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A systems genetics ...
A systems genetics approach to revealing the Pdgfb molecular network of the retina
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- Li, Shasha (author)
- Binzhou Med Univ, Med & Pharm Res Ctr, Shandong, Peoples R China.;Univ Tennessee, Hlth Sci Ctr, Dept Genet Genom & Informat, Memphis, TN USA.
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- Xu, Fuyi (author)
- Univ Tennessee, Hlth Sci Ctr, Dept Genet Genom & Informat, Memphis, TN USA.
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- Liu, Lin (author)
- Binzhou Med Univ, Med & Pharm Res Ctr, Shandong, Peoples R China.
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- Ju, Rong (author)
- Sun Yat Sen Univ, Zhongshan Ophthalm Ctr, State Key Lab Ophthalmol, Guangzhou, Guangdong, Peoples R China.
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- Bergquist, Jonas (author)
- Uppsala universitet,Analytisk kemi,Binzhou Med Univ, Med & Pharm Res Ctr, Shandong, Peoples R China
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- Zheng, Qing Yin (author)
- Case Western Reserve Univ, Sch Med, Transformat Otol & Neurosci Ctr, Cleveland, OH USA.;Case Western Reserve Univ, Sch Med, Dept Otolaryngol, Cleveland, OH USA.
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- Mi, Jia (author)
- Binzhou Med Univ, Med & Pharm Res Ctr, Shandong, Peoples R China.
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- Lu, Lu (author)
- Univ Tennessee, Hlth Sci Ctr, Dept Genet Genom & Informat, Memphis, TN USA.
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Li, Xuri (author)
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- Tian, Geng (author)
- Binzhou Med Univ, Med & Pharm Res Ctr, Shandong, Peoples R China.
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Binzhou Med Univ, Med & Pharm Res Ctr, Shandong, Peoples R China;Univ Tennessee, Hlth Sci Ctr, Dept Genet Genom & Informat, Memphis, TN USA. Univ Tennessee, Hlth Sci Ctr, Dept Genet Genom & Informat, Memphis, TN USA. (creator_code:org_t)
- MOLECULAR VISION, 2020
- 2020
- English.
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In: Molecular Vision. - : MOLECULAR VISION. - 1090-0535. ; 26, s. 459-471
- Related links:
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https://urn.kb.se/re...
Abstract
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- Purpose: Platelet-derived growth factor (PDGF) signaling is well known to be involved in vascular retinopathies. Among the PDGF family, the subunit B (PDGFB) protein is considered a promising therapeutic target. This study aimed to identify the genes and potential pathways through which PDGFB affects retinal phenotypes by using a systems genetics approach. Methods: Gene expression data had been previously generated in a laboratory for the retinas of 75 C57BL/6J(B6) X DBA/2J (BXD) recombinant inbred (RI) strains. Using this data, the genetic correlation method was used to identify genes correlated to Pdgfb. A correlation between intraocular pressure (TOP) and Pdgfb was calculated based on the Pearson correlation coefficient. A gene set enrichment analysis and the STRING database were used to evaluate gene function and to construct protein-protein interaction (PPI) networks. Results: Pdgfb was a cis-regulated gene in the retina; its expression had a significant correlation with IOP (r = 0.305; p value = 0.012). The expression levels of 2,477 genes also had significant correlations with Pdgfb expressions (p<0.05), among which Atf4 was the most positively correlated (r = 0.628; p value = 1.29e-10). Thus, Atf4 was highly expressed in the retina and shared the transcription factor (TF)Hnf4a binding site with Pdgfb. Gene Ontology and a pathway analysis revealed that Pdgfb and its covariates were highly involved in mitogen-activated protein kinase (MAPK) and vascular endothelial growth factor (VEGF) pathways. A generated gene network indicated that Pdgfb was directly connected to and interacted with other genes with similar biologic functions. Conclusions: A systems genetics analysis revealed that Pdgfb had significant interactions with Atf4 and other genes in MAPK and VEGF pathways, through which Pdgfb was important in maintaining retina function. These findings provided basic information regarding the Pdgfb regulation mechanism and potential therapy for vascular retinopathies.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
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- By the author/editor
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Li, Shasha
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Xu, Fuyi
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Liu, Lin
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Ju, Rong
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Bergquist, Jonas
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Zheng, Qing Yin
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show more...
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Mi, Jia
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Lu, Lu
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Li, Xuri
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Tian, Geng
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show less...
- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Cancer and Oncol ...
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
- Articles in the publication
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Molecular Vision
- By the university
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Uppsala University