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| Status |
Public on Aug 17, 2022 |
| Title |
Transcriptome sequencing and ceRNA (lncRNA-miRNA-mRNA) network construction identified the key molecular markers and signaling pathways of chronic thromboembolic pulmonary hypertension |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
For patients with chronic thromboembolic pulmonary hypertension (CTEPH), it can lead to death if left untreated. In this study, we attempted to identify key genes and pathways that could help in the diagnosis and treatment of CTEPH. It also provides research direction for further understanding the molecular mechanism of CTEPH.Firstly, we extract RNA from blood samples to construct the library. Then, qualified libraries were sequenced using PE100 strategy on BGIseq platform. Subsequently, the DESeq2 package in R was used to screen differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) of the CTEPH patient group and the normal control group. Afterwards, we performed functional enrichment and protein-protein interaction analysis of DEmRNAs. In addition, we also performed lncRNA-mRNA co-expression analysis and lncRNA-miRNA-mRNA network construction. A total of 437 DEmRNAs and 192 DElncRNAs were obtained. Subsequently, 205 pairs of interacting DEmRNAs and 232 pairs of lncRNA-mRNA relationship were obtained. Moreover, DEmRNAs were significantly enriched in chemokine signaling pathway, metabolic pathways, arachidonic acid metabolism and MAPK signaling pathway. In addition, only one regulation pathway of SOBP-has-miR-320b-LINC00472 was found through ceRNA network construction. In diagnostic analysis, the area under curve (AUC) of LINC00472, PIK3R6, SCN3A and TCL6 were greater than 0.7, which were 0.964, 0.893, 0.750 and 0.732, respectively. It is indicated that LINC00472, PIK3R6, SCN3A and TCL6 may as the potential diagnostic gene markers in CTEPH.
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| Overall design |
A total of 12 blood samples were included in this study, including 7 blood samples from CTEPH patients and 5 blood samples from normal control individual. Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System were used to detect the quality of the library. Qualified libraries were sequenced using PE100 strategy on BGIseq platform.
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| Contributor(s) |
Xu W, Deng M, Xie W, Liu M |
| Citation(s) |
35958401 |
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| Submission date |
Nov 16, 2021 |
| Last update date |
Aug 17, 2022 |
| Contact name |
Min Liu |
| E-mail(s) |
[email protected]
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| Organization name |
China-Japan Friendship Hospital
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| Street address |
No.2 Yinghua Dong Street, Hepingli, Chao Yang District
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100029 |
| Country |
China |
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| Platforms (1) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA780820 |
| SRA |
SRP346359 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE188938_lncRNA_gene.count.xlsx |
557.1 Kb |
(ftp)(http) |
XLSX |
| GSE188938_mRNA_gene.count.xlsx |
1.7 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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