WGCNA 联合网络

把基因和代谢物分别聚成共表达模块，在模块层面连接两组学，以及处理和水平。

主要发现：处理是模块层面最强的信号：基因模块 gyellow 与 gblue 和“R vs Y”的相关分别为 0.977 和 -0.965。R 中升高的 gyellow 富集苯丙烷生物合成，并与 R 中升高、富含类黄酮的代谢物模块 mturquoise 高度相关（r=0.960）；Y 中升高的 gblue 富集光合作用。

全局结果

模块规模共 30 行下载全表

module	type	n	hubs
brown	gene	2963	93
purple	gene	407	38
blue	gene	4887	677
salmon	gene	303	53
yellow	gene	2327	457
green	gene	1621	89
red	gene	919	62
pink	gene	516	43
black	gene	649	25
turquoise	gene	6685	559
lightcyan	gene	129	13
greenyellow	gene	342	28
cyan	gene	204	93
magenta	gene	484	17
tan	gene	308	8
midnightblue	gene	136	12
grey	gene	325	0
lightgreen	gene	37	12
grey60	gene	62	21
green	met	78	3
brown	met	197	9
turquoise	met	303	57
black	met	49	1
blue	met	213	11
grey	met	158	0
yellow	met	144	46
red	met	53	10
purple	met	14	7
pink	met	41	9
magenta	met	33	12

基因模块-性状相关预览前 40 行，共 216 行下载全表

a	b	trait_type	r	p	fdr
gyellow	R vs Y	treatment	0.9775	1.85e-20	4e-18
gblue	R vs Y	treatment	-0.9653	7.3e-18	7.88e-16
gturquoise	Level 1-5	level	0.7138	9.49e-06	0.00041
ggreen	Level 1-5	level	-0.7181	7.9e-06	0.00041
gbrown	Level 1-5	level	0.7147	9.12e-06	0.00041
gpurple	Level 1-5	level	-0.6478	0.000109	0.003918
gblack	R5	group	-0.638	0.000149	0.004599
ggreen	R5	group	-0.6335	0.000172	0.004632
gsalmon	Level 1-5	level	0.5799	0.000783	0.0188
gmagenta	R vs Y	treatment	0.557	0.00139	0.03002
gcyan	Level 1-5	level	-0.5075	0.0042	0.08248
gmagenta	R1	group	0.4871	0.006329	0.0855
gturquoise	R5	group	0.497	0.005204	0.0855
gmidnightblue	R vs Y	treatment	-0.4871	0.006333	0.0855
gred	R vs Y	treatment	0.5005	0.004847	0.0855
gbrown	R5	group	0.4882	0.006195	0.0855
gmagenta	Level 1-5	level	-0.4812	0.007103	0.09024
gcyan	R2	group	0.4764	0.007776	0.09331
ggreen	R4	group	-0.4664	0.009377	0.102
gblue	Y5	group	0.4653	0.009569	0.102
gyellow	R5	group	0.4633	0.00992	0.102
gmagenta	R3	group	0.4581	0.01091	0.1056
glightgreen	Y4	group	0.4564	0.01124	0.1056
gblack	Level 1-5	level	-0.4474	0.01318	0.1165
gbrown	R4	group	0.4461	0.01348	0.1165
gbrown	Y2	group	-0.4397	0.01503	0.1249
gbrown	R vs Y	treatment	0.4353	0.01621	0.1297
gmagenta	R2	group	0.4201	0.02082	0.155
gturquoise	Y5	group	0.4215	0.02036	0.155
gturquoise	R3	group	-0.4131	0.02329	0.1677
gmagenta	R5	group	-0.4024	0.02747	0.1914
glightgreen	R vs Y	treatment	-0.4001	0.02847	0.1921
ggreen	R vs Y	treatment	-0.397	0.02985	0.1954
ggreenyellow	Y4	group	0.3877	0.03426	0.2176
gturquoise	R1	group	-0.3835	0.03643	0.2248
gyellow	R4	group	0.3784	0.03919	0.2351
gyellow	Y2	group	-0.3683	0.04523	0.2505
ggrey60	R vs Y	treatment	0.3706	0.04381	0.2505
gsalmon	Y5	group	0.3689	0.04483	0.2505
gred	R3	group	0.3644	0.04774	0.2578

基因模块 KEGG 富集预览前 30 行，共 1,322 行下载全表

module	pid	name	n	bg	k	p	fdr
midnightblue	03010	Ribosome	60	321	81	4.81e-57	1.44e-55
pink	04141	Protein processing in endoplasmic reticulum	68	276	139	9e-52	5.94e-50
turquoise	03040	Spliceosome	133	216	1385	2.99e-28	4.19e-26
green	03440	Homologous recombination	63	178	446	1.4e-24	1.67e-22
turquoise	03013	Nucleocytoplasmic transport	73	119	1385	9.1e-16	6.37e-14
turquoise	03008	Ribosome biogenesis in eukaryotes	58	87	1385	3.99e-15	1.86e-13
blue	00195	Photosynthesis	43	64	1105	2.25e-15	3.09e-13
lightcyan	04075	Plant hormone signal transduction	12	298	15	3.94e-13	3.55e-12
green	03082	ATP-dependent chromatin remodeling	36	119	446	4.86e-12	2.89e-10
turquoise	03015	mRNA surveillance pathway	68	124	1385	1.61e-11	5.65e-10
grey60	00600	Sphingolipid metabolism	6	55	12	9.31e-10	5.58e-09
black	00190	Oxidative phosphorylation	27	131	260	1.42e-10	1.58e-08
magenta	00941	Flavonoid biosynthesis	10	29	131	9.72e-10	8.94e-08
blue	00196	Photosynthesis - antenna proteins	17	20	1105	1.95e-09	1.34e-07
red	00940	Phenylpropanoid biosynthesis	20	106	201	2.26e-09	2.03e-07
grey60	00905	Brassinosteroid biosynthesis	4	21	12	9.53e-08	2.86e-07
green	00190	Oxidative phosphorylation	33	131	446	7.5e-09	2.98e-07
blue	00860	Porphyrin metabolism	32	59	1105	2.34e-08	1.07e-06
black	03050	Proteasome	16	67	260	1.08e-07	6.01e-06
turquoise	03022	Basal transcription factors	31	53	1385	9e-07	2.52e-05
red	04075	Plant hormone signal transduction	30	298	201	8.82e-07	2.65e-05
red	00592	alpha-Linolenic acid metabolism	13	64	201	6.72e-07	2.65e-05
blue	03010	Ribosome	104	321	1105	1.02e-06	3.49e-05
green	03030	DNA replication	19	69	446	2.99e-06	8.88e-05
red	00901	Indole alkaloid biosynthesis	5	9	201	9.11e-06	0.000205
brown	04136	Autophagy - other	18	44	641	1.56e-06	0.000208
black	00020	Citrate cycle (TCA cycle)	13	64	260	1.2e-05	0.000444
purple	00600	Sphingolipid metabolism	7	55	72	8.66e-06	0.000476
blue	00710	Carbon fixation by Calvin cycle	33	79	1105	2.67e-05	0.000731
turquoise	03083	Polycomb repressive complex	33	67	1385	5.72e-05	0.001151

代谢物模块 KEGG 富集预览前 30 行，共 255 行下载全表

module	pid	name	n	bg	k	p	fdr
yellow	00970	Aminoacyl-tRNA biosynthesis	13	17	39	7.99e-09	3.35e-07
yellow	00470	D-Amino acid metabolism	13	21	39	4.39e-07	9.21e-06
yellow	00460	Cyanoamino acid metabolism	8	10	39	6.85e-06	9.59e-05
pink	00073	Cutin, suberine and wax biosynthesis	2	2	3	9.79e-05	0.000196
yellow	00290	Valine, leucine and isoleucine biosynthesis	4	4	39	0.000535	0.004367
yellow	00966	Glucosinolate metabolism	4	4	39	0.000535	0.004367
yellow	00260	Glycine, serine and threonine metabolism	7	12	39	0.000624	0.004367
magenta	00130	Ubiquinone and other terpenoid-quinone biosynthesis	1	3	1	0.0121	0.0121
yellow	00261	Monobactam biosynthesis	4	5	39	0.002367	0.0142
blue	00600	Sphingolipid metabolism	5	6	41	0.000525	0.01523
turquoise	00941	Flavonoid biosynthesis	9	14	53	0.000423	0.02032
yellow	00270	Cysteine and methionine metabolism	6	12	39	0.004698	0.02466
blue	00944	Flavone and flavonol biosynthesis	6	10	41	0.001828	0.02651
red	00250	Alanine, aspartate and glutamate metabolism	4	8	17	0.000909	0.03729
brown	00053	Ascorbate and aldarate metabolism	6	11	34	0.001211	0.05812
brown	00660	C5-Branched dibasic acid metabolism	4	6	34	0.003677	0.05883
brown	00020	Citrate cycle (TCA cycle)	4	6	34	0.003677	0.05883
yellow	00920	Sulfur metabolism	4	7	39	0.01299	0.06064
turquoise	00052	Galactose metabolism	10	20	53	0.002916	0.06999
pink	00564	Glycerophospholipid metabolism	1	6	3	0.07112	0.07112
red	00910	Nitrogen metabolism	2	2	17	0.00444	0.08677
red	00470	D-Amino acid metabolism	5	21	17	0.008465	0.08677
red	00630	Glyoxylate and dicarboxylate metabolism	4	13	17	0.007457	0.08677
black	00350	Tyrosine metabolism	3	6	18	0.005643	0.0903
black	00640	Propanoate metabolism	2	2	18	0.004995	0.0903
yellow	00999	Biosynthesis of various plant secondary metabolites	4	8	39	0.02303	0.09671
black	00240	Pyrimidine metabolism	4	13	18	0.009297	0.09917
red	00220	Arginine biosynthesis	3	8	17	0.01218	0.09987
brown	00562	Inositol phosphate metabolism	3	4	34	0.008626	0.1035
yellow	00280	Valine, leucine and isoleucine degradation	3	5	39	0.02883	0.1101

基因模块归属与 kME 代谢物模块归属

WGCNA 联合网络?

全局结果

模块规模

基因模块-性状相关

基因模块 KEGG 富集

代谢物模块 KEGG 富集

WGCNA 联合网络