2S', '3E', '4G', '5G']
+
+    kinase
+    EGFR         3.181
+    FGFR4        2.390
+    CSK          2.308
+    ZAP70        2.068
+    SYK          1.998
+    PDHK1_TYR    1.922
+    RET          1.732
+    MATK         1.688
+    FLT1         1.627
+    BMPR2_TYR    1.456
+    dtype: float64
+
+- So far [The kinase Library](https://kinase-library.phosphosite.org)
+  considers all ***tyr sequences*** in capital regardless of whether or
+  not they contain lower cases, which is a small bug and should be fixed
+  soon.
+- Kinase with “\_TYR” indicates it is a dual specificity kinase tested
+  in PSPA tyrosine setting, which has not been included in
+  kinase-library yet.
+
+We can also calculate the percentile score using a referenced score
+sheet.
+
+``` python
+# Percentile reference sheet
+y_pct = Data.get_pspa_tyr_pct()
+
+get_pct('AEEKEyHSEGG',**param_PSPA_y, pct_ref = y_pct)
+```
+
+    considering string: ['-5A', '-4E', '-3E', '-2K', '-1E', '0Y', '1H', '2S', '3E', '4G', '5G']
+
+
+
+|       | log2(score) | percentile |
+|-------|-------------|------------|
+| EGFR  | 3.181       | 96.787423  |
+| FGFR4 | 2.390       | 94.012303  |
+| CSK   | 2.308       | 95.201640  |
+| ZAP70 | 2.068       | 88.380041  |
+| SYK   | 1.998       | 85.522898  |
+| ...   | ...         | ...        |
+| EPHA1 | -3.501      | 12.139440  |
+| FES   | -3.699      | 21.216678  |
+| TNK1  | -4.269      | 5.481887   |
+| TNK2  | -4.577      | 2.050581   |
+| DDR2  | -4.920      | 10.403281  |
+
+
+
+## High-throughput substrate scoring on a dataframe
+
+### Load your csv
+
+``` python
+# df = pd.read_csv('your_file.csv')
+```
+
+### Load a demo df
+
+``` python
+# Load a demo df with phosphorylation sites
+df = Data.get_ochoa_site().head()
+df.iloc[:,-2:]
+```
+
+
+|     | site_seq        | gene_site      |
+|-----|-----------------|----------------|
+| 0   | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
+| 1   | YDSAGLLSDEDCMSV | A0A075B6Q4_S35 |
+| 2   | IADHLFWSEETKSRF | A0A075B6Q4_S57 |
+| 3   | KSRFTEYSMTSSVMR | A0A075B6Q4_S68 |
+| 4   | FTEYSMTSSVMRRNE | A0A075B6Q4_S71 |
+
+
+
+### Set the column name and param to calculate
+
+Here we choose param_CDDM_upper, as the sequences in the demo df are all
+in capital. You can also choose other params.
+
+``` python
+results = predict_kinase_df(df,'site_seq',**param_CDDM_upper)
+results
+```
+
+    input dataframe has a length 5
+    Preprocessing
+    Finish preprocessing
+    Calculating position: [-7, -6, -5, -4, -3, -2, -1, 0, 1, 2, 3, 4, 5, 6, 7]
+
+    100%|██████████| 289/289 [00:05<00:00, 56.64it/s]
+
+
+
+| kinase | SRC      | EPHA3    | FES      | NTRK3    | ALK      | EPHA8    | ABL1     | FLT3     | EPHB2    | FYN      | ... | MEK5     | PKN2     | MAP2K7   | MRCKB    | HIPK3    | CDK8     | BUB1     | MEKK3    | MAP2K3   | GRK1     |
+|--------|----------|----------|----------|----------|----------|----------|----------|----------|----------|----------|-----|----------|----------|----------|----------|----------|----------|----------|----------|----------|----------|
+| 0      | 0.991760 | 1.093712 | 1.051750 | 1.067134 | 1.013682 | 1.097519 | 0.966379 | 0.982464 | 1.054986 | 1.055910 | ... | 1.314859 | 1.635470 | 1.652251 | 1.622672 | 1.362973 | 1.797155 | 1.305198 | 1.423618 | 1.504941 | 1.872020 |
+| 1      | 0.910262 | 0.953743 | 0.942327 | 0.950601 | 0.872694 | 0.932586 | 0.846899 | 0.826662 | 0.915020 | 0.942713 | ... | 1.175454 | 1.402006 | 1.430392 | 1.215826 | 1.569373 | 1.716455 | 1.270999 | 1.195081 | 1.223082 | 1.793290 |
+| 2      | 0.849866 | 0.899910 | 0.848895 | 0.879652 | 0.874959 | 0.899414 | 0.839200 | 0.836523 | 0.858040 | 0.867269 | ... | 1.408003 | 1.813739 | 1.454786 | 1.084522 | 1.352556 | 1.524663 | 1.377839 | 1.173830 | 1.305691 | 1.811849 |
+| 3      | 0.803826 | 0.836527 | 0.800759 | 0.894570 | 0.839905 | 0.781001 | 0.847847 | 0.807040 | 0.805877 | 0.801402 | ... | 1.110307 | 1.703637 | 1.795092 | 1.469653 | 1.549936 | 1.491344 | 1.446922 | 1.055452 | 1.534895 | 1.741090 |
+| 4      | 0.822793 | 0.796532 | 0.792343 | 0.839882 | 0.810122 | 0.781420 | 0.805251 | 0.795022 | 0.790380 | 0.864538 | ... | 1.062617 | 1.357689 | 1.485945 | 1.249266 | 1.456078 | 1.422782 | 1.376471 | 1.089629 | 1.121309 | 1.697524 |
+
+
+
+## Phosphorylation sites
+
+Besides calculating sequence scores, we also provides multiple datasets
+of phosphorylation sites.
+
+### CPTAC pan-cancer phosphoproteomics
+
+``` python
+df = Data.get_cptac_ensembl_site()
+df.head(3)
+```
+
+
+
+|     | gene               | site  | site_seq        | protein           | gene_name | gene_site   | protein_site          |
+|-----|--------------------|-------|-----------------|-------------------|-----------|-------------|-----------------------|
+| 0   | ENSG00000003056.8  | S267  | DDQLGEESEERDDHL | ENSP00000000412.3 | M6PR      | M6PR_S267   | ENSP00000000412_S267  |
+| 1   | ENSG00000003056.8  | S267  | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR      | M6PR_S267   | ENSP00000440488_S267  |
+| 2   | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28     | USP28_S1053 | ENSP00000003302_S1053 |
+
+
+
+### [Ochoa et al. human phosphoproteome](https://www.nature.com/articles/s41587-019-0344-3)
+
+``` python
+df = Data.get_ochoa_site()
+df.head(3)
+```
+
+
+|     | uniprot    | position | residue | is_disopred | disopred_score | log10_hotspot_pval_min | isHotspot | uniprot_position | functional_score | current_uniprot | name             | gene | Sequence                                          | is_valid | site_seq        | gene_site      |
+|-----|------------|----------|---------|-------------|----------------|------------------------|-----------|------------------|------------------|-----------------|------------------|------|---------------------------------------------------|----------|-----------------|----------------|
+| 0   | A0A075B6Q4 | 24       | S       | True        | 0.91           | 6.839384               | True      | A0A075B6Q4_24    | 0.149257         | A0A075B6Q4      | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True     | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
+| 1   | A0A075B6Q4 | 35       | S       | True        | 0.87           | 9.192622               | False     | A0A075B6Q4_35    | 0.136966         | A0A075B6Q4      | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True     | YDSAGLLSDEDCMSV | A0A075B6Q4_S35 |
+| 2   | A0A075B6Q4 | 57       | S       | False       | 0.28           | 0.818834               | False     | A0A075B6Q4_57    | 0.125364         | A0A075B6Q4      | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True     | IADHLFWSEETKSRF | A0A075B6Q4_S57 |
+
+
+
+### PhosphoSitePlus human phosphorylation site
+
+``` python
+df = Data.get_psp_human_site()
+df.head(3)
+```
+
+
+|     | gene  | protein     | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq              | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site |
+|-----|-------|-------------|---------|------|-----------|-------------|---------|-----------------------|--------|--------|--------|----------|----------------|
+| 0   | YWHAB | 14-3-3 beta | P31946  | T2   | YWHAB_T2  | 15718712    | human   | \_\_\_\_\_\_MtMDksELV | NaN    | 3.0    | 1.0    | None     | 0              |
+| 1   | YWHAB | 14-3-3 beta | P31946  | S6   | YWHAB_S6  | 15718709    | human   | \_\_MtMDksELVQkAk     | NaN    | 8.0    | NaN    | None     | 0              |
+| 2   | YWHAB | 14-3-3 beta | P31946  | Y21  | YWHAB_Y21 | 3426383     | human   | LAEQAERyDDMAAAM       | NaN    | NaN    | 4.0    | None     | 0              |
+
+
+
+### Unique sites of combined Ochoa & PhosphoSitePlus
+
+``` python
+df = Data.get_combine_site_psp_ochoa()
+df.head(3)
+```
+
+
+|     | site_seq        | gene_site  | gene  | source | num_site | acceptor | -7  | -6  | -5  | -4  | ... | -2  | -1  | 0   | 1   | 2   | 3   | 4   | 5   | 6   | 7   |
+|-----|-----------------|------------|-------|--------|----------|----------|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
+| 0   | AAAAAAASGGAGSDN | PBX1_S136  | PBX1  | ochoa  | 1        | S        | A   | A   | A   | A   | ... | A   | A   | S   | G   | G   | A   | G   | S   | D   | N   |
+| 1   | AAAAAAASGGGVSPD | PBX2_S146  | PBX2  | ochoa  | 1        | S        | A   | A   | A   | A   | ... | A   | A   | S   | G   | G   | G   | V   | S   | P   | D   |
+| 2   | AAAAAAASGVTTGKP | CLASR_S349 | CLASR | ochoa  | 1        | S        | A   | A   | A   | A   | ... | A   | A   | S   | G   | V   | T   | T   | G   | K   | P   |
+
+
+
+## Phosphorylation site sequence example
+
+***All capital - 15 length (-7 to +7)***
+
+- QSEEEKLSPSPTTED
+- TLQHVPDYRQNVYIP
+- TMGLSARyGPQFTLQ
+
+***All capital - 10 length (-5 to +4)***
+
+- SRDPHYQDPH
+- LDNPDyQQDF
+- AAAAAsGGAG
+
+***With lowercase - (-7 to +7)***
+
+- QsEEEKLsPsPTTED
+- TLQHVPDyRQNVYIP
+- TMGLsARyGPQFTLQ
+
+***With lowercase - (-5 to +4)***
+
+- sRDPHyQDPH
+- LDNPDyQQDF
+- AAAAAsGGAG