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Bioinformatics Analysis of microRNA Time-Course Expression in Brown Rat (Rattus norvegicus): Spinal Cord Injury Self-Repair
- Source :
- Spine. 41(2)
- Publication Year :
- 2015
-
Abstract
- This is a bioinformatic study designed to investigate the time-course expression changes of microRNAs (miRNAs) after spinal cord injury (SCI).To investigate the mechanism of SCI self-repair at miRNAs level and target genes level.SCI results in loss of sensory and locomotor function, and SCI self-repair might provide clinical therapies; however, the mechanism of SCI self-repair remains unclear.The miRNA expression profile (GSE19890) of adult female Wistar brown rats (Rattus norvegicus) in SCI (laminectony and contusion), sham (laminectony but no contusion), and control (untreated) groups was downloaded from Gene Expression Omnibus. Totally, 35 chips were available, including five controls, five SCI-1-day, five SCI-3-day, five SCI-7-day, five sham-1-day, five sham-3-day, and five sham-7-day. Betr and limma package were used to screen time-course differentially expressed miRNAs (DEmiRNAs), followed by Bayesian hierarchical clustering (BHC), synergetic and functional enrichment analysis through BHC and cluster Profiler packages, respectively. Furthermore, STRING database and Cytoscape software were used to construct interaction networks between time-course DEmiRNAs, and GenCLip2.0 software was applied to pathway enrichment for key genes associated with nervous system.Totally, 68 time-course DEmiRNAs were identified and divided into 15 BHC clusters. Then, 100 time-course DEmiRNA pairs with synergetic function were identified, and time-course DEmiRNAs and target genes interaction networks were constructed, in which 10 genes (AKT1, VEGFA, CTNNB1, IGF1, APP, PTEN, CDC42, BDNF, SOD2, and IFNG) with highest degrees were found. Furthermore, key genes were significantly enriched in neurotrophin signaling pathway.After SCI, miRNAs might collectively regulate target genes, facilitating or inhibiting self-repair. Modulation of these miRNAs might provide novel therapies for SCI treatment.N/A.
- Subjects :
- 0301 basic medicine
Time Factors
Bioinformatics analysis
Brown rat
Biology
Bioinformatics
03 medical and health sciences
microRNA
Databases, Genetic
medicine
Animals
Cluster Analysis
Orthopedics and Sports Medicine
Gene Regulatory Networks
Rats, Wistar
Gene
Spinal cord injury
Spinal Cord Injuries
Oligonucleotide Array Sequence Analysis
Regulation of gene expression
Gene Expression Profiling
Computational Biology
Bayes Theorem
Spinal cord
medicine.disease
biology.organism_classification
Nerve Regeneration
Gene expression profiling
Disease Models, Animal
MicroRNAs
030104 developmental biology
medicine.anatomical_structure
Gene Expression Regulation
Spinal Cord
Female
Neurology (clinical)
Subjects
Details
- ISSN :
- 15281159
- Volume :
- 41
- Issue :
- 2
- Database :
- OpenAIRE
- Journal :
- Spine
- Accession number :
- edsair.doi.dedup.....8b4156c4510e60994c89638ca9aa89c3