Journal of Traditional Chinese Medicine ›› 2022, Vol. 42 ›› Issue (1): 108-115.DOI: 10.19852/j.cnki.jtcm.2022.01.007
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Xiaoli XIN1, Guodong WANG2, Ru HAN1, Yi JIANG1, Chang LIU1, Lingshuang LIU1(), Zhenye XU1()
Received:
2021-02-22
Accepted:
2021-05-14
Online:
2022-01-25
Published:
2022-01-25
Contact:
Lingshuang LIU,Zhenye XU
About author:
XU Zhenye, Longhua Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China. xuzhenye1947@126.comSupported by:
Xiaoli XIN, Guodong WANG, Ru HAN, Yi JIANG, Chang LIU, Lingshuang LIU, Zhenye XU. Mechanism underlying the effect of Liujunzi decoction (六君子汤) on advanced-stage non-small cell lung cancer in patients after first-line chemotherapy[J]. Journal of Traditional Chinese Medicine, 2022, 42(1): 108-115.
Figure 1 DEG expression heatmap (partial) DEGs satisfying FDR < 1.00, |lgFC| > 1.00 and P < 0.05 were screened out, DEG: differentially expressed genes; FDR: false discovery rate.
GO ID | Term | Percentage (%) | P value | Fold Enrichment | Number of DEGs |
---|---|---|---|---|---|
GO:0048666 | neuron development | 9.850 | 1.393×10-3 | 2.444 | 17 |
GO:0048483 | autonomic nervous system development | 2.318 | 3.336×10-3 | 13.214 | 4 |
GO:0010628 | positive regulation of gene expression | 13.326 | 4.019×10-3 | 1.886 | 23 |
GO:0003382 | epithelial cell morphogenesis | 2.318 | 4.872×10-3 | 11.563 | 4 |
GO:0007399 | nervous system development | 15.644 | 5.163×10-3 | 1.726 | 27 |
Table 1 GO enrichment analysis (BP)
GO ID | Term | Percentage (%) | P value | Fold Enrichment | Number of DEGs |
---|---|---|---|---|---|
GO:0048666 | neuron development | 9.850 | 1.393×10-3 | 2.444 | 17 |
GO:0048483 | autonomic nervous system development | 2.318 | 3.336×10-3 | 13.214 | 4 |
GO:0010628 | positive regulation of gene expression | 13.326 | 4.019×10-3 | 1.886 | 23 |
GO:0003382 | epithelial cell morphogenesis | 2.318 | 4.872×10-3 | 11.563 | 4 |
GO:0007399 | nervous system development | 15.644 | 5.163×10-3 | 1.726 | 27 |
GO ID | Term | Percentage (%) | P value | Fold Enrichment | Number of DEGs | |
---|---|---|---|---|---|---|
GO:0005578 | proteinaceous extracellular matrix | 4.056 | 0.042 | 2.735 | 7 | |
GO:0005615 | extracellular space | 9.850 | 0.044 | 1.660 | 17 | |
GO:0005576 | extracellular region | 24.335 | 0.045 | 1.281 | 42 |
Table 2 GO enrichment analysis (CC)
GO ID | Term | Percentage (%) | P value | Fold Enrichment | Number of DEGs | |
---|---|---|---|---|---|---|
GO:0005578 | proteinaceous extracellular matrix | 4.056 | 0.042 | 2.735 | 7 | |
GO:0005615 | extracellular space | 9.850 | 0.044 | 1.660 | 17 | |
GO:0005576 | extracellular region | 24.335 | 0.045 | 1.281 | 42 |
GO ID | Term | Percentage (%) | P value | Fold Enrichment | Number of DEGs | |
---|---|---|---|---|---|---|
GO:0005509 | Calcium ion binding | 6.953 | 0.018 | 2.233 | 12 | |
GO:0034584 | piRNA binding | 1.159 | 0.022 | 88.954 | 2 | |
GO:0001228 | Transcriptional activator activity, RNA polymerase Ⅱ transcription regulatory region sequence-specific binding | 4.056 | 0.035 | 2.865 | 7 | |
GO:0004252 | Serine-type endopeptidase activity | 3.476 | 0.042 | 3.140 | 6 |
Table 3 GO enrichment analysis (MF)
GO ID | Term | Percentage (%) | P value | Fold Enrichment | Number of DEGs | |
---|---|---|---|---|---|---|
GO:0005509 | Calcium ion binding | 6.953 | 0.018 | 2.233 | 12 | |
GO:0034584 | piRNA binding | 1.159 | 0.022 | 88.954 | 2 | |
GO:0001228 | Transcriptional activator activity, RNA polymerase Ⅱ transcription regulatory region sequence-specific binding | 4.056 | 0.035 | 2.865 | 7 | |
GO:0004252 | Serine-type endopeptidase activity | 3.476 | 0.042 | 3.140 | 6 |
KEGG ID | Term | Percentage (%) | P value | Fold Enrichment | Number of DEGs |
---|---|---|---|---|---|
hsa04060 | Cytokine-cytokine receptor interaction | 4.651 | 0.031 | 3.330 | 6 |
Table 4 KEGG pathway enrichment analysis
KEGG ID | Term | Percentage (%) | P value | Fold Enrichment | Number of DEGs |
---|---|---|---|---|---|
hsa04060 | Cytokine-cytokine receptor interaction | 4.651 | 0.031 | 3.330 | 6 |
Gene | Expression regulated | Node degree | MCODE score | Gene | Expression regulated | Node degree | MCODE score | |
---|---|---|---|---|---|---|---|---|
IL2 | up | 7 | 0.25 | XCL1 | down | 3 | 2 | |
PIWIL4 | down | 4 | 3 | IL22RA1 | up | 3 | 0.5 | |
DICER1 | down | 3 | 3 | ARHGAP11A | down | 3 | 0.5 | |
PIWIL2 | down | 3 | 3 | DCP1A | down | 3 | 3 | |
SAA1 | up | 3 | 2 | GDNF | down | 2 | 0.67 |
Table 5 Proteins with highest node degrees in PPI analysis
Gene | Expression regulated | Node degree | MCODE score | Gene | Expression regulated | Node degree | MCODE score | |
---|---|---|---|---|---|---|---|---|
IL2 | up | 7 | 0.25 | XCL1 | down | 3 | 2 | |
PIWIL4 | down | 4 | 3 | IL22RA1 | up | 3 | 0.5 | |
DICER1 | down | 3 | 3 | ARHGAP11A | down | 3 | 0.5 | |
PIWIL2 | down | 3 | 3 | DCP1A | down | 3 | 3 | |
SAA1 | up | 3 | 2 | GDNF | down | 2 | 0.67 |
GO ID | Categories | Terms | FDR |
---|---|---|---|
GO:0010608 | Biological process | posttranscriptional regulation of gene expression | 7.88 × 10-5 |
GO:0010629 | Biological process | negative regulation of gene expression | 0.0015 |
GO:0016070 | Biological process | RNA metabolic process | 0.0134 |
GO:1990904 | Cellular component | ribonucleoprotein complex | 0.00016 |
GO:0003723 | Molecular function | RNA binding | 0.0001 |
Table 6 GO enrichment analysis by STRING 10.0 (PIWIL4, DICER1, PIWIL2, and DCP1A)
GO ID | Categories | Terms | FDR |
---|---|---|---|
GO:0010608 | Biological process | posttranscriptional regulation of gene expression | 7.88 × 10-5 |
GO:0010629 | Biological process | negative regulation of gene expression | 0.0015 |
GO:0016070 | Biological process | RNA metabolic process | 0.0134 |
GO:1990904 | Cellular component | ribonucleoprotein complex | 0.00016 |
GO:0003723 | Molecular function | RNA binding | 0.0001 |
KEGG ID | Terms | matching proteins in network | FDR |
---|---|---|---|
HSA-211000 | Gene Silencing by RNA | DICER1,PIWIL2,PIWIL4 | 7.77×10-6 |
HSA-5601884 | piRNA biogenesis | PIWIL2,PIWIL4 | 9.45×10-5 |
Table 7 KEGG enrichment analysis by STRING 10.0 (PIWIL4, DICER1, PIWIL2, and DCP1A)
KEGG ID | Terms | matching proteins in network | FDR |
---|---|---|---|
HSA-211000 | Gene Silencing by RNA | DICER1,PIWIL2,PIWIL4 | 7.77×10-6 |
HSA-5601884 | piRNA biogenesis | PIWIL2,PIWIL4 | 9.45×10-5 |
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