Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning

Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).

Citation and bibliographic coupling between authors in the field of social network analysis

Purpose:We analyzed the structure of a community of authors working in the field of social network analysis(SNA)based on citation indicators:direct citation and bibliographic coupling metrics.We observed patterns at the micro,meso,and macro levels of analysis.Design/methodology/approach:We used bibliometric network analysis,including the“temporal quantities”approach proposed to study temporal networks.Using a two-mode network linking publications with authors and a one-mode network of citations between the works,we constructed and analyzed the networks of citation and bibliographic coupling among authors.We used an iterated saturation data collection approach.Findings:At the macro-level,we observed the global structural features of citations between authors,showing that 80%of authors have not more than 15 citations from other works.At the meso-level,we extracted the groups of authors citing each other and similar to each other according to their citation patterns.We have seen a division of authors in SNA into groups of social scientists and physicists,as well as into other groups of authors from different disciplines.We found some examples of brokerage between different groups that maintained the common identity of the field.At the micro-level,we extracted authors with extremely high values of received citations,who can be considered as the most prominent authors in the field.We examined the temporal properties of the most popular authors.Research limitations:The main challenge in this approach is the resolution of the author’s name(synonyms and homonyms).We faced the author disambiguation,or“multiple personalities”(Harzing,2015)problem.To remain consistent and comparable with our previously published articles,we used the same SNA data collected up to 2018.The analysis and conclusions on the activity,productivity,and visibility of the authors are relative only to the field of SNA.Practical implications:The proposed approach can be utilized for similar objectives and identifying key structures and characteristics in other disciplines.This may potentially inspire the application of network approaches in other research areas,creating more authors collaborating in the field of SNA.Originality/value:We identified and applied an innovative approach and methods to study the structure of scientific communities,which allowed us to get the findings going beyond those obtained with other methods.We used a new approach to temporal network analysis,which is an important addition to the analysis as it provides detailed information on different measures for the authors and pairs of authors over time.

A Multilayer Network Constructed for Herb and Prescription Efficacy Analysis

Chinese Medicine(CM)has been widely used as an important avenue for disease prevention and treatment in China especially in the form of CM prescriptions combining sets of herbs to address patients’symptoms and syndromes.However,the selection and compatibility of herbs are complex and abstract due to intrinsic relationships between herbal properties and their overall functions.Network analysis is applied to demonstrate the complex relationships between individual herbal efficacy and the overall function of CM prescriptions.To illustrate their connections and correlations,prescription function(PF),prescription herb(PH),and herbal efficacy(HE)intranetworks are proposed based on CM theory to identify relationships between herbs and prescriptions.These three networks are then connected by PF-PH and PH-HE interlayer networks adopting herb dosage to form a multidimensional heterogeneous network,a Prescription-Herb-Function Network(PHFN).The network is applied to 112 classic prescriptions from Treatise on Exogenous Febrile and Miscellaneous Diseases to illustrate the application of PHFN.The PHFN is constructed including 146 functions in PF intra network,89 herbs in the PH intra network,and 163 herbal efficacies in the HE intra network.The results show that herb pairs with synergistic actions have stronger relevance,such as licorice-cassia twig,licorice-Chinese date,fresh ginger-Chinese date,etc.The integration of dosage to the network helps to indicate the main herbs for cluster analysis and automatic formulation.PHFN also reveals the internal relationships between the functions of prescriptions and composed herbal efficacies.

Analysis of Urban Agglomeration Network Structure Based on Baidu Migration Data: A Case Study of the Guangdong-Hong Kong-Macao Greater Bay Urban Agglomeration

The inter-city linkage heat data provided by Baidu Migration is employed as a characterization of inter-city linkages in order to facilitate the study of the network linkage characteristics and hierarchical structure of urban agglomeration in the Greater Bay Area through the use of social network analysis method.This is the inaugural application of big data based on location services in the study of urban agglomeration network structure,which represents a novel research perspective on this topic.The study reveals that the density of network linkages in the Greater Bay Area urban agglomeration has reached 100%,indicating a mature network-like spatial structure.This structure has given rise to three distinct communities:Shenzhen-Dongguan-Huizhou,Guangzhou-Foshan-Zhaoqing,and Zhuhai-Zhongshan-Jiangmen.Additionally,cities within the Greater Bay Area urban agglomeration play different roles,suggesting that varying development strategies may be necessary to achieve staggered development.The study demonstrates that large datasets represented by LBS can offer novel insights and methodologies for the examination of urban agglomeration network structures,contingent on the appropriate mining and processing of the data.

Weighted gene co-expression network analysis reveals similarities and differences of molecular features between dilated and ischemic cardiomyopathies

Cardiomyopathies represent the most common clinical and genetic heterogeneous group of diseases that affect the heart function.Though progress has been made to elucidate the process,molecular mechanisms of different classes of cardiomyopathies remain elusive.This paper aims to describe the similarities and differences in molecular features of dilated cardiomyopathy(DCM)and ischemic cardiomyopathy(ICM).We firstly detected the co-expressed modules using the weighted gene co-expression network analysis(WGCNA).Significant modules associated with DCM/ICM were identified by the Pearson correlation coefficient(PCC)between the modules and the phenotype of DCM/ICM.The differentially expressed genes in the modules were selected to perform functional enrichment.The potential transcription factors(TFs)prediction was conducted for transcription regulation of hub genes.Apoptosis and cardiac conduction were perturbed in DCM and ICM,respectively.TFs demonstrated that the biomarkers and the transcription regulations in DCM and ICM were different,which helps make more accurate discrimination between them at molecular levels.In conclusion,comprehensive analyses of the molecular features may advance our understanding of DCM and ICM causes and progression.Thus,this understanding may promote the development of innovative diagnoses and treatments.

Identification of key genes underlying clinical features of hepatocellular carcinoma based on weighted gene co‑expression network analysis and bioinformatics analysis

Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagnosis and treatment. Methods: GSE84598 chip data were downloaded from the GEO database, and module genes closely related to the clinical features of HCC were extracted by comprehensive weighted gene co‑expression network analysis. Hub genes were identified through protein interaction network analysis by the maximum clique centrality (MCC) algorithm;Finally, the expression of hub genes was validated by TCGA database and the Kaplan Meier plotter online database was used to evaluate the prognostic relationship between hub genes and HCC patients. Results: By comparing the gene expression data between HCC tissue samples and normal liver tissue samples, a total of 6 262 differentially expressed genes were obtained, of which 2 207 were upregulated and 4 055 were downregulated. Weighted gene co‑expression network analysis was applied to identify 120 genes of key modules. By intersecting with the differentially expressed genes, 115 candidate hub genes were obtained. The results of enrichment analysis showed that the candidate hub genes were closely related to cell mitosis, p53 signaling pathway and so on. Further application of the MCC algorithm to the protein interaction network of 115 candidate hub genes identified five hub genes, namely NUF2, RRM2, UBE2C, CDC20 and MAD2L1. Validation of hub genes by TCGA database revealed that all five hub genes were significantly upregulated in HCC tissues compared to normal liver tissues;Moreover, survival analysis revealed that high expression of hub genes was closely associated with poor prognosis in HCC patients. Conclusions: This study identifies five hub genes by combining multiple databases, which may provide directions for the clinical diagnosis and treatment of HCC.

Network Analysis of Road Traffic Crash and Rescue Operations in Federal Capital City

Abuja is witnessing an upsurge of victims from Road Traffic Crash (RTC) which is mostly due to the attendant rapid increase in the volume of vehicles, traffic jams, bad driving, over speeding, insufficient road signs and bad conditions of vehicles that ply the roads. The problem is compounded by a lack of early emergency response. Geographic Information System (GIS) based travel time model was applied in the street network analysis to identify RTC black spots that are outside the close reach of Federal Road Safety Commission (FRSC) rescue points/health facilities in Federal Capital City (FCC). Five minutes, Ten minutes and Fifteen minutes travel times were used as the impedance factor. Remote Sensing and GIS techniques were used to carry out network analysis. This was achieved by conducting the closest facility operation in the ArcGIS network analyst extension using the time of travel from each FRSC zebra point location to the RTC black spot zones/health facility. The results were presented on road network maps and bar graphs. The areas where quick response and medical facilities are insufficient were identified. It was concluded that the available health centres can sufficiently service RTC black spots in FCC, but the FRSC zebra points are insufficient which renders rescue operations inefficient and thereby exposes RTC victims to more danger. In order to ensure that there is sufficient coverage for response times, it was suggested that additional zebra points be created.

City Network Evolution Characteristics of Smart Industry: Evidence from Yangtze River Delta, China

The dual-path model of industrial evolution and spatial progression has been widely acknowledged and incorporated into the strategic planning to promote the development of urban industries and regional collaborations.However,current research on inter-enter-prise city networks mainly focuses on the single sector of flows on all enterprise branches,such as product value chains and production factors,but neglects that of particular industry department.Built upon the new economic geography and city networks theory,this paper develops a methodological framework that focuses on the analysis of city network evolution characteristics of smart industry.Particu-larly,a conceptual model of smart industry enterprise-industry-city is proposed and then applied to a case study of smart industry in the Yangtze River Delta Region,China.Using enterprise supplier-customer data,a city network of smart industry is constructed and sub-sequently analyzed with the proposed model.Findings indicate that the smart industry network in Yangtze River Delta Region exhibits a hierarchical structure and the expansion of the network presents a small-world network characteristic.The study not only makes a meth-odological contribution for revealing the industrial and spatial evolution path of the current smart industry,but also provides empirical support for the formulation of new economic development policies focused on smart industries,demonstrating the role of city clusters as carriers of regional synergistic development.

Transcriptome analysis reveals the genetic basis of crest cushion formation in duck

The Chinese crested duck is a unique duck breed having a bulbous feather shape on its duck head.However,the mechanisms involved in its formation and development are unclear.In the present study,RNA sequencing analysis was performed on the crested tissues of 6 Chinese crested ducks and the scalp tissues of 6 cherry valley ducks(CVs)from 2 developmental stages.This study identified 261 differentially expressed genes(DEGs),122 upregulated and 139 downregulated,in the E28 stage and 361 DEGs,154 upregulated and 207 downregulated in the D42 stage between CC and CV ducks.The subsequent results of weighted gene co-expression network analysis(WGCNA)revealed that the turquoise and cyan modules were associated with the crest trait in the D42 stage,meanwhile,the green,brown,and pink modules were associated with the crest trait in the E28 stage.Venn analysis of the DEGs and WGCNA showed that 145 and 45 genes are associated between the D42 and E28 stages,respectively.The expression of WNT16,BMP2,SLC35F2,SLC6A15,APOBEC2,ABHD6,TNNC2,MYL1,and TNNI2 were verified by real-time quantitative PCR.This study provides an approach to reveal the molecular mechanisms underlying the crested trait development.

Evolution and Governance of the Structure of Marine Economic Networks in China’s Coastal Areas: Based on Sea-related A-share Listed Companies

Data on discrete,isolated attributes of the marine economy are often used in traditional marine economic research.However,as the focus of urban research shifts from internal static attributes to external dynamic linkages,the importance of marine economic net-work research is beginning to emerge.The construction of the marine economic network in China’s coastal areas is necessary to change the flow of land and sea resources and optimize regional marine economic development.Employing data from headquarters and branches of sea-related A-share listed enterprises to construct the marine economic network in China,we use social network analysis(SNA)to discuss the characteristics of its evolution as of 2010,2015,and 2020 and its governance.The following results were obtained.1)In terms of topological characteristics,the scale of the marine economic network in China’s coastal areas has accelerated and expan-ded,and the connections have become increasingly close;thus,this development has complex network characteristics.2)In terms of spatial structure,the intensity of the connection fluctuates and does not form stable development support;the group structure gradually becomes clear,but the overall pattern is fragmented;there are spatial differences in marine economic agglomeration radiation;the radi-ation effect of the eastern marine economic circle is obvious;and the polarization effect of northern and southern marine economic circles is significant.On this basis,we construct a framework for the governance of a marine economic network with the market,the government,and industry as the three governing bodies.By clarifying the driving factors and building objectives of marine economic network construction,this study aims to foster the high-quality development of China’s marine economy.

Structural Characteristics and Influencing Factors of Carbon Emission Spatial Association Network:A Case Study of Yangtze River Delta City Cluster,China

City cluster is an effective platform for encouraging regionally coordinated development.Coordinated reduction of carbon emissions within city cluster via the spatial association network between cities can help coordinate the regional carbon emission management,realize sustainable development,and assist China in achieving the carbon peaking and carbon neutrality goals.This paper applies the improved gravity model and social network analysis(SNA)to the study of spatial correlation of carbon emissions in city clusters and analyzes the structural characteristics of the spatial correlation network of carbon emissions in the Yangtze River Delta(YRD)city cluster in China and its influencing factors.The results demonstrate that:1)the spatial association of carbon emissions in the YRD city cluster exhibits a typical and complex multi-threaded network structure.The network association number and density show an upward trend,indicating closer spatial association between cities,but their values remain generally low.Meanwhile,the network hierarchy and network efficiency show a downward trend but remain high.2)The spatial association network of carbon emissions in the YRD city cluster shows an obvious‘core-edge’distribution pattern.The network is centered around Shanghai,Suzhou and Wuxi,all of which play the role of‘bridges’,while cities such as Zhoushan,Ma'anshan,Tongling and other cities characterized by the remote location,single transportation mode or lower economic level are positioned at the edge of the network.3)Geographic proximity,varying levels of economic development,different industrial structures,degrees of urbanization,levels of technological innovation,energy intensities and environmental regulation are important influencing factors on the spatial association of within the YRD city cluster.Finally,policy implications are provided from four aspects:government macro-control and market mechanism guidance,structural characteristics of the‘core-edge’network,reconfiguration and optimization of the spatial layout of the YRD city cluster,and the application of advanced technologies.

Bibliometric analysis of microphthalmos and anophthalmos over 20 years:from 2004 to 2023

AIM:To conduct a bibliometric analysis of studies on microphthalmos and anophthalmos(M/A),explore research hotspots,and provide information on future research interests in this field to benefit clinicians and researchers.METHODS:Totally 751 publications related to M/A from the year 2004 to 2023 were collected from the Web of Science Core Collection database.These publications consist of both original and review articles,that are composed in English.The contributions of different countries,institutions,journals,and authors were analyzed,and network analysis was conducted by using Microsoft Excel 2021,VOSviewer,and R Studio to visualize research hotspots.RESULTS:Among all publications included,the highest number of publications came from USA(218,29.03%).China followed with 99 publications(13.18%),and England with 86 publications(11.45%).The publications from the USA had the highest frequency of citations,with 16699 citations,and the highest H-index of 49.The American Journal of Medical Genetics Part A(43,5.73%)published the largest number of papers,and the University of London had the most publications(41,5.46%).The genetic and molecular mechanisms of M/A were still unclear and the clinical intervention for M/A had gained a lot of attention as an emerging area of interest.CONCLUSION:Data have been gathered on the yearly count of published materials and citations,as well as the rise in publication trends,the efficiency of regions or countries,authors,journals,and organizations,along with the high-cited publications in M/A.The recent trend of research has shifted from genetic mechanisms to different clinical phenotypes and corresponding clinical interventions,which can give direction to future research.

Trends and hotspots in gastrointestinal neoplasms risk assessment: A bibliometric analysis from 1984 to 2022

BACKGROUND Gastrointestinal neoplasm(GN)significantly impact the global cancer burden and mortality,necessitating early detection and treatment.Understanding the evolution and current state of research in this field is vital.AIM To conducts a comprehensive bibliometric analysis of publications from 1984 to 2022 to elucidate the trends and hotspots in the GN risk assessment research,focusing on key contributors,institutions,and thematic evolution.METHODS This study conducted a bibliometric analysis of data from the Web of Science Core Collection database using the"bibliometrix"R package,VOSviewer,and CiteSpace.The analysis focused on the distribution of publications,contributions by institutions and countries,and trends in keywords.The methods included data synthesis,network analysis,and visualization of international collaboration networks.RESULTS This analysis of 1371 articles on GN risk assessment revealed a notable evolution in terms of research focus and collaboration.It highlights the United States'critical role in advancing this field,with significant contributions from institutions such as Brigham and Women's Hospital and the National Cancer Institute.The last five years,substantial advancements have been made,representing nearly 45%of the examined literature.Publication rates have dramatically increased,from 20 articles in 2002 to 112 in 2022,reflecting intensified research efforts.This study underscores a growing trend toward interdisciplinary and international collaboration,with the Journal of Clinical Oncology standing out as a key publication outlet.This shift toward more comprehensive and collaborative research methods marks a significant step in addressing GN risks.CONCLUSION This study underscores advancements in GN risk assessment through genetic analyses and machine learning and reveals significant geographical disparities in research emphasis.This calls for enhanced global collaboration and integration of artificial intelligence to improve cancer prevention and treatment accuracy,ultimately enhancing worldwide patient care.

Network Analysis of Research Project Members in Grant-in-Aid for Scientific Research in Japan

The researcher network that appeared in research projects funded by the Japanese government was analyzed. Several static and dynamic network analysis methods were applied to the data for 20 years to explore the fine structure of the researcher’s network for grants. Our analysis shows that the long-term trend of researchers’ group sizes has become smaller, particularly rapidly decreasing in recent years. Some findings on researcher behavior in joining a project have also been reported.

Transglutaminase 2 serves as a pathogenic hub gene of KRAS mutant colon cancer based on integrated analysis

BACKGROUND Colon cancer is acknowledged as one of the most common malignancies worldwide,ranking third in United States regarding incidence and mortality.Notably,approximately 40%of colon cancer cases harbor oncogenic KRAS mutations,resulting in the continuous activation of epidermal growth factor receptor signaling.AIM To investigate the key pathogenic genes in KRAS mutant colon cancer holds considerable importance.METHODS Weighted gene co-expression network analysis,in combination with additional bioinformatics analysis,were conducted to screen the key factors driving the progression of KRAS mutant colon cancer.Meanwhile,various in vitro experiments were also conducted to explore the biological function of transglutaminase 2(TGM2).RESULTS Integrated analysis demonstrated that TGM2 acted as an independent prognostic factor for progression-free survival.Immunohistochemical analysis on tissue microarrays revealed that TGM2 was associated with an elevated probability of perineural invasion in patients with KRAS mutant colon cancer.Additionally,biological roles of the key gene TGM2 was also assessed,suggesting that the downregulation of TGM2 attenuated the proliferation,invasion,and migration of the KRAS mutant colon cancer cell line.CONCLUSION This study underscores the potential significance of TGM2 in the progression of KRAS mutant colon cancer.This insight not only offers a theoretical foundation for therapeutic approaches but also highlights the need for additional clinical trials and fundamental research to support our preliminary findings.

Exploring the molecular mechanism of Suoquan pill in the treatment of diabetic kidney disease based on network pharmacology,molecular docking,in vitro experiment

Background:Diabetic kidney disease(DKD)is a microvascular complication of diabetes mellitus and is the main cause of end-stage renal failure.Suoquan pills(SQP)has a variety of pharmacological activities and multiple therapeutic effects,and it is used clinically as a basic formula for the treatment of DKD.Methods:Public databases were used to identify SQP compounds and the potential targets of SQP and DKD.A drug-component-therapeutic target network was constructed.Protein-protein interaction network analysis,Gene Ontology functional analysis,and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were used to analyse the potential molecular mechanisms of SQP based on common targets of drugs and diseases.Molecular docking simulations were conducted to confirm the binding abity of the core compounds to key targets.The efficacy and predicted molecular mechanisms of SQP were validated using cell counting kit-8 assay,flow cytometry,and western blotting with HK-2 cells as a model.Results:Network pharmacology analysis showed that 26 compounds and 207 potential targets of SQP were involved in the treatment of DKD;boldine,denudatin B,pinocembrin,kaempferoid,and quercetin were considered core compounds,and epidermal growth factor receptor(EGFR)and proto-oncogene,non-receptor tyrosine kinase(SRC)were considered key targets.Gene Ontology enrichment analysis indicated that protein phosphorylation and negative regulation of apoptotic processes are important biological processes in the treatment of DKD by SQP.Molecular docking confirmed the excellent binding abilities of boldine,denudatin B,kaempferide,and quercetin to EGFR and SRC.The results of in vitro experiments showed that treatment with an ethanolic extract of SQP significantly protected HK-2 cells from high glucose-induced cell damage.In addition,the SQP ethanol extract inhibited the phosphorylation of EGFR and SRC,suppressed the apoptosis rate,and regulated apoptosis-related proteins in HK-2 cells under high glucose stress.Conclusion:This study systematically and intuitively illustrated the possible pharmacological mechanisms of SQP against DKD through multiple components,targets,and signalling pathways,especially the inhibition of EGFR and SRC phosphorylation and apoptosis.

Discovering hidden information of gene ontology based on complex networks analysis

To resolve the ontology understanding problem, the structural features and the potential important terms of a large-scale ontology are investigated from the perspective of complex networks analysis. Through the empirical studies of the gene ontology with various perspectives, this paper shows that the whole gene ontology displays the same topological features as complex networks including ＂small world＂ and ＂scale-free＂,while some sub-ontologies have the ＂scale-free＂ property but no ＂small world＂ effect.The potential important terms in an ontology are discovered by some famous complex network centralization methods.An evaluation method based on information retrieval in MEDLINE is designed to measure the effectiveness of the discovered important terms.According to the relevant literature of the gene ontology terms,the suitability of these centralization methods for ontology important concepts discovering is quantitatively evaluated.The experimental results indicate that the betweenness centrality is the most appropriate method among all the evaluated centralization measures.

Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis

AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.

Identification of key genes involved in axon regeneration and Wallerian degeneration by weighted gene co-expression network analysis

Peripheral nerve injury repair requires a certain degree of cooperation between axon regeneration and Wallerian degeneration.Therefore,investigating how axon regeneration and degeneration work together to repair peripheral nerve injury may uncover the molecular mechanisms and signal cascades underlying peripheral nerve repair and provide potential strategies for improving the low axon regeneration capacity of the central nervous system.In this study,we applied weighted gene co-expression network analysis to identify differentially expressed genes in proximal and distal sciatic nerve segments from rats with sciatic nerve injury.We identified 31 and 15 co-expression modules from the proximal and distal sciatic nerve segments,respectively.Functional enrichment analysis revealed that the differentially expressed genes in proximal modules promoted regeneration,while the differentially expressed genes in distal modules promoted neurodegeneration.Next,we constructed hub gene networks for selected modules and identified a key hub gene,Kif22,which was up-regulated in both nerve segments.In vitro experiments confirmed that Kif22 knockdown inhibited proliferation and migration of Schwann cells by modulating the activity of the extracellular signal-regulated kinase signaling pathway.Collectively,our findings provide a comparative framework of gene modules that are co-expressed in injured proximal and distal sciatic nerve segments,and identify Kif22 as a potential therapeutic target for promoting peripheral nerve injury repair via Schwann cell proliferation and migration.All animal experiments were approved by the Institutional Animal Ethics Committee of Nantong University,China(approval No.S20210322-008)on March 22,2021.

A spillover network analysis of the global crude oil market:Evidence from the post-financial crisis era

The frequent occurrence of geopolitical crises in the post-financial crisis era is driving the rethinking behind whether the global crude oil market is still a highly connected"great pool".Using the spillover network model suggested by Baruník and Krehlík(2018),and the daily data of 31 global crude oil markets from 2009 to 2019,this study examines the return and volatility spillover effects and their timevarying behavior in six crude oil market segments at different timescales.The findings indicate that heterogeneity exists in the co-movements between global crude oil markets in the post-financial crisis era.In the medium term,both return and volatility spillover effects are not significant,which makes the diversified portfolio strategy useful.Prices in the Europe and Central Asian regions take the lead in return spillovers.In contrast,Asia-Pacific regional prices contribute the most in terms of volatility spillovers.Long-term volatility spillovers increase sharply when confronted with oil-related events in the postfinancial crisis era.Therefore,policymakers should take effective measures to prevent any large-scale risk transmission in the long run.