ArticleHuman genomics2018
Identify Down syndrome transcriptome associations using integrative analysis of microarray database and correlation-interaction network.
Article in Human genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 20 citations in OpenAlex.
- DYRK1A Up-Regulation Specifically Impairs a Presynaptic Form of Long-Term Potentiation.Life (Basel, Switzerland) · 2025Article
- Regulating the lncRNA DSCR9/RPLP2/PI3K/AKT axis: an important mechanism of Xinfeng capsules in improving rheumatoid arthritis.Frontiers in immunology · 2024Article
- Article
- Competing endogenous RNA analysis identified lncRNA DSCR9 as a novel prognostic biomarker associated with metastasis and tumor microenvironment in renal cell carcinoma.Oncology letters · 2023Article
- Effects ofFrontiers in genetics · 2023Article
- DSCR9/miR-21-5p axis inhibits pancreatic cancer proliferation and resistance to gemcitabine via BTG2 signaling.Acta biochimica et biophysica Sinica · 2022Article
- Altered Gene Expression Profiles in Neural Stem Cells Derived from Duchenne Muscular Dystrophy Patients with Intellectual Disability.Experimental neurobiology · 2021Article
- Comparative analysis of the down syndrome hippocampal non-coding RNA transcriptomes using a mouse model.Genes & genomics · 2020Article
- Existing bitter medicines for fighting 2019-nCoV-associated infectious diseases.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2020Article
- Systematic prediction of the biological functions of TAS2R10 using positive co-expression analysis.Experimental and therapeutic medicine · 2020Article
- Down syndrome and Alzheimer's disease: common molecular traits beyond the amyloid precursor protein.Aging · 2020Review
- Downregulation of miR‑224‑5p in prostate cancer and its relevant molecular mechanism via TCGA, GEO database and in silico analyses.Oncology reports · 2018Article
- Bioinformatics Investigation and Contribution of Other Chromosomes Besides Chromosome 21 in the Risk of Down Syndrome Development.Basic and clinical neuroscienceArticle
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Authors and funding
12 authors at 6 institutions in 2 countries.
Funding
Abstract
backgroundLong non-coding RNAs (lncRNAs) have previously been emerged as key players in a series of biological processes. Dysregulation of lncRNA is correlated to human diseases including neurological disorders. Here, we developed a multi-step bioinformatics analysis to study the functions of a particular Down syndrome-associated gene DSCR9 including the lncRNAs. The method is named correlation-interaction-network (COIN), based on which a pipeline is implemented. Co-expression gene network analysis and biological network analysis results are presented.
methodsWe identified the regulation function of DSCR9, a lncRNA transcribed from the Down syndrome critical region (DSCR) of chromosome 21, by analyzing its co-expression genes from over 1700 sets and nearly 60,000 public Affymetrix human U133-Plus 2 transcriptional profiling microarrays. After proper evaluations, a threshold is chosen to filter the data and get satisfactory results. Microarray data resource is from EBI database and protein-protein interaction (PPI) network information is incorporated from the most complete network databases. PPI integration strategy guarantees complete information regarding DSCR9. Enrichment analysis is performed to identify significantly correlated pathways.
resultsWe found that the most significant pathways associated with the top DSCR9 co-expressed genes were shown to be involved in neuro-active ligand-receptor interaction (GLP1R, HTR4, P2RX2, UCN3, and UTS2R), calcium signaling pathway (CACNA1F, CACNG4, HTR4, P2RX2, and SLC8A3), neuronal system (KCNJ5 and SYN1) by the KEGG, and GO analysis. The A549 and U251 cell lines with stable DSCR9 overexpression were constructed. We validated 10 DSCR9 co-expression genes by qPCR in both cell lines with over 70% accuracy.
conclusionsDSCR9 was highly correlated with genes that were known as important factors in the developments and functions of nervous system, indicating that DSCR9 may regulate neurological proteins regarding Down syndrome and other neurological-related diseases. The pipeline can be properly adjusted to other applications.
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