Mining for genes related to choroidal neovascularization based on the shortest path algorithm and protein interaction information

Zhang, Jian; Sai, Yan; Zhang, Yuhang; Zhang, Qing; Chen, Xijia; Xu, Xun; Lu, Wei

doi:10.1016/j.bbagen.2016.03.015

Cited by 8 publications

(8 citation statements)

References 127 publications

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“…Many of the genes and pathways implicated in our meta-analysis have also been previously associated with AMD, CNV, and/or cataract in humans. Extracellular matrix remodeling 77 – 79 , activation of immune/inflammatory processes (particularly within the complement system) 80 – 86 , and oxidative stress 87 – 91 have all been implicated in AMD and CNV pathogenesis. Oxidative damage is also thought to be a major factor in the pathogenesis of age-related cataract 92 , 93 .…”

Section: Discussionmentioning

confidence: 99%

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Novel evidence for complement system activation in chick myopia and hyperopia models: a meta-analysis of transcriptome datasets

Riddell

2017

Sci Rep

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Myopia (short-sightedness) and hyperopia (long-sightedness) occur when the eye grows too long or short, respectively, for its refractive power. There are currently approximately 1.45 billion myopes worldwide and prevalence is rising dramatically. Although high myopia significantly increases the risk of developing a range of sight-threatening disorders, the molecular mechanisms underlying ocular growth regulation and its relationship to these secondary complications remain poorly understood. Thus, this study meta-analyzed transcriptome datasets collected in the commonly used chick model of optically-induced refractive error. Fifteen datasets (collected across five previous studies) were obtained from GEO, preprocessed in Bioconductor, and divided into 4 conditions representing early (≤1 day) and late (>1 day) myopia and hyperopia induction. Differentially expressed genes in each condition were then identified using Rank Product meta-analysis. The results provide novel evidence for transcriptional activation of the complement system during both myopia and hyperopia induction, and confirm existing literature implicating cell signaling, mitochondrial, and structural processes in refractive error. Further comparisons demonstrated that the meta-analysis results also significantly improve concordance with broader omics data types (i.e., human genetic association and animal proteomics studies) relative to previous transcriptome studies, and show extensive similarities with the genes linked to age-related macular degeneration, choroidal neovascularization, and cataract.

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Section: Discussionmentioning

confidence: 99%

“… 79 Genes linked to CNV were sourced from Supplementary Material I of Zhang et al . 86 Genes associated with POAG and its endophenotypes were sourced from Supplementary Table S1 of Iglesias et al . 107 Genes associated with cataract were sourced from Cat-Map 108 on 2017/02/26.…”

Section: Methodsmentioning

confidence: 99%

Novel evidence for complement system activation in chick myopia and hyperopia models: a meta-analysis of transcriptome datasets

Riddell

2017

Sci Rep

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“…We kept genes with MIS value greater than 900 and obtained 27 genes. Finally, for each of the 27 genes, we calculated the MFS and selected genes with an MFS value greater than 0.9, resulting in a final list of 11 3 BioMed Research International CNV-related genes, which is totally different from previous discoveries [22]. The selected numbers of putative genes in different steps of LHD are shown in Table 1, and the detailed information of the 11 final candidate CNV-associated genes is listed in Table 2.…”

Section: Resultsmentioning

confidence: 99%

“…In recent years, with the development of high-throughput sequencing, bioinformatics algorithms have provided us a novel and more effective approach for identifying CNV-associated genes. In 2016, a systematic prediction [ 22 ] based on all the identified CNV-related genes, protein–protein interaction (PPI) network, and shortest path algorithm identified various genes associated with CNV, including ANK1 , ITGA4 , and CD44 . Most of these genes have already been identified to contribute to abnormal angiogenesis or antiangiogenesis in the choroid [ 22 ], validating the efficacy and accuracy of computational prediction on disease-associated genes.…”

Section: Introductionmentioning

confidence: 99%

Identification of Novel Choroidal Neovascularization‐Related Genes Using Laplacian Heat Diffusion Algorithm

Sheng

Cai

Cheng

et al. 2021

BioMed Research International

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Choroidal neovascularization (CNV) is a type of eye disease that can cause vision loss. In recent years, many studies have attempted to investigate the major pathological processes and molecular pathogenic mechanisms of CNV. Because many diseases are related to genes, the genes associated with CNV need to be identified. In this study, we proposed a network-based approach for identifying novel CNV-associated genes. To execute such method, we first employed a protein-protein interaction network reported in STRING. Then, we applied a network diffusion algorithm, Laplacian heat diffusion, on this network by selecting validated CNV-related genes as the seed nodes. As a result, some novel genes that had unknown but strong relationships with validated genes were identified. Furthermore, we used a screening procedure to extract the most essential genes. Eleven latent CNV-related genes were finally obtained. Extensive analyses were performed to confirm that these genes are novel CNV-related genes.

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“…Some trials were also conducted in the bioinformatics field. Zhang et al [ 25 ] presented a specific computational routine for the identification of CNV-associated genes, indicating the efficacy and accuracy of computational application in such field.…”

Section: Introductionmentioning

confidence: 99%

Computational Approach to Investigating Key GO Terms and KEGG Pathways Associated with CNV

Luo

Yan

Zhang

et al. 2018

BioMed Research International

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Choroidal neovascularization (CNV) is a severe eye disease that leads to blindness, especially in the elderly population. Various endogenous and exogenous regulatory factors promote its pathogenesis. However, the detailed molecular biological mechanisms of CNV have not been fully revealed. In this study, by using advanced computational tools, a number of key gene ontology (GO) terms and KEGG pathways were selected for CNV. A total of 29 validated genes associated with CNV and 17,639 nonvalidated genes were encoded based on the features derived from the GO terms and KEGG pathways by using the enrichment theory. The widely accepted feature selection method—maximum relevance and minimum redundancy (mRMR)—was applied to analyze and rank the features. An extensive literature review for the top 45 ranking features was conducted to confirm their close associations with CNV. Identifying the molecular biological mechanisms of CNV as described by the GO terms and KEGG pathways may contribute to improving the understanding of the pathogenesis of CNV.

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Mining for genes related to choroidal neovascularization based on the shortest path algorithm and protein interaction information

Cited by 8 publications

References 127 publications

Novel evidence for complement system activation in chick myopia and hyperopia models: a meta-analysis of transcriptome datasets

Novel evidence for complement system activation in chick myopia and hyperopia models: a meta-analysis of transcriptome datasets

Identification of Novel Choroidal Neovascularization‐Related Genes Using Laplacian Heat Diffusion Algorithm

Computational Approach to Investigating Key GO Terms and KEGG Pathways Associated with CNV

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