ArticlePloS one2011
Identification of hub genes related to the recovery phase of irradiation injury by microarray and integrated gene network analysis.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 23 citations in OpenAlex.
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- Epigenetics in radiation-induced fibrosis.Oncogene · 2015Review
- A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury.Journal of neuroscience research · 2015Article
- Total body irradiation is permissive for mesenchymal stem cell-mediated new bone formation following local transplantation.Tissue engineering. Part A · 2014Article
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- Systems level analysis and identification of pathways and networks associated with liver fibrosis.PloS one · 2014Article
- Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes.Frontiers in genetics · 2014Article
- MicroRNA-gene expression network in murine liver during Schistosoma japonicum infection.PloS one · 2013Article
- Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge.BMC bioinformatics · 2012Article
- Chapter 4: Protein interactions and disease.PLoS computational biology · 2012Article
- Mouse genetic approaches applied to the normal tissue radiation response.Frontiers in oncology · 2012Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIrradiation commonly causes long-term bone marrow injury charactertized by defective HSC self-renewal and a decrease in HSC reserve. However, the effect of high-dose IR on global gene expression during bone marrow recovery remains unknown. METHODOLOGY: Microarray analysis was used to identify differentially expressed genes that are likely to be critical for bone marrow recovery. Multiple bioinformatics analyses were conducted to identify key hub genes, pathways and biological processes. PRINCIPAL
findings1) We identified 1302 differentially expressed genes in murine bone marrow at 3, 7, 11 and 21 days after irradiation. Eleven of these genes are known to be HSC self-renewal associated genes, including Adipoq, Ccl3, Ccnd1, Ccnd2, Cdkn1a, Cxcl12, Junb, Pten, Tal1, Thy1 and Tnf; 2) These 1302 differentially expressed genes function in multiple biological processes of immunity, including hematopoiesis and response to stimuli, and cellular processes including cell proliferation, differentiation, adhesion and signaling; 3) Dynamic Gene Network analysis identified a subgroup of 25 core genes that participate in immune response, regulation of transcription and nucleosome assembly; 4) A comparison of our data with known irradiation-related genes extracted from literature showed 42 genes that matched the results of our microarray analysis, thus demonstrated consistency between studies; 5) Protein-protein interaction network and pathway analyses indicated several essential protein-protein interactions and signaling pathways, including focal adhesion and several immune-related signaling pathways.
conclusionsComparisons to other gene array datasets indicate that global gene expression profiles of irradiation damaged bone marrow show significant differences between injury and recovery phases. Our data suggest that immune response (including hematopoiesis) can be considered as a critical biological process in bone marrow recovery. Several critical hub genes that are key members of significant pathways or gene networks were identified by our comprehensive analysis.
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