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Bioinformatics Analysis of Key micro-RNAs and mRNAs under the Hand, Foot, and Mouth Disease Virus Infection

SHENG LIN
SHENG LIN
, 
LIU YANG
LIU YANG
, 
SHIBIAO WANG
SHIBIAO WANG
, 
BIN WENG
BIN WENG
 and 
MIN LIN
MIN LIN
   | Dec 27, 2020
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Article Category: original-paper
Published Online: Dec 27, 2020
Page range: 479 - 490
Received: Oct 12, 2020
Accepted: Nov 09, 2020
DOI: https://doi.org/10.33073/pjm-2020-052
Keywords
© 2020 Sheng Lin et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Fig. 1.

Differentially expressed miRNAs after HFMD virus infection in 16HBE cells based on the GSE85829 dataset.(A) Left: EV71 infection-induced 25 DE-miRNAs; Right: CA16 infection-induced 13 DE-miRNAs.(B) The Venn diagram of 7 common DE-miRNAs between EV71 and CA16 infection.
Differentially expressed miRNAs after HFMD virus infection in 16HBE cells based on the GSE85829 dataset.(A) Left: EV71 infection-induced 25 DE-miRNAs; Right: CA16 infection-induced 13 DE-miRNAs.(B) The Venn diagram of 7 common DE-miRNAs between EV71 and CA16 infection.

Fig. 2.

Differentially expressed miRNAs after HFMD virus infection in the HUVEC cell line based on the GSE94551 dataset.(A) Left: 39 DE-miRNAs were observed after EV71 infection; Right: 99 DE-miRNAs were found after CA16 infection.(B) The Venn diagram of 7 common DE-miRNAs between EV71 and CA16 infection.(C) The Venn diagram of common DE-miRNAs among four groups of HFMD virus infection.
Differentially expressed miRNAs after HFMD virus infection in the HUVEC cell line based on the GSE94551 dataset.(A) Left: 39 DE-miRNAs were observed after EV71 infection; Right: 99 DE-miRNAs were found after CA16 infection.(B) The Venn diagram of 7 common DE-miRNAs between EV71 and CA16 infection.(C) The Venn diagram of common DE-miRNAs among four groups of HFMD virus infection.

Fig. 3.

MicroRNAs in serum exosomes from HFMD patients were analyzed based on the GSE52780 dataset.(A) Heatmap of 258 DE-miRNAs was found, including 85 up-regulated and 173 down-regulated ones.(B) The top ten up-regulated and down-regulated DE-miRNAs.
MicroRNAs in serum exosomes from HFMD patients were analyzed based on the GSE52780 dataset.(A) Heatmap of 258 DE-miRNAs was found, including 85 up-regulated and 173 down-regulated ones.(B) The top ten up-regulated and down-regulated DE-miRNAs.

Fig. 4.

GO and KEGG enrichment of key miRNAs and DE-mRNAs. Based on the above five key miRNAs, GO functional, and KEGG pathway enrichment was performed using the miRPath v. 3 database.(A) GO enrichment based on the intersection targets of the five key miRNAs (only four miRNAs were included in the miRPath database).(B) KEGG enrichment based on the intersection targets of the four key miRNAs.(C) GO enrichment verification through the union of key miRNA related GO terms, presented as a heatmap.(D) Verification of KEGG pathway through the union of key miRNA related KEGG pathways presented as a heatmap.(E) The enriched GO functions of up-regulated DEGs in SH-SY5Y cells infected by EV71 from the GSE45589 dataset.(F) The enriched GO functions of down-regulated DEGs in SH-SY5Y cells infected by EV71 from the GSE45589 dataset.(G) Enriched KEGG pathways in SH-SY5Y cells infected by EV71 from the GSE45589 dataset.
GO and KEGG enrichment of key miRNAs and DE-mRNAs. Based on the above five key miRNAs, GO functional, and KEGG pathway enrichment was performed using the miRPath v. 3 database.(A) GO enrichment based on the intersection targets of the five key miRNAs (only four miRNAs were included in the miRPath database).(B) KEGG enrichment based on the intersection targets of the four key miRNAs.(C) GO enrichment verification through the union of key miRNA related GO terms, presented as a heatmap.(D) Verification of KEGG pathway through the union of key miRNA related KEGG pathways presented as a heatmap.(E) The enriched GO functions of up-regulated DEGs in SH-SY5Y cells infected by EV71 from the GSE45589 dataset.(F) The enriched GO functions of down-regulated DEGs in SH-SY5Y cells infected by EV71 from the GSE45589 dataset.(G) Enriched KEGG pathways in SH-SY5Y cells infected by EV71 from the GSE45589 dataset.

Fig. 5.

Common differential mRNAs and PPI network.(A) Using the TarBase V8 tool, we acquired 1,520 potential targets (mRNA) from the 5 key DE-miRNAs, among which 11 DEGs were also included by the 159 DE-mRNAs in the GSE45589 dataset: MACF1, MARS, SF3B3, SMARCC1, BRMS1L, SMC1A, SPHK2, LIG1, CSF3, CYR61, and FGFR1OP.(B) GO functional analysis showed three terms might be enriched according to these DEGs.(C) These common DEGs showed a PPI network mainly connected by SMC1A, SMARCC1, SF3B3, LIG1, and BRMS1L.(D) The PPI network constructed by the 159 DE-mRNAs in the GSE45589 dataset (the isolated nodes were removed).
Common differential mRNAs and PPI network.(A) Using the TarBase V8 tool, we acquired 1,520 potential targets (mRNA) from the 5 key DE-miRNAs, among which 11 DEGs were also included by the 159 DE-mRNAs in the GSE45589 dataset: MACF1, MARS, SF3B3, SMARCC1, BRMS1L, SMC1A, SPHK2, LIG1, CSF3, CYR61, and FGFR1OP.(B) GO functional analysis showed three terms might be enriched according to these DEGs.(C) These common DEGs showed a PPI network mainly connected by SMC1A, SMARCC1, SF3B3, LIG1, and BRMS1L.(D) The PPI network constructed by the 159 DE-mRNAs in the GSE45589 dataset (the isolated nodes were removed).
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