2022 Fiscal Year Research-status Report
Trans-omics analysis of the difference between Cortical and Trabecular bone.
| Project/Area Number |
21K09998
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| Research Institution | Niigata University |
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Principal Investigator |
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| Co-Investigator(Kenkyū-buntansha) |
加来 賢 新潟大学, 医歯学系, 准教授 (30547542)
魚島 勝美 新潟大学, 医歯学系, 教授 (50213400)
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| Project Period (FY) |
2021-04-01 – 2024-03-31
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| Keywords | trans-omics / extracellular matrix / bone phenotype / bone regeneration |
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| Outline of Annual Research Achievements |
In this study, a bioinformatic methodology employing trans-omics analysis and the Matrisome database is being employed to investigate the differences in extracellular matrix composition and the associated regulatory networks between cortical and trabecular bone.
During this period, FASTQ files analysis workflow was stablished and Gene Read Counts trials were performed. RNA sequencing environment for Weighted gene co-expression network analysis setting was completed to identify modules or groups of genes that exhibit similar expression patterns across different samples. This method assigns weights to gene-gene connections based on the strength of their co-expression relationships, allowing the identification of highly interconnected gene modules and the functional relationships and regulatory mechanisms underlying biological processes by identifying key genes within modules and elucidating their potential roles in specific biological pathways or diseases.
DESeq2/Limma for fold change and gene list environment was set for Pathway analysis to perform enrichment analysis and visualize the results, to gain insights into the bone biological systems and to identify potential targets for therapeutic intervention.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
Progressing Rather Smoothly
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| Strategy for Future Research Activity |
Mouse samples of Cortical and trabecular bone will be isolated, Mass Spectrometry will be performed, data will be annotated with the UniProt database. All identified proteins will be further curated by the Matrisome database.
Pathway analysis/Enrichment analysis, GO termas and KEGG pathway will be performed to gain insights into the underlying biological processes and interactions among genes or proteins within bone biological system. A systematic examination of gene expression, protein-protein interaction data will be performed to identify and interpret the enrichment of genes or proteins in specific biological pathways or functional categories. This analysis will provide a comprehensive view of the molecular mechanisms and signaling pathways involved bone differentiation and may help us to identify key pathways and molecules that play crucial roles in these complex biological phenomena and facilitating the development of targeted therapies and interventions.
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| Causes of Carryover |
The reasons for incurring an amount to be used in the next fiscal year and the associated usage plan are multifaceted. Firstly, budget allocation and planning are crucial to ensure efficient resource utilization and meet organizational goals and objectives.
During this period of time, effort where allocated mainly in the computational analysis and software settings.
For the upcoming fiscal year, it is expected to use the bugged in the laboratory materials and samples.
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