The C value of each DE ncRNA is equal to the sum of BP value, CC value, MF value and KEGG value
We calculated the C value of each DE miRNA in skeletal muscle denervation, prostate cancer, Alzheimer's disease and gastric cancer data sets respectively. In addition, we calculate the C value of each lncRNA in skeletal muscle denervation and adipocyte differentiation data sets. The details of these data were aggregated into a table (Table 1). Using the mathematical model we designed, the C values of each DE ncRNA based on biological process (BP), cellular component (CC), molecular function (MF) and KEGG analysis can be obtained, and we call these C values as BP value, CC value, MF value and KEGG value respectively. The total C value of each DE ncRNA is equal to the sum of BP value, CC value, MF value and KEGG value. The DE miRNAs were sorted with the total C value to obtain the 10 DE miRNAs with maximum C value, named as top10 C value miRNAs (Table 2). The top10 DE miRNAs with maximum absolute Log2 FC (top10 FC miRNAs), and the top10 DE miRNAs with minimum P value (top10 P value miRNAs), were obtained by sorting the DE miRNAs according to the absolute Log2 fold FC and P value respectively (Supplementary Table 1-2). Similarly, DE lncRNAs are processed in the same way to obtain top5 C value lncRNAs, top5 FC lncRNAs, top5 P value lncRNAs for adipocyte differentiation and top10 C value lncRNAs, top10 FC lncRNAs, top10 P value lncRNAs for skeletal muscle denervation. (Table 3,Supplementary Table 3-6).
Table 1. Description of publicly available data sets used in the meta-analysis.
RNA
|
Gene Expression Platforms
|
Status
|
Tissue
|
Organism
|
Ref.
|
MicroRNA
|
Illumina HiSeq X
|
Nerve resection
|
Muscle
|
Mus Musculus
|
11
|
MicroRNA
|
Illumina HiSeq 2500
|
Alzheimer’s disease
|
Brain
|
Mus Musculus
|
GSE13217712
|
MicroRNA
|
Agilent-019118
|
Prostate cancer
|
Tumor tissue
|
Homo sapiens
|
GSE6431816
|
MicroRNA
|
Illumina HiSeq 2000 miRNAseq
|
Gastric cancer
|
Tumor tissue
|
Homo sapiens
|
14
|
LncRNA
|
Illumina HiSeq X
|
Nerve resection
|
Muscle
|
Mus Musculus
|
11
|
LncRNA
|
Illumina HiSeq 1500
|
Adipocyte differentiated stem cell
|
Adipose-derived stem cell
|
Homo sapiens
|
GSE11325315
|
Ref: reference.
Table 2 The top10 miRNAs according to C value
|
miRNAs
|
KEGG value
|
BP value
|
CC value
|
MF value
|
C value
|
skeletal muscle denervation
|
|
|
|
|
mmu-miR-1943-5p
|
33.2298
|
816.2096
|
57.7971
|
86.4830
|
993.7195
|
mmu-miR-322-5p
|
30.8406
|
752.9168
|
68.5535
|
79.5975
|
931.9084
|
mmu-miR-497a-5p
|
30.7342
|
748.7866
|
69.7075
|
79.4659
|
928.6942
|
mmu-miR-674-5p
|
27.1606
|
715.4414
|
58.0113
|
72.7104
|
873.3236
|
mmu-miR-377-3p
|
27.4901
|
693.5040
|
53.2729
|
72.8327
|
847.0997
|
mmu-miR-378d
|
23.2596
|
680.9893
|
61.2806
|
72.2897
|
837.8192
|
mmu-miR-486a-3p
|
26.8248
|
657.0155
|
50.6866
|
69.4835
|
804.0103
|
mmu-miR-34a-5p
|
26.6988
|
659.2445
|
53.4273
|
63.0869
|
802.4575
|
mmu-miR-34c-5p
|
26.6988
|
659.2445
|
53.4273
|
63.0869
|
802.4575
|
mmu-miR-485-5p
|
24.7998
|
631.6504
|
56.8839
|
69.4729
|
782.8069
|
Alzheimer’s disease
|
|
|
|
|
mmu-miR-340-5p
|
43.5208
|
1010.0391
|
99.4072
|
95.1248
|
1248.0919
|
mmu-miR-128-3p
|
32.3406
|
702.2785
|
72.0400
|
72.0975
|
878.7565
|
mmu-miR-1912-3p
|
31.4818
|
665.3036
|
71.0238
|
65.4024
|
833.2115
|
mmu-miR-3065-5p
|
28.5725
|
635.0081
|
59.7389
|
60.1966
|
783.5160
|
mmu-miR-30e-5p
|
25.0791
|
603.9772
|
61.3365
|
55.3197
|
745.7125
|
mmu-miR-30b-5p
|
24.3197
|
578.0747
|
60.5463
|
54.1156
|
717.0563
|
mmu-miR-369-3p
|
21.9838
|
578.5994
|
50.7141
|
53.2306
|
704.5279
|
mmu-miR-30f
|
23.9495
|
503.5940
|
55.6817
|
48.9650
|
632.1902
|
mmu-miR-16-5p
|
24.3638
|
493.9211
|
47.4183
|
46.5204
|
612.2236
|
mmu-miR-3470a
|
18.4495
|
405.6942
|
42.6480
|
40.2364
|
507.0280
|
prostate cancer
|
|
|
|
|
|
hsa-miR-374a-5p
|
4.3985
|
118.2693
|
5.2133
|
10.0440
|
137.9250
|
hsa-miR-513a-5p
|
5.6572
|
112.0295
|
6.9103
|
12.5930
|
137.1900
|
hsa-miR-95-5p
|
3.4669
|
116.9228
|
5.4779
|
9.5689
|
135.4365
|
hsa-miR-374b-5p
|
3.8076
|
113.5990
|
5.3002
|
11.6734
|
134.3802
|
hsa-miR-498
|
4.7281
|
107.2751
|
5.8249
|
10.8348
|
128.6630
|
hsa-miR-20a-5p
|
4.1156
|
109.1116
|
5.6328
|
8.0808
|
126.9408
|
hsa-miR-30e-5p
|
3.6117
|
102.8695
|
5.2738
|
8.0756
|
119.8306
|
hsa-miR-96-5p
|
3.0537
|
94.3429
|
5.1002
|
6.5807
|
109.0776
|
hsa-miR-148a-5p
|
3.3918
|
90.1048
|
4.5191
|
6.8996
|
104.9153
|
hsa-miR-429
|
3.2433
|
85.7535
|
5.0370
|
7.6430
|
101.6768
|
gastric cancer
|
|
|
|
|
|
hsa-miR-153-5p
|
18.2391
|
362.6950
|
64.0236
|
71.7660
|
516.7236
|
hsa-miR-3662
|
15.3946
|
317.1733
|
49.4005
|
52.8578
|
434.8263
|
hsa-miR-548f-3p
|
14.2178
|
286.8668
|
49.4087
|
47.7987
|
398.2921
|
hsa-miR-5680
|
13.2793
|
242.4315
|
42.3071
|
49.8912
|
347.9091
|
hsa-miR-944
|
14.7858
|
239.0951
|
40.7592
|
49.7775
|
344.4176
|
hsa-miR-7-2-3p
|
13.3438
|
249.0496
|
38.5958
|
38.1965
|
339.1857
|
hsa-miR-4677-5p
|
8.4194
|
187.5756
|
34.2620
|
30.5864
|
260.8433
|
hsa-miR-20a-5p
|
7.5578
|
178.5451
|
36.1427
|
28.2557
|
250.5012
|
hsa-miR-4728-5p
|
10.0061
|
161.1989
|
32.7904
|
31.1540
|
235.1493
|
hsa-miR-6507-5p
|
10.3778
|
162.0089
|
28.4527
|
26.2513
|
227.0907
|
BP, biological process; CC, cellular component; MF, molecular function
Table 3 The top lncRNAs according to C value
|
miRNAs
|
KEGG value
|
BP value
|
CC value
|
MF value
|
C value
|
adipocyte differentiation
|
|
|
|
|
MIAT
|
0.7422
|
33.6464
|
1.7731
|
4.2158
|
40.3777
|
CYTOR
|
0.5408
|
27.4816
|
1.6461
|
3.5501
|
33.2186
|
LINC02202
|
0.8555
|
23.7874
|
1.6544
|
2.7816
|
29.0790
|
OSER1-DT
|
0.7450
|
22.7320
|
1.7143
|
2.1406
|
27.3320
|
LINC01119
|
0.3521
|
21.7651
|
1.1976
|
2.0853
|
25.4002
|
skeletal muscle denervation
|
|
|
|
|
LNC_000596
|
19.4847
|
283.7968
|
35.8261
|
40.4197
|
379.5275
|
ENSMUST00000138653.7
|
18.6985
|
268.8787
|
31.0684
|
39.4189
|
358.0646
|
ENSMUST00000131642.1
|
17.0027
|
256.5569
|
30.1589
|
32.2753
|
335.9940
|
LNC_000057
|
15.5034
|
232.4060
|
29.6239
|
28.7508
|
306.2843
|
LNC_000040
|
17.5395
|
215.5778
|
28.0434
|
30.6050
|
291.7658
|
ENSMUST00000152365.1
|
14.3560
|
227.8362
|
26.2226
|
22.5889
|
291.0038
|
ENSMUST00000137810.2
|
13.5911
|
218.9375
|
25.9034
|
24.7821
|
283.2142
|
LNC_000279
|
12.8857
|
217.3779
|
26.5701
|
26.3653
|
283.1992
|
LNC_000353
|
15.4114
|
207.9657
|
27.1850
|
29.2075
|
279.7697
|
ENSMUST00000154414.1
|
12.3479
|
211.8834
|
24.6985
|
27.0541
|
275.9841
|
BP, biological process; CC, cellular component; MF, molecular function
C value is superior to log2 FC and P value in miRNAs operation results
In each data set, the most significant enriched BP term, CC term, MF term, KEGG pathway were obtained by DEGs enrichment analysis. We took the intersections of DEGs with the predicted target genes of top10 C value miRNAs, top10 FC miRNAs and top10 P value miRNAs respectively, and then calculated the proportion of these intersections in the above pathways/terms. It was found that the proportion of top10 C Value miRNAs target genes was significantly larger than that of top10 FC miRNAs, top10 P value miRNAs in the above terms/pathways (Fig. 1). We built several PPI networks based on DEGs, and calculated the degree of each node. The node with a larger degree had a darker color and was closer to the center. Then we divided these nodes into core region (top 20% of degree), subcore region (top 20%-50% of degree) and noncore region (bottom 50% of degree) (Fig. 2a, e, i and m). In the PPI network, the predicted target genes of top10 C value miRNAs, top10 FC miRNAs and top10 p value miRNAs were labeled in red (Fig. 2). It was found that the number of top10 C value miRNAs’ target genes in each region were larger than those of top10 FC miRNAs, and top10 P value miRNAs, and the C value group are more concentrated in core region (Fig. 3) (Table 4).
Based on extensive literature, we identified 14 skeletal muscle growth regulatory miRNAs, 6 Alzheimer’s disease associated miRNAs, 7 prostate cancer associated miRNAs, 6 gastric cancer associated miRNAs and found that when DE miRNAs were sorted by C value, the sequence number accumulation value of these miRNAs was significantly smaller than that of the other two indexes, which means that these miRNAs sequences increased integrally (Fig. 4). When sorting by C value versus sorting by absolute Log2 FC/ P value, most of the disease critical miRNAs ranked up (Fig. 4).
Table 4 The ratio of the number of genes in each group in different regions.
|
FC group
|
P value group
|
C value group
|
|
Core region
|
Subcore region
|
Noncore region
|
Core region
|
Subcore region
|
Noncore region
|
Core region
|
Subcore region
|
Noncore region
|
Skeletal muscle denervation
|
0.1752
|
0.3424
|
0.4824
|
0.1805
|
0.3268
|
0.4927
|
0.2020
|
0.3459
|
0.4522
|
Prostate cancer
|
0.6607
|
0.2857
|
0.0536
|
0.5152
|
0.3030
|
0.1818
|
0.7045
|
0.2727
|
0.0227
|
Alzheimer's disease
|
0.2274
|
0.3271
|
0.4455
|
0.2225
|
0.3549
|
0.4225
|
0.2460
|
0.3524
|
0.4016
|
Gastric cancer
|
0.2166
|
0.3076
|
0.4759
|
0.2125
|
0.3188
|
0.4687
|
0.2391
|
0.3095
|
0.4514
|
C value is superior to log2 FC and P value in lncRNAs operation results
In skeletal muscle denervation data set, we calculated the proportion of the predicted target genes of top10 C value lncRNAs, top10 FC lncRNAs, and top10 P value lncRNAs in the most enriched terms/pathways respectively, and found that the proportion of the genes regulated by top10 C value lncRNAs was larger than that of top10 FC lncRNAs and top10 P value lncRNAs (Fig. 5a). It was found that the number of top10 C value lncRNAs’ target genes in each region were larger than those of top10 FC lncRNAs, and top10 P value lncRNAs and the C value group are more concentrated in core region (Fig. 5b-f) (Table 5).
Since there are relatively few DE lncRNAs and DE mRNAs in adipocyte differentiation data set, we take top5 C value lncRNAs, top5 FC lncRNAs, top5 P value lncRNAs. The proportion of the genes regulated by top5 C value lncRNAs was larger than that of top5 FC lncRNAs and top5 P value lncRNAs in enriched term/pathway (Fig. 6a). It was found that the number of top5 C value lncRNAs’ target genes in each region were larger than those of top5 FC lncRNAs, and top5 P value lncRNAs and the C value group are more concentrated in core region (Fig. 6b-f) (Table 5). And when DE lncRNAs were sorted by C value, the adipocyte differentiation associated lncRNAs sequences increased integrally than that of the other two indexes (Fig. 6g-h).
Table 5 The ratio of the number of genes in each group in different regions.
|
FC group
|
P value group
|
C value group
|
|
Core region
|
Subcore region
|
Noncore region
|
Core region
|
Subcore region
|
Noncore region
|
Core region
|
Subcore region
|
Noncore region
|
Skeletal muscle denervation
|
0.0990
|
0.3453
|
0.5555
|
0.0946
|
0.3438
|
0.5615
|
0.1915
|
0.3856
|
0.4229
|
Adipocyte differentiation
|
0.2727
|
0.3636
|
0.3636
|
0.3000
|
0.3000
|
0.4000
|
0.4800
|
0.3600
|
0.1600
|