<no title>

[32]:

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from scipy.spatial import distance
from sklearn.metrics import roc_curve, auc
import random
from scipy.optimize import curve_fit
import seaborn as sns
from scipy.stats import *
from scipy import stats
import copy
import re
from sklearn.preprocessing import StandardScaler
import warnings
warnings.filterwarnings('ignore')
import pylab as py

from Slim_TPCA import Slim_TPCA

[2]:

# Select four temperature points
# The Data_dir here is the relative directory of the data file to the script
Data_dir = '..\\..\\project_1_data\\pj10_source\\'
col_list = [0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18]
TPCA_table1 = pd.read_excel(Data_dir + 'aan0346_Tables_S1_to_S18.xlsx', sheet_name=0, usecols=col_list, header=2)
TPCA_table1.columns = ['Accession','T_37','T_40','T_43','T_46','T_49','T_52','T_55','T_58','T_61','T_64']

col_list = [0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18]
TPCA_table7 = pd.read_excel(Data_dir + 'aan0346_Tables_S1_to_S18.xlsx', sheet_name=6, usecols=col_list, header=2)
TPCA_table7.columns = ['Accession','T_37','T_40','T_43','T_46','T_49','T_52','T_55','T_58','T_61','T_64']

col_list = [0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18]
TPCA_DMSO = pd.read_excel(Data_dir + 'aan0346_Tables_S1_to_S18.xlsx', sheet_name=14, usecols=col_list, header=2)
TPCA_DMSO.columns = ['Accession','T_37','T_40','T_43','T_46','T_49','T_52','T_55','T_58','T_61','T_64']

col_list = [0, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]
TPCA_MTX = pd.read_excel(Data_dir + 'aan0346_Tables_S1_to_S18.xlsx', sheet_name=14, usecols=col_list, header=2)
TPCA_MTX.columns = ['Accession','T_37','T_40','T_43','T_46','T_49','T_52','T_55','T_58','T_61','T_64']
# Filter out some proteins with abnormal changes in thermal stability
TPCA_table1 = TPCA_table1[np.sum(TPCA_table1.iloc[:,1:]>1.2, axis=1)==0].reset_index(drop=True)
TPCA_table7 = TPCA_table7[np.sum(TPCA_table7.iloc[:,1:]>1.2, axis=1)==0].reset_index(drop=True)
TPCA_DMSO = TPCA_DMSO[np.sum(TPCA_DMSO.iloc[:,1:]>1.2, axis=1)==0].reset_index(drop=True)
TPCA_MTX = TPCA_MTX[np.sum(TPCA_MTX.iloc[:,1:]>1.2, axis=1)==0].reset_index(drop=True)

TPCA_table1_4t = TPCA_table1.iloc[:,[0,1,4,7,9]]
TPCA_table7_4t = TPCA_table7.iloc[:,[0,1,4,7,9]]
TPCA_DMSO_4t = TPCA_DMSO.iloc[:,[0,1,4,7,9]]
TPCA_MTX_4t = TPCA_MTX.iloc[:,[0,1,4,7,9]]

[8]:

TPCA_table1_4t

[8]:

	Accession	T_37	T_46	T_55	T_61
0	P06733	0.996324	1.016098	0.938197	0.737465
1	P08238	0.996324	0.925673	0.192489	0.083953
2	P60709	0.996324	0.859558	0.184996	0.096016
3	P07900	0.996324	0.935755	0.177301	0.065293
4	P63261	0.996324	0.862699	0.185592	0.092703
...	...	...	...	...	...
7344	Q9Y219	0.996324	0.996797	0.495677	0.350349
7345	Q9Y4I5	0.996324	0.938674	0.540570	0.407048
7346	Q9Y587	0.996324	0.790674	0.361195	0.196616
7347	Q9Y5B6	0.996324	0.775120	0.406555	0.272317
7348	Q9Y5L2	0.996324	0.811529	0.527748	0.456675

7349 rows × 5 columns

[9]:

TPCA_table7_4t

[9]:

	Accession	T_37	T_46	T_55	T_61
0	A0AV96	0.999317	0.767114	0.236343	0.271086
1	A0AVF1	0.999317	0.630179	0.170644	0.081662
2	A0AVI2	0.999317	0.975093	0.751207	0.435817
3	A0AVT1	0.999317	0.932444	0.117044	0.060957
4	A0FGR8	0.999317	0.776876	0.292422	0.144480
...	...	...	...	...	...
7504	R4GMX3	0.999317	0.823301	0.154396	0.065230
7505	R4GMY8	0.999317	1.102146	0.233735	0.049690
7506	R4GN35	0.999317	0.852296	0.209799	0.099568
7507	R4GNH3	0.999317	1.064515	0.388299	0.099491
7508	S4R3N1	0.999317	1.027315	0.622019	0.560280

7509 rows × 5 columns

[10]:

TPCA_DMSO_4t

[10]:

	Accession	T_37	T_46	T_55	T_61
0	A0AVT1	0.993418	0.840974	0.179851	0.082742
1	A0FGR8	0.993418	0.738062	0.272239	0.146445
2	A0JNW5	0.993418	0.834989	0.241493	0.080578
3	A0MZ66	0.993418	0.703659	0.181131	0.102229
4	A1A5D9	0.993418	1.124804	1.010595	0.859623
...	...	...	...	...	...
5691	Q9Y6Y0	0.993418	0.636364	0.160605	0.085604
5692	Q9Y6Y8	0.993418	0.759312	0.227500	0.134417
5693	R4GMX3	0.993418	0.637131	0.143294	0.060596
5694	R4GNH3	0.993418	0.911211	0.384059	0.060962
5695	S4R3N1	0.993418	1.017978	0.899409	0.694829

5696 rows × 5 columns

[11]:

TPCA_MTX_4t

[11]:

	Accession	T_37	T_46	T_55	T_61
0	A0AVT1	0.996284	0.870993	0.162564	0.075434
1	A0FGR8	0.996284	0.856500	0.385548	0.172577
2	A0JNW5	0.996284	0.992454	0.347952	0.115628
3	A0MZ66	0.996284	0.797549	0.225280	0.118198
4	A1A5D9	0.996284	0.904087	0.604036	0.418830
...	...	...	...	...	...
5654	Q9Y6Y0	0.996284	0.771987	0.194220	0.104885
5655	Q9Y6Y8	0.996284	0.878918	0.267283	0.166219
5656	R4GMX3	0.996284	0.780070	0.189431	0.079288
5657	R4GNH3	0.996284	0.925082	0.447936	0.114163
5658	S4R3N1	0.996284	1.022142	1.105067	0.880167

5659 rows × 5 columns

[12]:

# Obtain a table with credible protein pair information reported in at least two papers
pair_table0 = pd.read_excel(Data_dir + 'TPCA_table2.xlsx')
pair_table1 = pair_table0[pair_table0['No. of Publications']>2].reset_index(drop=True)
pair_table1

[12]:

	Protein A	Protein B	No. of Publications
0	P40337	Q16665	79
1	O14920	Q9Y6K9	66
2	P22681	P62993	64
3	P42345	Q8N122	60
4	P05412	P45983	58
...	...	...	...
5485	Q12769	Q9BW27	3
5486	O43143	P52756	3
5487	Q16576	Q8WXI9	3
5488	O15151	P27348	3
5489	Q13347	Q99613	3

5490 rows × 3 columns

[13]:

# Get information about protein complexes in the corum database
col_list = [0, 1, 2, 5, 9, 12]
corum = pd.read_csv(Data_dir + 'allComplexes.txt', sep='\t', usecols=col_list)
corum

[13]:

	ComplexID	ComplexName	Organism	subunits(UniProt IDs)	GO description	subunits(Gene name)
0	1	BCL6-HDAC4 complex	Human	P41182;P56524	DNA topological change;negative regulation of ...	BCL6;HDAC4
1	2	BCL6-HDAC5 complex	Human	P41182;Q9UQL6	DNA topological change;negative regulation of ...	BCL6;HDAC5
2	3	BCL6-HDAC7 complex	Human	P41182;Q8WUI4	DNA topological change;negative regulation of ...	BCL6;HDAC7
3	4	Multisubunit ACTR coactivator complex	Human	Q09472;Q92793;Q92831;Q9Y6Q9	positive regulation of transcription, DNA-temp...	EP300;CREBBP;KAT2B;NCOA3
4	9	6S-nuclear aryl hydrocarbon (Ah) receptor liga...	Mouse	P30561;P53762	regulation of RNA biosynthetic process;regulat...	Ahr;Arnt
...	...	...	...	...	...	...
4269	7588	APP(AICD)-FOXO1 complex	Human	P05067;Q12778	cell death;cytoplasm;apoptotic process	APP;FOXO1
4270	7589	APP(AICD)-FOXO4 complex	Human	P05067;P98177	cell death;cytoplasm;apoptotic process	APP;FOXO4
4271	7592	Meiob-Rpa2-Spata22 complex	Mouse	Q5SV06;Q62193;Q9D513	chromatin DNA binding	Spata22;Rpa2;Meiob
4272	7593	AKAP13-MAP2K3-MAP3K20-MAPK14-PKN1 complex	Human	P46734;Q12802;Q16512;Q16539;Q9NYL2	MAPK cascade	MAP2K3;AKAP13;PKN1;MAPK14;MAP3K20
4273	7594	Meis2-Pbx1-Pdx1 complex	Mouse	P41778;P52946;P97367	nucleus;regulation of transcription, DNA-templ...	Pbx1;Pdx1;Meis2

4274 rows × 6 columns

[5]:

# Using boxplot to show the trend of data
sns.boxplot(data = TPCA_table7, showfliers=False)

[5]:

<AxesSubplot:>

../_images/notebooks_Slim_TPCA_test_8_1.png

[6]:

# Using ROC curve to evaluate the prediction
Slim_TPCA.roc_plot(TPCA_table7, pair_table1)

../_images/notebooks_Slim_TPCA_test_9_0.png

[7]:

# Calculate TPCA signatures of complexes by sampling
table7_random_sample_4t, table7_sig_sample_4t = Slim_TPCA.complex_signature_sample(TPCA_table7_4t, corum)

[14]:

table7_random_sample_4t

[14]:

	3	4	5	6	7	8	9	10	11	12	...	29	31	32	35	43	57	65	69	82	121
0	0.779244	0.649008	0.564714	0.518125	0.610693	0.594234	0.557421	0.555023	0.529464	0.505033	...	0.615243	0.599833	0.593519	0.584435	0.561588	0.549724	0.534998	0.566381	0.549865	0.556998
1	0.343141	0.648300	0.622926	0.545459	0.593774	0.639406	0.682846	0.639320	0.678559	0.675339	...	0.484884	0.472681	0.474262	0.558945	0.514685	0.575610	0.577161	0.541165	0.592101	0.563332
2	0.773273	0.382246	0.622980	0.745530	0.727845	0.674314	0.582740	0.652440	0.572770	0.567719	...	0.526473	0.566758	0.602624	0.603471	0.576615	0.573653	0.566111	0.561316	0.582207	0.566660
3	0.349296	0.616668	0.732306	0.684266	0.526539	0.603072	0.555510	0.486570	0.505072	0.456243	...	0.625528	0.595571	0.546429	0.508919	0.586783	0.539033	0.584882	0.562064	0.481345	0.592664
4	0.734995	0.785656	0.602765	0.687350	0.602336	0.528106	0.447551	0.236086	0.416708	0.513488	...	0.551322	0.648130	0.658150	0.606709	0.523009	0.552707	0.488379	0.567467	0.656345	0.538608
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
9995	0.385319	0.779954	0.597345	0.537456	0.772089	0.476241	0.429126	0.612893	0.588293	0.612771	...	0.597774	0.675950	0.529701	0.602357	0.573796	0.560113	0.580977	0.601052	0.541679	0.544367
9996	0.681380	0.797056	0.578530	0.630504	0.387264	0.326173	0.710226	0.447887	0.556621	0.650238	...	0.568941	0.484094	0.622397	0.511496	0.552091	0.575063	0.595143	0.533166	0.585816	0.524210
9997	0.532761	0.514534	0.839380	0.478747	0.558719	0.612183	0.714550	0.470922	0.301195	0.367962	...	0.643930	0.626394	0.474924	0.638773	0.479897	0.583882	0.577249	0.581806	0.521220	0.518727
9998	0.666261	0.736488	0.844754	0.320485	0.384130	0.850851	0.520765	0.534594	0.421263	0.500090	...	0.502745	0.624295	0.653327	0.617367	0.597130	0.602753	0.518709	0.560822	0.623126	0.516156
9999	0.335644	0.548753	0.516765	1.051003	0.847589	0.731600	0.210459	0.648981	0.718236	0.480978	...	0.512698	0.529668	0.719490	0.487595	0.561799	0.586503	0.541819	0.651817	0.605211	0.610317

10000 rows × 33 columns

[15]:

table7_sig_sample_4t

[15]:

	ComplexID	ComplexName	Organism	subunits(UniProt IDs)	GO description	subunits(Gene name)	Subunit_Found	No_Subunit_Found	Avg_Dist	Avg_Dist_Derived	TPCA_Sig_P-value	TPCA_Sig_Z-score
0	4	Multisubunit ACTR coactivator complex	Human	Q09472;Q92793;Q92831;Q9Y6Q9	positive regulation of transcription, DNA-temp...	EP300;CREBBP;KAT2B;NCOA3	Q09472;Q92793;Q9Y6Q9	3	0.171014	0.853961	0.0316	1.835605
1	10	Condensin I complex	Human	O95347;Q15003;Q15021;Q9BPX3;Q9NTJ3	M phase;mitotic nuclear division;chromosome co...	SMC2;NCAPH;NCAPD2;NCAPG;SMC4	O95347;Q15003;Q15021;Q9BPX3;Q9NTJ3	5	0.047746	0.954429	0.0000	3.996365
2	12	BLOC-2 (biogenesis of lysosome-related organel...	Human	Q86YV9;Q969F9;Q9UPZ3	endosome organization;lysosome organization;va...	HPS6;HPS3;HPS5	Q86YV9;Q969F9;Q9UPZ3	3	0.113091	0.898399	0.0071	2.258323
3	15	NCOR complex	Human	O15379;O60907;O75376;Q13227;Q92828;Q9BZK7	DNA topological change;negative regulation of ...	HDAC3;TBL1X;NCOR1;GPS2;CORO2A;TBL1XR1	O15379;O60907;O75376;Q92828;Q9BZK7	5	0.216056	0.822330	0.0125	2.258320
4	23	BLOC-1 (biogenesis of lysosome-related organel...	Human	O95295;P78537;Q6QNY0;Q6QNY1;Q8TDH9;Q96EV8;Q9NU...	None	SNAPIN;BLOC1S1;BLOC1S3;BLOC1S2;BLOC1S5;DTNBP1;...	O95295;P78537;Q6QNY0;Q6QNY1;Q8TDH9;Q96EV8;Q9NUP1	7	0.176741	0.849804	0.0008	3.176014
...	...	...	...	...	...	...	...	...	...	...	...	...
1087	7582	ESR2-TRAP/Mediator coactivator complex	Human	O43513;O60244;O75448;O75586;P24863;P49336;Q094...	mediator complex;mRNA transcription;nucleus;re...	MED7;MED14;MED24;MED6;CCNC;CDK8;EP300;MED21;ME...	O43513;O60244;P24863;P49336;Q09472;Q13503;Q156...	14	0.211030	0.825743	0.0000	4.241964
1088	7583	CDK8 subcomplex (CCNC, CDK8, MED12, MED13)	Human	P24863;P49336;Q93074;Q9UHV7	histone kinase activity	CCNC;CDK8;MED12;MED13	P24863;P49336;Q93074;Q9UHV7	4	0.222320	0.818116	0.0312	1.866946
1089	7584	CDK8 subcomplex (CCNC, CDK8, MED12)	Human	P24863;P49336;Q93074	histone kinase activity	CCNC;CDK8;MED12	P24863;P49336;Q93074	3	0.249921	0.800051	0.1006	1.322658
1090	7585	CDK8 subcomplex (CCNC, CDK8, MED13)	Human	P24863;P49336;Q9UHV7	histone kinase activity	CCNC;CDK8;MED13	P24863;P49336;Q9UHV7	3	0.139880	0.877285	0.0156	2.057495
1091	7593	AKAP13-MAP2K3-MAP3K20-MAPK14-PKN1 complex	Human	P46734;Q12802;Q16512;Q16539;Q9NYL2	MAPK cascade	MAP2K3;AKAP13;PKN1;MAPK14;MAP3K20	P46734;Q12802;Q16512;Q16539;Q9NYL2	5	0.192688	0.838442	0.0079	2.470446

1092 rows × 12 columns

[16]:

# Calculate TPCA signatures of complexes by Beta distribution fitting
table7_random_beta_4t, table7_sig_beta_4t = Slim_TPCA.complex_signature_beta(TPCA_table7_4t, corum)
sig_result = pd.DataFrame({'Sample':table7_sig_sample_4t['TPCA_Sig_P-value'], 'Beta':table7_sig_beta_4t['TPCA_Sig_P-value']})
sig_result = sig_result[np.sum(sig_result==0, axis=1)==0].reset_index(drop=True)

[17]:

sig_result

[17]:

	Sample	Beta
0	0.0316	0.009652
1	0.0545	0.026748
2	0.2684	0.250098
3	0.1623	0.156690
4	0.0251	0.004361
...	...	...
824	0.3747	0.363433
825	0.1730	0.162725
826	0.5883	0.571875
827	0.0312	0.011850
828	0.1006	0.090829

829 rows × 2 columns

[18]:

sns.pairplot(data=sig_result)

[18]:

<seaborn.axisgrid.PairGrid at 0x2ba78100820>

../_images/notebooks_Slim_TPCA_test_15_1.png

[19]:

# Calculate TPCA dynamic modulation signatures of complexes by sampling and absolute distance
MTX_dynamic_absolute_random_4t, MTX_dynamic_absolute_sample_4t = Slim_TPCA.dynamic_complex_absolute_sample(TPCA_DMSO_4t, TPCA_MTX_4t, corum)

[20]:

MTX_dynamic_absolute_random_4t

[20]:

	3	4	5	6	7	8	9	10	11	12	...	28	31	34	38	42	66	67	68	85	126
0	0.019390	0.017768	-0.005482	0.014657	0.004218	0.005317	0.020310	0.027237	0.063059	0.027803	...	-0.012784	-0.013336	-0.008926	-0.014170	-0.015879	0.005040	0.006060	0.007865	-0.023312	-0.043110
1	0.034352	-0.016493	0.055331	0.057159	0.031395	0.025806	-0.005620	0.005728	-0.016734	-0.020292	...	-0.010159	0.015728	0.028059	-0.014992	-0.029510	-0.093621	-0.095533	-0.087212	-0.057435	-0.009502
2	0.048409	0.096671	0.051531	0.034073	0.084055	-0.056832	-0.039717	-0.057635	-0.102303	-0.037304	...	-0.052334	-0.128422	-0.131161	-0.079601	-0.070588	0.002906	0.005883	0.000034	0.005669	-0.057841
3	0.039388	0.061160	0.038627	-0.083045	-0.150321	-0.042767	-0.029652	-0.056840	-0.018775	-0.042738	...	-0.083454	-0.035295	-0.037749	-0.061469	-0.049153	-0.018021	-0.042806	-0.040088	-0.071188	-0.012680
4	0.040657	0.041840	-0.124119	-0.032774	-0.010920	-0.067074	-0.002381	-0.012825	0.042552	0.102479	...	-0.038015	-0.072640	-0.050444	0.046777	0.034189	-0.087155	-0.062412	-0.068550	-0.027857	-0.026515
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
9995	-0.448212	-0.030953	-0.531915	0.023555	0.002192	-0.070471	-0.085362	0.080573	0.016617	0.063970	...	-0.020822	0.028467	-0.030114	-0.009254	0.015827	-0.039435	-0.007448	-0.014886	-0.015587	-0.007732
9996	0.034874	0.027597	0.116606	0.022516	-0.025259	0.037002	-0.120146	-0.106739	-0.141229	0.076553	...	-0.035181	0.013102	-0.026978	-0.045025	-0.033807	-0.000484	-0.032710	-0.025255	0.003104	-0.017043
9997	0.064068	-0.089895	0.019111	-0.009754	-0.088511	0.067880	0.015009	-0.132397	-0.099199	-0.129614	...	0.003447	-0.018253	-0.011799	-0.043683	0.034941	-0.043117	-0.002664	-0.010679	-0.057793	-0.022571
9998	-0.078887	-0.018101	0.033638	-0.030903	-0.040812	-0.116837	-0.000939	-0.143596	-0.028123	0.000261	...	0.003203	-0.018020	-0.005822	-0.072891	-0.048994	-0.029375	-0.011082	-0.024573	-0.010859	-0.021181
9999	-0.048656	-0.284772	0.018244	-0.086161	-0.020684	-0.136642	0.074967	-0.109238	0.090591	-0.025404	...	-0.044014	-0.048583	-0.011635	-0.056760	-0.003554	-0.029622	-0.054354	-0.044017	-0.037601	-0.061629

10000 rows × 32 columns

[21]:

MTX_dynamic_absolute_sample_4t

[21]:

	ComplexID	ComplexName	Organism	subunits(UniProt IDs)	GO description	subunits(Gene name)	Subunit_Found	No_Subunit_Found	Avg_Dist_1	Avg_Dist_Derived_1	Avg_Dist_2	Avg_Dist_Derived_2	Avg_Dist_change	Dynamic_P
0	4	Multisubunit ACTR coactivator complex	Human	Q09472;Q92793;Q92831;Q9Y6Q9	positive regulation of transcription, DNA-temp...	EP300;CREBBP;KAT2B;NCOA3	Q09472;Q92793;Q9Y6Q9	3	0.155208	0.865645	0.309147	0.763856	-0.153939	0.8295
1	10	Condensin I complex	Human	O95347;Q15003;Q15021;Q9BPX3;Q9NTJ3	M phase;mitotic nuclear division;chromosome co...	SMC2;NCAPH;NCAPD2;NCAPG;SMC4	O95347;Q15003;Q15021;Q9BPX3;Q9NTJ3	5	0.069342	0.935154	0.082957	0.923397	-0.013615	0.4574
2	15	NCOR complex	Human	O15379;O60907;O75376;Q13227;Q92828;Q9BZK7	DNA topological change;negative regulation of ...	HDAC3;TBL1X;NCOR1;GPS2;CORO2A;TBL1XR1	O15379;O60907;O75376;Q92828;Q9BZK7	5	0.199575	0.833629	0.208486	0.827482	-0.008911	0.4375
3	23	BLOC-1 (biogenesis of lysosome-related organel...	Human	O95295;P78537;Q6QNY0;Q6QNY1;Q8TDH9;Q96EV8;Q9NU...	None	SNAPIN;BLOC1S1;BLOC1S3;BLOC1S2;BLOC1S5;DTNBP1;...	O95295;P78537;Q6QNY0;Q6QNY1;Q8TDH9;Q9NUP1	6	0.161005	0.861323	0.207986	0.827824	-0.046981	0.6077
4	27	Arp2/3 protein complex	Human	O15143;O15144;O15145;O15511;P59998;P61158;P61160	None	ARPC1B;ARPC2;ARPC3;ARPC5;ARPC4;ACTR3;ACTR2	O15143;O15144;O15145;O15511;P61158;P61160	6	0.104131	0.905690	0.137539	0.879091	-0.033409	0.5433
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
968	7582	ESR2-TRAP/Mediator coactivator complex	Human	O43513;O60244;O75448;O75586;P24863;P49336;Q094...	mediator complex;mRNA transcription;nucleus;re...	MED7;MED14;MED24;MED6;CCNC;CDK8;EP300;MED21;ME...	O43513;O60244;P24863;P49336;Q09472;Q13503;Q156...	14	0.336775	0.748069	0.236984	0.808418	0.099791	0.0196
969	7583	CDK8 subcomplex (CCNC, CDK8, MED12, MED13)	Human	P24863;P49336;Q93074;Q9UHV7	histone kinase activity	CCNC;CDK8;MED12;MED13	P24863;P49336;Q93074;Q9UHV7	4	0.331881	0.750818	0.230481	0.812690	0.101400	0.1235
970	7584	CDK8 subcomplex (CCNC, CDK8, MED12)	Human	P24863;P49336;Q93074	histone kinase activity	CCNC;CDK8;MED12	P24863;P49336;Q93074	3	0.390432	0.719201	0.204315	0.830348	0.186117	0.0642
971	7585	CDK8 subcomplex (CCNC, CDK8, MED13)	Human	P24863;P49336;Q9UHV7	histone kinase activity	CCNC;CDK8;MED13	P24863;P49336;Q9UHV7	3	0.238089	0.807696	0.239161	0.806998	-0.001071	0.4350
972	7593	AKAP13-MAP2K3-MAP3K20-MAPK14-PKN1 complex	Human	P46734;Q12802;Q16512;Q16539;Q9NYL2	MAPK cascade	MAP2K3;AKAP13;PKN1;MAPK14;MAP3K20	P46734;Q16512;Q16539;Q9NYL2	4	0.179285	0.847972	0.312733	0.761770	-0.133448	0.8312

973 rows × 14 columns

[22]:

# Calculate TPCA dynamic modulation signatures of complexes by sampling and relative distance
MTX_dynamic_relative_random_4t, MTX_dynamic_relative_sample_4t = Slim_TPCA.dynamic_complex_relative_sample(TPCA_DMSO_4t, TPCA_MTX_4t, corum)

[23]:

MTX_dynamic_relative_random_4t

[23]:

	3	4	5	6	7	8	9	10	11	12	...	28	31	34	38	42	66	67	68	85	126
0	0.023128	0.027158	-0.009782	0.024337	0.006653	0.008839	0.034995	0.049368	0.092965	0.042967	...	-0.025028	-0.025496	-0.017671	-0.028789	-0.032067	0.009922	0.012013	0.015667	-0.047833	-0.088375
1	0.059584	-0.025738	0.096637	0.078314	0.052546	0.048502	-0.011637	0.011561	-0.038652	-0.045429	...	-0.021186	0.031760	0.055357	-0.029428	-0.060190	-0.202821	-0.206779	-0.182207	-0.127442	-0.020396
2	0.065637	0.113542	0.075658	0.124848	0.152586	-0.105422	-0.071454	-0.098210	-0.230921	-0.085703	...	-0.106689	-0.301913	-0.314302	-0.184408	-0.147784	0.005742	0.011760	0.000072	0.011463	-0.121327
3	0.047519	0.249740	0.115203	-0.139785	-0.410005	-0.085813	-0.079520	-0.131622	-0.037971	-0.082798	...	-0.193141	-0.072309	-0.070683	-0.131715	-0.119987	-0.040880	-0.096639	-0.090551	-0.146248	-0.023762
4	0.152591	0.111447	-0.187802	-0.058212	-0.025923	-0.142500	-0.004127	-0.028245	0.087967	0.167320	...	-0.073127	-0.172043	-0.135089	0.080447	0.064934	-0.180951	-0.127110	-0.141397	-0.054413	-0.053216
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
9995	-0.613216	-0.055618	-1.914915	0.035726	0.004367	-0.123910	-0.162555	0.154026	0.032416	0.167114	...	-0.040209	0.054413	-0.058004	-0.017720	0.032455	-0.082592	-0.012120	-0.029175	-0.030579	-0.014395
9996	0.029636	0.035179	0.299595	0.036169	-0.057698	0.059426	-0.261549	-0.207192	-0.271436	0.097041	...	-0.064533	0.024960	-0.055048	-0.106153	-0.065022	-0.000955	-0.068949	-0.046759	0.005013	-0.031995
9997	0.102269	-0.229968	0.037984	-0.014785	-0.165130	0.099108	0.048536	-0.254152	-0.162986	-0.314088	...	0.006163	-0.046404	-0.024594	-0.093102	0.071504	-0.081467	-0.004802	-0.018533	-0.116650	-0.042849
9998	-0.239752	-0.041495	0.104274	-0.062770	-0.103611	-0.338762	-0.002922	-0.489829	-0.044895	0.000596	...	0.006169	-0.034268	-0.010196	-0.123801	-0.094515	-0.059106	-0.021109	-0.055275	-0.019417	-0.041803
9999	-0.120136	-0.857046	0.028468	-0.182802	-0.027375	-0.346494	0.121898	-0.164044	0.150409	-0.061691	...	-0.076623	-0.097372	-0.021855	-0.087365	-0.008408	-0.063540	-0.109164	-0.098985	-0.071881	-0.136919

10000 rows × 32 columns

[24]:

MTX_dynamic_relative_sample_4t

[24]:

	ComplexID	ComplexName	Organism	subunits(UniProt IDs)	GO description	subunits(Gene name)	Subunit_Found	No_Subunit_Found	Avg_Dist_1	Avg_Dist_Derived_1	Avg_Dist_2	Avg_Dist_Derived_2	Avg_Dist_relative_change	Dynamic_P
0	4	Multisubunit ACTR coactivator complex	Human	Q09472;Q92793;Q92831;Q9Y6Q9	positive regulation of transcription, DNA-temp...	EP300;CREBBP;KAT2B;NCOA3	Q09472;Q92793;Q9Y6Q9	3	0.155208	0.865645	0.309147	0.763856	-0.991822	0.9630
1	10	Condensin I complex	Human	O95347;Q15003;Q15021;Q9BPX3;Q9NTJ3	M phase;mitotic nuclear division;chromosome co...	SMC2;NCAPH;NCAPD2;NCAPG;SMC4	O95347;Q15003;Q15021;Q9BPX3;Q9NTJ3	5	0.069342	0.935154	0.082957	0.923397	-0.196348	0.7489
2	15	NCOR complex	Human	O15379;O60907;O75376;Q13227;Q92828;Q9BZK7	DNA topological change;negative regulation of ...	HDAC3;TBL1X;NCOR1;GPS2;CORO2A;TBL1XR1	O15379;O60907;O75376;Q92828;Q9BZK7	5	0.199575	0.833629	0.208486	0.827482	-0.044649	0.4917
3	23	BLOC-1 (biogenesis of lysosome-related organel...	Human	O95295;P78537;Q6QNY0;Q6QNY1;Q8TDH9;Q96EV8;Q9NU...	None	SNAPIN;BLOC1S1;BLOC1S3;BLOC1S2;BLOC1S5;DTNBP1;...	O95295;P78537;Q6QNY0;Q6QNY1;Q8TDH9;Q9NUP1	6	0.161005	0.861323	0.207986	0.827824	-0.291800	0.8696
4	27	Arp2/3 protein complex	Human	O15143;O15144;O15145;O15511;P59998;P61158;P61160	None	ARPC1B;ARPC2;ARPC3;ARPC5;ARPC4;ACTR3;ACTR2	O15143;O15144;O15145;O15511;P61158;P61160	6	0.104131	0.905690	0.137539	0.879091	-0.320834	0.8911
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
968	7582	ESR2-TRAP/Mediator coactivator complex	Human	O43513;O60244;O75448;O75586;P24863;P49336;Q094...	mediator complex;mRNA transcription;nucleus;re...	MED7;MED14;MED24;MED6;CCNC;CDK8;EP300;MED21;ME...	O43513;O60244;P24863;P49336;Q09472;Q13503;Q156...	14	0.336775	0.748069	0.236984	0.808418	0.296313	0.0011
969	7583	CDK8 subcomplex (CCNC, CDK8, MED12, MED13)	Human	P24863;P49336;Q93074;Q9UHV7	histone kinase activity	CCNC;CDK8;MED12;MED13	P24863;P49336;Q93074;Q9UHV7	4	0.331881	0.750818	0.230481	0.812690	0.305531	0.0544
970	7584	CDK8 subcomplex (CCNC, CDK8, MED12)	Human	P24863;P49336;Q93074	histone kinase activity	CCNC;CDK8;MED12	P24863;P49336;Q93074	3	0.390432	0.719201	0.204315	0.830348	0.476695	0.0279
971	7585	CDK8 subcomplex (CCNC, CDK8, MED13)	Human	P24863;P49336;Q9UHV7	histone kinase activity	CCNC;CDK8;MED13	P24863;P49336;Q9UHV7	3	0.238089	0.807696	0.239161	0.806998	-0.004500	0.4375
972	7593	AKAP13-MAP2K3-MAP3K20-MAPK14-PKN1 complex	Human	P46734;Q12802;Q16512;Q16539;Q9NYL2	MAPK cascade	MAP2K3;AKAP13;PKN1;MAPK14;MAP3K20	P46734;Q16512;Q16539;Q9NYL2	4	0.179285	0.847972	0.312733	0.761770	-0.744333	0.9666

973 rows × 14 columns

[33]:

# Calculate TPCA dynamic modulation signatures of complexes by Beta distribution fitting and absolute distance
MTX_dynamic_absolute_beta_4t = Slim_TPCA.dynamic_complex_absolute_beta(TPCA_DMSO_4t, TPCA_MTX_4t, corum)

[34]:

MTX_dynamic_absolute_beta_4t

[34]:

	ComplexID	ComplexName	Organism	subunits(UniProt IDs)	GO description	subunits(Gene name)	Subunit_Found	No_Subunit_Found	Avg_Dist_1	Avg_Dist_Derived_1	Avg_Dist_2	Avg_Dist_Derived_2	Avg_Dist_change	Dynamic_P
0	4	Multisubunit ACTR coactivator complex	Human	Q09472;Q92793;Q92831;Q9Y6Q9	positive regulation of transcription, DNA-temp...	EP300;CREBBP;KAT2B;NCOA3	Q09472;Q92793;Q9Y6Q9	3	0.155208	0.865645	0.309147	0.763856	-0.153939	0.851209
1	10	Condensin I complex	Human	O95347;Q15003;Q15021;Q9BPX3;Q9NTJ3	M phase;mitotic nuclear division;chromosome co...	SMC2;NCAPH;NCAPD2;NCAPG;SMC4	O95347;Q15003;Q15021;Q9BPX3;Q9NTJ3	5	0.069342	0.935154	0.082957	0.923397	-0.013615	0.456708
2	15	NCOR complex	Human	O15379;O60907;O75376;Q13227;Q92828;Q9BZK7	DNA topological change;negative regulation of ...	HDAC3;TBL1X;NCOR1;GPS2;CORO2A;TBL1XR1	O15379;O60907;O75376;Q92828;Q9BZK7	5	0.199575	0.833629	0.208486	0.827482	-0.008911	0.436275
3	23	BLOC-1 (biogenesis of lysosome-related organel...	Human	O95295;P78537;Q6QNY0;Q6QNY1;Q8TDH9;Q96EV8;Q9NU...	None	SNAPIN;BLOC1S1;BLOC1S3;BLOC1S2;BLOC1S5;DTNBP1;...	O95295;P78537;Q6QNY0;Q6QNY1;Q8TDH9;Q9NUP1	6	0.161005	0.861323	0.207986	0.827824	-0.046981	0.612971
4	27	Arp2/3 protein complex	Human	O15143;O15144;O15145;O15511;P59998;P61158;P61160	None	ARPC1B;ARPC2;ARPC3;ARPC5;ARPC4;ACTR3;ACTR2	O15143;O15144;O15145;O15511;P61158;P61160	6	0.104131	0.905690	0.137539	0.879091	-0.033409	0.554722
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
968	7582	ESR2-TRAP/Mediator coactivator complex	Human	O43513;O60244;O75448;O75586;P24863;P49336;Q094...	mediator complex;mRNA transcription;nucleus;re...	MED7;MED14;MED24;MED6;CCNC;CDK8;EP300;MED21;ME...	O43513;O60244;P24863;P49336;Q09472;Q13503;Q156...	14	0.336775	0.748069	0.236984	0.808418	0.099791	0.001455
969	7583	CDK8 subcomplex (CCNC, CDK8, MED12, MED13)	Human	P24863;P49336;Q93074;Q9UHV7	histone kinase activity	CCNC;CDK8;MED12;MED13	P24863;P49336;Q93074;Q9UHV7	4	0.331881	0.750818	0.230481	0.812690	0.101400	0.102595
970	7584	CDK8 subcomplex (CCNC, CDK8, MED12)	Human	P24863;P49336;Q93074	histone kinase activity	CCNC;CDK8;MED12	P24863;P49336;Q93074	3	0.390432	0.719201	0.204315	0.830348	0.186117	0.029471
971	7585	CDK8 subcomplex (CCNC, CDK8, MED13)	Human	P24863;P49336;Q9UHV7	histone kinase activity	CCNC;CDK8;MED13	P24863;P49336;Q9UHV7	3	0.238089	0.807696	0.239161	0.806998	-0.001071	0.452023
972	7593	AKAP13-MAP2K3-MAP3K20-MAPK14-PKN1 complex	Human	P46734;Q12802;Q16512;Q16539;Q9NYL2	MAPK cascade	MAP2K3;AKAP13;PKN1;MAPK14;MAP3K20	P46734;Q16512;Q16539;Q9NYL2	4	0.179285	0.847972	0.312733	0.761770	-0.133448	0.840978

973 rows × 14 columns

[35]:

# Calculate TPCA dynamic modulation signatures of complexes by Beta distribution fitting and relative distance
MTX_dynamic_relative_beta_4t = Slim_TPCA.dynamic_complex_relative_beta(TPCA_DMSO_4t, TPCA_MTX_4t, corum)

[36]:

MTX_dynamic_relative_beta_4t

[36]:

	ComplexID	ComplexName	Organism	subunits(UniProt IDs)	GO description	subunits(Gene name)	Subunit_Found	No_Subunit_Found	Avg_Dist_1	Avg_Dist_Derived_1	Avg_Dist_2	Avg_Dist_Derived_2	Avg_Dist_relative_change	Dynamic_P
0	4	Multisubunit ACTR coactivator complex	Human	Q09472;Q92793;Q92831;Q9Y6Q9	positive regulation of transcription, DNA-temp...	EP300;CREBBP;KAT2B;NCOA3	Q09472;Q92793;Q9Y6Q9	3	0.155208	0.865645	0.309147	0.763856	-0.991822	0.993636
1	10	Condensin I complex	Human	O95347;Q15003;Q15021;Q9BPX3;Q9NTJ3	M phase;mitotic nuclear division;chromosome co...	SMC2;NCAPH;NCAPD2;NCAPG;SMC4	O95347;Q15003;Q15021;Q9BPX3;Q9NTJ3	5	0.069342	0.935154	0.082957	0.923397	-0.196348	0.765366
2	15	NCOR complex	Human	O15379;O60907;O75376;Q13227;Q92828;Q9BZK7	DNA topological change;negative regulation of ...	HDAC3;TBL1X;NCOR1;GPS2;CORO2A;TBL1XR1	O15379;O60907;O75376;Q92828;Q9BZK7	5	0.199575	0.833629	0.208486	0.827482	-0.044649	0.497697
3	23	BLOC-1 (biogenesis of lysosome-related organel...	Human	O95295;P78537;Q6QNY0;Q6QNY1;Q8TDH9;Q96EV8;Q9NU...	None	SNAPIN;BLOC1S1;BLOC1S3;BLOC1S2;BLOC1S5;DTNBP1;...	O95295;P78537;Q6QNY0;Q6QNY1;Q8TDH9;Q9NUP1	6	0.161005	0.861323	0.207986	0.827824	-0.291800	0.883416
4	27	Arp2/3 protein complex	Human	O15143;O15144;O15145;O15511;P59998;P61158;P61160	None	ARPC1B;ARPC2;ARPC3;ARPC5;ARPC4;ACTR3;ACTR2	O15143;O15144;O15145;O15511;P61158;P61160	6	0.104131	0.905690	0.137539	0.879091	-0.320834	0.905778
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
968	7582	ESR2-TRAP/Mediator coactivator complex	Human	O43513;O60244;O75448;O75586;P24863;P49336;Q094...	mediator complex;mRNA transcription;nucleus;re...	MED7;MED14;MED24;MED6;CCNC;CDK8;EP300;MED21;ME...	O43513;O60244;P24863;P49336;Q09472;Q13503;Q156...	14	0.336775	0.748069	0.236984	0.808418	0.296313	0.000000
969	7583	CDK8 subcomplex (CCNC, CDK8, MED12, MED13)	Human	P24863;P49336;Q93074;Q9UHV7	histone kinase activity	CCNC;CDK8;MED12;MED13	P24863;P49336;Q93074;Q9UHV7	4	0.331881	0.750818	0.230481	0.812690	0.305531	0.016065
970	7584	CDK8 subcomplex (CCNC, CDK8, MED12)	Human	P24863;P49336;Q93074	histone kinase activity	CCNC;CDK8;MED12	P24863;P49336;Q93074	3	0.390432	0.719201	0.204315	0.830348	0.476695	0.001570
971	7585	CDK8 subcomplex (CCNC, CDK8, MED13)	Human	P24863;P49336;Q9UHV7	histone kinase activity	CCNC;CDK8;MED13	P24863;P49336;Q9UHV7	3	0.238089	0.807696	0.239161	0.806998	-0.004500	0.482795
972	7593	AKAP13-MAP2K3-MAP3K20-MAPK14-PKN1 complex	Human	P46734;Q12802;Q16512;Q16539;Q9NYL2	MAPK cascade	MAP2K3;AKAP13;PKN1;MAPK14;MAP3K20	P46734;Q16512;Q16539;Q9NYL2	4	0.179285	0.847972	0.312733	0.761770	-0.744333	0.987882

973 rows × 14 columns

[37]:

dynamic_result = pd.DataFrame({'Absolute_Sample':MTX_dynamic_absolute_sample_4t['Dynamic_P'], 'Relative_Sample':MTX_dynamic_relative_sample_4t['Dynamic_P'],
                               'Absolute_Beta':MTX_dynamic_absolute_beta_4t['Dynamic_P'], 'Relative_Beta':MTX_dynamic_relative_beta_4t['Dynamic_P']})

[38]:

dynamic_result

[38]:

	Absolute_Sample	Relative_Sample	Absolute_Beta	Relative_Beta
0	0.8295	0.9630	0.851209	0.993636
1	0.4574	0.7489	0.456708	0.765366
2	0.4375	0.4917	0.436275	0.497697
3	0.6077	0.8696	0.612971	0.883416
4	0.5433	0.8911	0.554722	0.905778
...	...	...	...	...
968	0.0196	0.0011	0.001455	0.000000
969	0.1235	0.0544	0.102595	0.016065
970	0.0642	0.0279	0.029471	0.001570
971	0.4350	0.4375	0.452023	0.482795
972	0.8312	0.9666	0.840978	0.987882

973 rows × 4 columns

[39]:

sns.pairplot(data=dynamic_result)

[39]:

<seaborn.axisgrid.PairGrid at 0x2ba7f8a1670>

../_images/notebooks_Slim_TPCA_test_28_1.png

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