Characterization of Core Components

This notebook demonstrates the tutorial workflow for MultiModulon analysis.

[1]:

# Import required libraries
from multimodulon import MultiModulon
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt

# Set display options
pd.set_option('display.max_columns', None)
pd.set_option('display.max_rows', 50)

Step 1: Load MultiModulon object

Load the saved MultiModulon object from Tutorial_1_Create_multiModulon_object.ipynb

[2]:

multiModulon = MultiModulon.load_json_multimodulon("./multiModulon_E_coli_comparison_demo.json.gz")

[3]:

multiModulon.species_palette

[3]:

{'BL21': '#B24C4C', 'MG1655': '#4C6AB2', 'W3110': '#88B24C'}

Step 2: Visualize the core components (Available Functions)

Visualize the core and unique components by view_iModulon_weights and view_core_iModulon_weights

[4]:

multiModulon.view_iModulon_weights(
    species="MG1655",
    component="Core_1",
    fig_size=(8, 5),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf",
    show_COG=True,
    show_gene_names=True
)

../_images/examples_characterization_core_components_6_0.png

[5]:

multiModulon.view_iModulon_genes(
    species="MG1655",
    component="Core_1"
)

[5]:

	M_weight	Preferred_name	gene_name	accession	start	end	strand	old_locus_tag	gene_product	ncbi_protein	seed_ortholog	evalue	score	eggNOG_OGs	max_annot_lvl	COG_category	Description	GOs	EC	KEGG_ko	KEGG_Pathway	KEGG_Module	KEGG_Reaction	KEGG_rclass	BRITE	KEGG_TC	CAZy	BiGG_Reaction	PFAMs
b0583	0.128547	entD	entD	U00096.3	609459	610079	-	NaN	phosphopantetheinyl transferase EntD	AAC73684.2	316407.85674704	1.240000e-150	423.0	COG2977@1\|root,COG2977@2\|Bacteria,1MZK2@1224\|P...	2\|Bacteria	H	Involved in the biosynthesis of the siderophor...	GO:0003674,GO:0003824,GO:0005575,GO:0005622,GO...	6.3.2.14	ko:K02362	ko01053,ko01110,ko01130,map01053,map01110,map0...	-	R07644	RC00162,RC03046	ko00000,ko00001,ko01000	-	-	iAPECO1_1312.APECO1_1466,iECO111_1330.ECO111_0...	ACPS
b0584	0.170337	fepA	fepA	U00096.3	610254	612494	-	NaN	ferric enterobactin outer membrane transporter	AAC73685.1	316407.4062212	0.000000e+00	1519.0	COG1629@1\|root,COG4771@2\|Bacteria,1MUC1@1224\|P...	2\|Bacteria	P	This protein is involved in the initial step o...	GO:0000041,GO:0003674,GO:0005215,GO:0005488,GO...	-	ko:K16089,ko:K19611	ko02020,map02020	-	-	-	ko00000,ko00001,ko02000	1.B.14.1,1.B.14.1.22,1.B.14.1.3,1.B.14.1.5,1.B...	-	iECABU_c1320.ECABU_c06330,iECO103_1326.ECO103_...	Plug,TonB_dep_Rec
b0585	0.163971	fes	fes	U00096.3	612737	613939	+	NaN	ferric enterobactin esterase	AAC73686.2	511145.b0585	1.160000e-313	851.0	COG2382@1\|root,COG2382@2\|Bacteria,1MXJN@1224\|P...	2\|Bacteria	P	esterase	GO:0003674,GO:0003824,GO:0005575,GO:0005622,GO...	-	ko:K07214	-	-	-	-	ko00000	-	-	iECNA114_1301.ECNA114_0527,iSbBS512_1146.SbBS5...	DUF3327,Esterase
b4511	0.163414	ybdZ	ybdZ	U00096.3	613942	614160	+	NaN	enterobactin biosynthesis protein YbdZ	ABD18641.1	316407.85674706	5.410000e-51	160.0	COG3251@1\|root,COG3251@2\|Bacteria,1N87J@1224\|P...	2\|Bacteria	S	Involved in the biosynthesis of the siderophor...	GO:0005575,GO:0005622,GO:0005623,GO:0005737,GO...	-	ko:K05375,ko:K07214	ko00261,ko01130,map00261,map01130	M00736	R10880	RC00064,RC00141,RC03296,RC03297,RC03298	ko00000,ko00001,ko00002	-	-	-	MbtH
b0586	0.151540	entF	entF	U00096.3	614157	618038	+	NaN	apo-serine activating enzyme	AAC73687.1	316407.85674707	0.000000e+00	2562.0	COG1020@1\|root,COG3319@1\|root,COG1020@2\|Bacter...	2\|Bacteria	Q	Activates the carboxylate group of L-serine vi...	GO:0003674,GO:0003824,GO:0005488,GO:0005575,GO...	6.3.2.14	ko:K02364	ko01053,ko01110,ko01130,map01053,map01110,map0...	-	R07644	RC00162,RC03046	ko00000,ko00001,ko01000,ko01008	-	-	iECO111_1330.ECO111_0616,iECO26_1355.ECO26_066...	AMP-binding,AMP-binding_C,Condensation,PP-bind...
b0588	0.094940	fepC	fepC	U00096.3	619384	620199	-	NaN	ferric enterobactin ABC transporter ATP bindin...	AAC73689.1	316407.85674709	7.490000e-195	540.0	COG1120@1\|root,COG1120@2\|Bacteria,1MUNG@1224\|P...	2\|Bacteria	P	Probably responsible for energy coupling to th...	GO:0000041,GO:0000166,GO:0003674,GO:0005215,GO...	3.6.3.34	ko:K02013	ko02010,map02010	M00240	-	-	ko00000,ko00001,ko00002,ko01000,ko02000	3.A.1.14	-	iAF1260.b0588,iB21_1397.B21_00544,iBWG_1329.BW...	ABC_tran
b0589	0.081723	fepG	fepG	U00096.3	620196	621188	-	NaN	ferric enterobactin ABC transporter membrane s...	AAC73690.1	316407.85674710	3.590000e-218	604.0	COG4779@1\|root,COG4779@2\|Bacteria,1NXD0@1224\|P...	2\|Bacteria	P	Belongs to the binding-protein-dependent trans...	GO:0000041,GO:0003674,GO:0005215,GO:0005575,GO...	-	ko:K02015	ko02010,map02010	M00240	-	-	ko00000,ko00001,ko00002,ko02000	3.A.1.14	-	iAPECO1_1312.APECO1_1460,iEC55989_1330.EC55989...	FecCD
b0590	0.093200	fepD	fepD	U00096.3	621185	622189	-	NaN	ferric enterobactin ABC transporter membrane s...	AAC73691.1	511145.b0590	5.450000e-215	596.0	COG0609@1\|root,COG0609@2\|Bacteria,1MYYG@1224\|P...	2\|Bacteria	P	Belongs to the binding-protein-dependent trans...	GO:0000041,GO:0003674,GO:0005215,GO:0005575,GO...	-	ko:K02015	ko02010,map02010	M00240	-	-	ko00000,ko00001,ko00002,ko02000	3.A.1.14	-	iB21_1397.B21_04117,iEC042_1314.EC042_4777,iEC...	FecCD
b0591	0.096287	entS	entS	U00096.3	622300	623550	+	NaN	enterobactin exporter EntS	AAC73692.1	316407.85674712	9.810000e-280	767.0	COG0477@1\|root,COG0477@2\|Bacteria,1MXZ3@1224\|P...	2\|Bacteria	EGP	Exports the siderophore enterobactin out of th...	GO:0005575,GO:0005623,GO:0005886,GO:0006810,GO...	-	ko:K08225	-	-	-	-	ko00000,ko02000	2.A.1.38	-	iECABU_c1320.ECABU_c06410,iSBO_1134.SBO_0452	MFS_1,MFS_3
b0592	0.086034	fepB	fepB	U00096.3	623554	624510	-	NaN	ferric enterobactin ABC transporter periplasmi...	AAC73693.1	316407.85674713	2.450000e-219	606.0	COG4592@1\|root,COG4592@2\|Bacteria,1NPCN@1224\|P...	2\|Bacteria	P	part of the binding-protein- dependent transpo...	GO:0000041,GO:0005575,GO:0005623,GO:0006810,GO...	-	ko:K02016	ko02010,map02010	M00240	-	-	ko00000,ko00001,ko00002,ko02000	3.A.1.14	-	iECNA114_1301.ECNA114_0535	Peripla_BP_2
b0593	0.179651	entC	entC	U00096.3	624885	626060	+	NaN	isochorismate synthase EntC	AAC73694.1	316407.85674714	6.640000e-279	763.0	COG1169@1\|root,COG1169@2\|Bacteria,1MVB7@1224\|P...	2\|Bacteria	HQ	Involved in the biosynthesis of the siderophor...	GO:0000162,GO:0000287,GO:0003674,GO:0003824,GO...	5.4.4.2	ko:K01851,ko:K02361,ko:K02552	ko00130,ko01053,ko01100,ko01110,ko01130,map001...	M00116	R01717	RC00588	ko00000,ko00001,ko00002,ko01000	-	-	iEC55989_1330.EC55989_0585,iECABU_c1320.ECABU_...	Chorismate_bind
b0594	0.173730	entE	entE	U00096.3	626070	627680	+	NaN	2%2C3-dihydroxybenzoate-AMP ligase	AAC73695.1	316407.85674715	0.000000e+00	1068.0	COG1021@1\|root,COG1021@2\|Bacteria,1NSN8@1224\|P...	2\|Bacteria	Q	Involved in the biosynthesis of the siderophor...	GO:0003674,GO:0003824,GO:0005575,GO:0005622,GO...	2.7.7.58,6.3.2.14	ko:K02363,ko:K12238	ko01053,ko01110,ko01130,map01053,map01110,map0...	-	R07644	RC00162,RC03046	ko00000,ko00001,ko01000,ko01008	-	-	iSF_1195.SF0508,iSSON_1240.SSON_0545,iS_1188.S...	AMP-binding,AMP-binding_C
b0595	0.157571	entB	entB	U00096.3	627694	628551	+	NaN	enterobactin synthase component B	AAC73696.1	316407.85674716	3.090000e-210	580.0	COG1535@1\|root,COG3433@1\|root,COG1535@2\|Bacter...	2\|Bacteria	Q	Involved in the biosynthesis of the siderophor...	GO:0000287,GO:0003674,GO:0003824,GO:0004463,GO...	3.3.2.1,6.3.2.14	ko:K01252	ko01053,ko01110,ko01130,map01053,map01110,map0...	-	R03037,R07644	RC00162,RC00350,RC02148,RC03046	ko00000,ko00001,ko01000,ko01008	-	-	iSFV_1184.SFV_0543	Isochorismatase,PP-binding
b0596	0.146970	entA	entA	U00096.3	628551	629297	+	NaN	2%2C3-dihydro-2%2C3-dihydroxybenzoate dehydrog...	AAC73697.1	316407.85674717	1.270000e-170	477.0	COG1028@1\|root,COG1028@2\|Bacteria,1MUD2@1224\|P...	2\|Bacteria	IQ	Involved in the biosynthesis of the siderophor...	GO:0003674,GO:0003824,GO:0005488,GO:0005515,GO...	1.3.1.28	ko:K00216	ko01053,ko01110,ko01130,map01053,map01110,map0...	-	R01505	RC00534	ko00000,ko00001,ko01000	-	-	iECNA114_1301.ECNA114_0539,iECSF_1327.ECSF_053...	adh_short_C2
b0597	0.146853	entH	entH	U00096.3	629300	629713	+	NaN	proofreading thioesterase in enterobactin bios...	AAC73698.1	316407.85674718	5.720000e-99	286.0	COG2050@1\|root,COG2050@2\|Bacteria,1MYE0@1224\|P...	2\|Bacteria	Q	Required for optimal enterobactin synthesis. A...	GO:0003674,GO:0003824,GO:0005488,GO:0005515,GO...	3.1.2.28	ko:K02614,ko:K19222	ko00130,ko00360,ko01100,ko01110,map00130,map00...	M00116	R07262,R09840	RC00004,RC00014,RC00174	ko00000,ko00001,ko00002,ko01000	-	-	-	4HBT,Hydrolase_3
b0683	-0.106083	fur	fur	U00096.3	710200	710646	-	NaN	DNA-binding transcriptional dual regulator Fur	AAC73777.1	316407.1651290	2.650000e-107	308.0	COG0735@1\|root,COG0735@2\|Bacteria,1RDWJ@1224\|P...	2\|Bacteria	K	Acts as a global negative controlling element,...	GO:0000976,GO:0001067,GO:0001130,GO:0001216,GO...	-	ko:K03711,ko:K09823	ko02024,map02024	-	-	-	ko00000,ko00001,ko03000	-	-	-	FUR
b0803	0.076955	ybiI	ybiI	U00096.3	838190	838456	-	NaN	zinc finger domain-containing protein YbiI	AAC73890.1	316407.4062364	4.120000e-60	184.0	COG1734@1\|root,COG1734@2\|Bacteria,1MZIB@1224\|P...	2\|Bacteria	T	zinc ion binding	-	-	ko:K06204	ko02026,map02026	-	-	-	ko00000,ko00001,ko03000,ko03009,ko03021	-	-	-	zf-dskA_traR
b0804	0.135791	ybiX	ybiX	U00096.3	838530	839207	-	NaN	PKHD-type hydroxylase YbiX	AAC73891.2	316407.85674765	1.830000e-163	457.0	COG3128@1\|root,COG3128@2\|Bacteria,1MUI7@1224\|P...	2\|Bacteria	S	PKHD-type hydroxylase YbiX	GO:0006873,GO:0006875,GO:0006879,GO:0006950,GO...	-	ko:K07336	-	-	-	-	ko00000,ko01000	-	-	-	2OG-FeII_Oxy_3
b0805	0.169354	fiu	fiu	U00096.3	839249	841531	-	NaN	Fe catecholate outer membrane transporter Fiu	AAC73892.1	316407.4062366	0.000000e+00	1514.0	COG4774@1\|root,COG4774@2\|Bacteria,1MV0X@1224\|P...	2\|Bacteria	P	Involved in the active transport across the ou...	GO:0005575,GO:0005623,GO:0006810,GO:0008150,GO...	-	ko:K16090	-	-	-	-	ko00000,ko02000	1.B.14.1.11	-	iLF82_1304.LF82_0668,iNRG857_1313.NRG857_03600...	Plug,TonB_dep_Rec
b1102	0.130277	fhuE	fhuE	U00096.3	1159362	1161551	-	NaN	ferric coprogen/ferric rhodotorulic acid outer...	AAC74186.1	316407.1651542	0.000000e+00	1473.0	COG4773@1\|root,COG4773@2\|Bacteria,1MW5E@1224\|P...	2\|Bacteria	P	Outer-membrane receptor for Fe(III)-coprogen, ...	GO:0005575,GO:0005623,GO:0009279,GO:0016020,GO...	-	ko:K16088	-	-	-	-	ko00000,ko02000	1.B.14.1.10,1.B.14.1.3,1.B.14.1.8	-	iSDY_1059.SDY_2048	Plug,STN,TonB_dep_Rec
b1452	0.101367	yncE	yncE	U00096.3	1523307	1524368	+	NaN	PQQ-like domain-containing protein YncE	AAC74534.1	316407.85674972	2.170000e-226	627.0	COG3391@1\|root,COG3391@2\|Bacteria,1PDS2@1224\|P...	2\|Bacteria	S	DNA binding	GO:0003674,GO:0003676,GO:0003677,GO:0005488,GO...	-	-	-	-	-	-	-	-	-	-	PQQ_2
b1656	-0.107184	sodB	sodB	U00096.3	1735378	1735959	+	NaN	superoxide dismutase (Fe)	AAC74728.1	316407.1742729	8.250000e-142	399.0	COG0605@1\|root,COG0605@2\|Bacteria,1MVW2@1224\|P...	2\|Bacteria	C	radicals which are normally produced within th...	GO:0000302,GO:0000303,GO:0000305,GO:0003674,GO...	1.15.1.1,3.1.11.6	ko:K03601,ko:K04564	ko03430,ko04013,ko04068,ko04146,ko04211,ko0421...	-	-	-	ko00000,ko00001,ko01000,ko03400	-	-	iAF1260.b1656,iAPECO1_1312.APECO1_736,iB21_139...	Sod_Fe_C,Sod_Fe_N
b1705	0.102622	NaN	ydiE	U00096.3	1789613	1789804	+	NaN	PF10636 family protein YdiE	AAC74775.1	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
b2155	0.168631	cirA	cirA	U00096.3	2244778	2246769	-	NaN	Fe-catecholate outer membrane transporter CirA	AAC75216.1	511145.b2155	0.000000e+00	1360.0	COG1629@1\|root,COG4771@2\|Bacteria,1MUC1@1224\|P...	2\|Bacteria	P	Colicin I receptor	GO:0000041,GO:0003674,GO:0005215,GO:0005488,GO...	-	ko:K16089,ko:K19611	ko02020,map02020	-	-	-	ko00000,ko00001,ko02000	1.B.14.1,1.B.14.1.22,1.B.14.1.3,1.B.14.1.5,1.B...	-	iECO103_1326.ECO103_2630,iSDY_1059.SDY_0512	Plug,TonB_dep_Rec
b2673	0.116194	nrdH	nrdH	U00096.3	2800723	2800968	+	NaN	glutaredoxin-like protein NrdH	AAC75720.1	316407.85675518	1.570000e-54	170.0	COG0695@1\|root,COG0695@2\|Bacteria,1N7YD@1224\|P...	2\|Bacteria	O	Electron transport system for the ribonucleoti...	GO:0003674,GO:0003824,GO:0006091,GO:0008150,GO...	-	ko:K06191	-	-	-	-	ko00000	-	-	-	Glutaredoxin
b2674	0.110272	nrdI	nrdI	U00096.3	2800965	2801375	+	NaN	dimanganese-tyrosyl radical cofactor maintenan...	AAC75721.1	316407.85675519	5.970000e-96	279.0	COG1780@1\|root,COG1780@2\|Bacteria,1RGYF@1224\|P...	2\|Bacteria	F	Probably involved in ribonucleotide reductase ...	GO:0000166,GO:0003674,GO:0005488,GO:0006464,GO...	-	ko:K03647	-	-	-	-	ko00000	-	-	-	Flavodoxin_NdrI
b2675	0.108159	nrdE	nrdE	U00096.3	2801348	2803492	+	NaN	ribonucleoside-diphosphate reductase 2 subunit...	AAC75722.1	316407.85675520	0.000000e+00	1424.0	COG0209@1\|root,COG0209@2\|Bacteria,1MUJ8@1224\|P...	2\|Bacteria	F	Provides the precursors necessary for DNA synt...	GO:0000166,GO:0003674,GO:0003824,GO:0004748,GO...	1.17.4.1	ko:K00525	ko00230,ko00240,ko01100,map00230,map00240,map0...	M00053	R02017,R02018,R02019,R02024	RC00613	ko00000,ko00001,ko00002,ko01000,ko03400	-	-	iAPECO1_1312.APECO1_3846,iSDY_1059.SDY_2428,iY...	RNR_N,Ribonuc_red_lgC,Ribonuc_red_lgN
b2676	0.100969	nrdF	nrdF	U00096.3	2803502	2804461	+	NaN	ribonucleoside-diphosphate reductase 2 subunit...	AAC75723.1	316407.1800064	3.560000e-233	641.0	COG0208@1\|root,COG0208@2\|Bacteria,1MWUS@1224\|P...	2\|Bacteria	F	Provides the precursors necessary for DNA synt...	GO:0003674,GO:0005488,GO:0005506,GO:0005515,GO...	1.17.4.1	ko:K00526	ko00230,ko00240,ko01100,map00230,map00240,map0...	M00053	R02017,R02018,R02019,R02024	RC00613	ko00000,ko00001,ko00002,ko01000,ko03400	-	-	iAPECO1_1312.APECO1_4325,iECNA114_1301.ECNA114...	Ribonuc_red_sm
b4291	0.081580	fecA	fecA	U00096.3	4514353	4516677	-	NaN	ferric citrate outer membrane transporter	AAC77247.1	316407.85677032	0.000000e+00	1573.0	COG4772@1\|root,COG4772@2\|Bacteria,1MWDG@1224\|P...	2\|Bacteria	P	receptor	GO:0000041,GO:0003674,GO:0005215,GO:0005381,GO...	-	ko:K16091	-	-	-	-	ko00000,ko02000	1.B.14.1.14	-	iEC042_1314.EC042_4780	Plug,STN,TonB_dep_Rec
b4292	0.098783	fecR	fecR	U00096.3	4516764	4517717	-	NaN	ferric citrate regulator FecR	AAC77248.1	316407.85677033	2.210000e-226	624.0	COG3712@1\|root,COG3712@2\|Bacteria,1N28G@1224\|P...	2\|Bacteria	PT	Fe2 -dicitrate sensor, membrane component	GO:0005575,GO:0005623,GO:0042597,GO:0044464	-	ko:K07165	-	-	-	-	ko00000	-	-	-	DUF4880,DUF4974,FecR
b4293	0.096825	fecI	fecI	U00096.3	4517714	4518235	-	NaN	RNA polymerase sigma factor FecI	AAC77249.1	316407.85677034	4.510000e-118	338.0	COG1595@1\|root,COG1595@2\|Bacteria,1RHRW@1224\|P...	2\|Bacteria	K	Belongs to the sigma-70 factor family. ECF sub...	-	-	ko:K03088	-	-	-	-	ko00000,ko03021	-	-	-	Sigma70_r2,Sigma70_r4_2
b4367	0.098091	fhuF	fhuF	U00096.3	4604875	4605663	-	NaN	ferric-siderophore reductase FhuF	AAC77323.1	316407.85677107	5.510000e-197	545.0	COG4114@1\|root,COG4114@2\|Bacteria,1MWSR@1224\|P...	2\|Bacteria	S	ferric iron reductase	GO:0003674,GO:0005488,GO:0005575,GO:0005622,GO...	-	ko:K13255	-	-	-	-	ko00000	-	-	iE2348C_1286.E2348C_4666,iECH74115_1262.ECH741...	FhuF,FhuF_C
b4567	0.192312	yjjZ	yjjZ	U00096.3	4605804	4606040	+	NaN	DUF1435 domain-containing protein YjjZ	ABD18719.1	511145.b4567	6.590000e-48	153.0	2CF73@1\|root,32RSY@2\|Bacteria,1N033@1224\|Prote...	2\|Bacteria	S	Protein of unknown function (DUF1435)	-	-	-	-	-	-	-	-	-	-	-	DUF1435

[6]:

multiModulon['MG1655'].presence_matrix

[6]:

	Core_1	Core_2	Core_3	Core_4	Core_5	Core_6	Core_7	Core_8	Core_9	Core_10	Core_11	Core_12	Core_13	Core_14	Core_15	Core_16	Core_17	Core_18	Core_19	Core_20	Core_21	Core_22	Core_23	Unique_1	Unique_2	Unique_3	Unique_4	Unique_5	Unique_6	Unique_7	Unique_8	Unique_9	Unique_10	Unique_11
b0001	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
b0002	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
b0003	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
b0004	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
b0005	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
b4400	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
b4401	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
b4402	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0
b4824	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0
b4403	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

4305 rows × 34 columns

[7]:

multiModulon['MG1655'].sample_sheet

[7]:

	Run	ReleaseDate	LoadDate	spots	bases	spots_with_mates	avgLength	size_MB	AssemblyName	download_path	LibraryName	LibraryStrategy	LibrarySelection	LibrarySource	LibraryLayout	InsertSize	InsertDev	Platform	Model	SRAStudy	BioProject	Study_Pubmed_id	ProjectID	Sample	BioSample	SampleType	TaxID	ScientificName	SampleName	g1k_pop_code	source	g1k_analysis_group	Subject_ID	Sex	Disease	Tumor	Affection_Status	Analyte_Type	Histological_Type	Body_Site	CenterName	Submission	dbgap_study_accession	Consent	RunHash	ReadHash	R1	R2	Strain	biosample_genotype	reference_sequence	project	condition	reference_condition	strain_description	base_media	carbon_source	nitrogen_source	aerobicity	supplement	temperature	pH	growth_phase	OD	additional_notes	knockout	biological_replicate	technical replicates	sampleID	culture_type	Swift
SRX8684872	SRR12170059	2022-09-25 23:05:26	2022-09-25 23:01:55	5516734.0	1.641596e+09	5516734.0	297.0	407.0	NC_000913	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/s...	MG1655_F133_MID_1	RNA-Seq	cDNA	TRANSCRIPTOMIC	PAIRED	0.0	0.0	ILLUMINA	Illumina HiSeq 4000	SRP270849	PRJNA644668	NaN	644668.0	SRS6963815	SAMN15470650	simple	511145.0	Escherichia coli str. K-12 substr. MG1655	MG1655_F133_MID	NaN	NaN	NaN	NaN	NaN	NaN	no	NaN	NaN	NaN	NaN	UNIVERSITY OF CALIFORNIA- SAN DIEGO	SRA1096109	NaN	public	A2811478FA75C0725C9C8ABAC24F6CE5	2D157C081C3A732986637377ACA14205	s3://modulome/multi_ecoli/MG1655/raw_rna/SRX86...	s3://modulome/multi_ecoli/MG1655/raw_rna/SRX86...	MG1655	F133_MID	U00096.3	multi_ALE	F133_MID	WT	F133_MID	M9	glucose	NH4Cl	Aerobic	NaN	37	NaN	NaN	NaN	NaN	WT	1	1	NaN	Batch	0
SRX8684873	SRR12170058	2022-09-25 23:05:26	2022-09-25 23:02:21	6904986.0	2.054524e+09	6904986.0	297.0	510.0	NC_000913	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/s...	MG1655_F133_MID_2	RNA-Seq	cDNA	TRANSCRIPTOMIC	PAIRED	0.0	0.0	ILLUMINA	Illumina HiSeq 4000	SRP270849	PRJNA644668	NaN	644668.0	SRS6963815	SAMN15470650	simple	511145.0	Escherichia coli str. K-12 substr. MG1655	MG1655_F133_MID	NaN	NaN	NaN	NaN	NaN	NaN	no	NaN	NaN	NaN	NaN	UNIVERSITY OF CALIFORNIA- SAN DIEGO	SRA1096109	NaN	public	6F1624C35020E2950400EAA843FBE4A1	B224CA3555520A964DE7D3934CAD3D73	s3://modulome/multi_ecoli/MG1655/raw_rna/SRX86...	s3://modulome/multi_ecoli/MG1655/raw_rna/SRX86...	MG1655	F133_MID	U00096.3	multi_ALE	F133_MID	WT	F133_MID	M9	glucose	NH4Cl	Aerobic	NaN	37	NaN	NaN	NaN	NaN	WT	2	1	NaN	Batch	0
SRX8684874	SRR12170057	2022-09-25 23:07:04	2022-09-25 23:04:27	16293212.0	2.205682e+09	14341258.0	135.0	426.0	GCA_000005845.2	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/s...	MG1655_F001_MID_1	RNA-Seq	cDNA	TRANSCRIPTOMIC	PAIRED	0.0	0.0	ILLUMINA	Illumina HiSeq 4000	SRP270849	PRJNA644668	NaN	644668.0	SRS6963816	SAMN15470648	simple	511145.0	Escherichia coli str. K-12 substr. MG1655	MG1655_F001_MID	NaN	NaN	NaN	NaN	NaN	NaN	no	NaN	NaN	NaN	NaN	UNIVERSITY OF CALIFORNIA- SAN DIEGO	SRA1096109	NaN	public	CBDA566CCB1AC327D08A7D29E5D0E5B9	EBA2468F6BD5786912663646206B0606	s3://modulome/multi_ecoli/MG1655/raw_rna/SRX86...	s3://modulome/multi_ecoli/MG1655/raw_rna/SRX86...	MG1655	F001_MID	U00096.3	multi_ALE	F001_MID	WT	F001_MID	M9	glucose	NH4Cl	Aerobic	NaN	37	NaN	NaN	NaN	NaN	WT	1	1	NaN	Batch	0
SRX8684875	SRR12170056	2022-09-25 23:05:26	2022-09-25 23:01:48	7318390.0	9.946296e+08	6495910.0	135.0	185.0	GCA_000005845.2	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/s...	MG1655_F001_MID_2	RNA-Seq	cDNA	TRANSCRIPTOMIC	PAIRED	0.0	0.0	ILLUMINA	Illumina HiSeq 4000	SRP270849	PRJNA644668	NaN	644668.0	SRS6963816	SAMN15470648	simple	511145.0	Escherichia coli str. K-12 substr. MG1655	MG1655_F001_MID	NaN	NaN	NaN	NaN	NaN	NaN	no	NaN	NaN	NaN	NaN	UNIVERSITY OF CALIFORNIA- SAN DIEGO	SRA1096109	NaN	public	643DCE4D30004666B1915811EC00AB96	B9AEE80BABB7F175FDE99637F60849F9	s3://modulome/multi_ecoli/MG1655/raw_rna/SRX86...	s3://modulome/multi_ecoli/MG1655/raw_rna/SRX86...	MG1655	F001_MID	U00096.3	multi_ALE	F001_MID	WT	F001_MID	M9	glucose	NH4Cl	Aerobic	NaN	37	NaN	NaN	NaN	NaN	WT	2	1	NaN	Batch	0
SRX8684876	SRR12170055	2020-07-08 01:02:36	2020-07-08 01:00:21	4835538.0	1.450661e+09	4835538.0	300.0	392.0	NC_000913	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/s...	MG1655_F057_MID_1	RNA-Seq	cDNA	TRANSCRIPTOMIC	PAIRED	0.0	0.0	ILLUMINA	Illumina HiSeq 4000	SRP270849	PRJNA644668	NaN	644668.0	SRS6963817	SAMN15470649	simple	511145.0	Escherichia coli str. K-12 substr. MG1655	MG1655_F057_MID	NaN	NaN	NaN	NaN	NaN	NaN	no	NaN	NaN	NaN	NaN	UNIVERSITY OF CALIFORNIA- SAN DIEGO	SRA1096109	NaN	public	38EF20DF6206A513E0C21E0370DCFCA0	BD4EAEB626E9C690E0051523F7DFCC1D	s3://modulome/multi_ecoli/MG1655/raw_rna/SRX86...	s3://modulome/multi_ecoli/MG1655/raw_rna/SRX86...	MG1655	F057_MID	U00096.3	multi_ALE	F057_MID	WT	F057_MID	M9	glucose	NH4Cl	Aerobic	NaN	37	NaN	NaN	NaN	NaN	WT	1	1	NaN	Batch	0
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
p1k_00506	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	PAIRED	NaN	NaN	ILLUMINA	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	MG1655	WT	U00096.3	P1K	m9p	M9_glucose	WT	M9-P	glucose	NH4Cl	Aerobic	NaN	37	7.0	NaN	NaN	NaN	WT	2	1	NaN	Batch	True
p1k_00507	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	PAIRED	NaN	NaN	ILLUMINA	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	MG1655	WT	U00096.3	P1K	01xLB_pyruvate	M9_glucose	WT	01xLB	NaN	NaN	Aerobic	100uM Pyruvate	37	7.0	NaN	NaN	NaN	WT	1	1	NaN	Batch	True
p1k_00508	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	PAIRED	NaN	NaN	ILLUMINA	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	MG1655	WT	U00096.3	P1K	01xLB_pyruvate	M9_glucose	WT	01xLB	NaN	NaN	Aerobic	100uM Pyruvate	37	7.0	NaN	NaN	NaN	WT	2	1	NaN	Batch	True
p1k_00509	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	PAIRED	NaN	NaN	ILLUMINA	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	MG1655	WT	U00096.3	P1K	ZnCl2_LB	M9_glucose	WT	LB	NaN	NaN	Aerobic	1mM ZnCl2	37	7.0	NaN	NaN	NaN	WT	1	1	NaN	Batch	True
p1k_00510	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	PAIRED	NaN	NaN	ILLUMINA	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	MG1655	WT	U00096.3	P1K	ZnCl2_LB	M9_glucose	WT	LB	NaN	NaN	Aerobic	1mM ZnCl2	37	7.0	NaN	NaN	NaN	WT	2	1	NaN	Batch	True

69 rows × 71 columns

[8]:

multiModulon.view_iModulon_activities(
    species="MG1655",
    component="Core_1",
    fig_size=(6, 4),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf"
)

../_images/examples_characterization_core_components_10_0.png

[9]:

multiModulon.compare_core_iModulon_activity(
    component='Core_1',
    fig_size=(4, 3),
    species_in_comparison=['MG1655','BL21', 'W3110'],
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf",
    condition_list=['M9_glucose:in_house_2', 'LiAcet:in_house_2', 'acetate:in_house_2'],
    legend_title='Strain',
    title=None
)

../_images/examples_characterization_core_components_11_0.png

[10]:

multiModulon.show_iModulon_activity_change(
    species='MG1655',
    condition_1='acetate:in_house_2',
    condition_2='LiAcet:in_house_2',
    fig_size=(5, 5),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf"
)

../_images/examples_characterization_core_components_12_0.png

[11]:

multiModulon.show_gene_iModulon_correlation(
    gene='b0583',
    component='Core_1',
    fig_size=(4, 3),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf"
    )

../_images/examples_characterization_core_components_13_0.png

Step 3: Compare Gene Membership for Core components

Visualize the core and unique components by view_iModulon_weights and view_core_iModulon_weights

[12]:

multiModulon.view_core_iModulon_weights(
    component="Core_1",
    fig_size=(6, 4),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf",
    reference_order=['MG1655', 'BL21', 'W3110'],
    show_COG=True
)

../_images/examples_characterization_core_components_15_0.png

[13]:

Core_1_comparison = multiModulon.compare_core_iModulon(
    component='Core_1',
    y_label='Strains',
    reference_order=['MG1655', 'BL21', 'W3110'],
    fig_size=(20, 6),
    font_path="/usr/share/fonts/truetype/msttcorefonts/Arial.ttf",
    show_gene_names=False
    # save_path="./Output_iModulon_Figures/"
    )

../_images/examples_characterization_core_components_16_0.png

[14]:

Core_1_comparison

[14]:

	b0583	b0584	b0585	b0586	b0588	b0589	b0590	b0591	b0592	b0593	b0594	b0595	b0596	b0597	b0805	b1102	b1452	b1656	b1705	b2155	b2673	b2674	b2675	b2676	b4292	b4293	b4367	b4511	b4567	b0803	b0804	b1018	b1679	b1680	b1681	b1682	b1683	b3337	b4291	b0150	b0151	b0152	b0153	b0468	b0587	b0683	b1019	b1252	b1494	b1495	b1496	b1905	b2211	b3005	b3006	b3070	ECD_01019	JW5326	b1684
MG1655	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	-1	-1	0
BL21	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	1	1	1	1	1	-1	-1
W3110	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-1	1	1