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 empiri...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.展开更多
A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology(GO)annotations together.The operation system was based on Debian Linux 3.1,with Apache as the web server and Mysql data...A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology(GO)annotations together.The operation system was based on Debian Linux 3.1,with Apache as the web server and Mysql database as the data storage system.FASTA files with GO annotations were taken as the sequence source for blast alignment,which were formatted by wu-formatdb program.The GoBlast system includes three Bioperl modules in Perl:a data input module,a data process module and a data output module.A GoBlast query starts with an amino acid or nucleotide sequence.It ends with an output in an html page,presenting high scoring gene products which are of a high homology to the queried sequence and listing associated GO terms beside respective gene poducts.A simple click on a GO term leads to the detailed explanation of the specific gene function.This avails gene function prediction by Blast.GoBlast can be a very useful tool for functional genome research and is available for free at http://bioq.org/goblast.展开更多
Background Clustering is a useful exploratory technique for interpreting gene expression data to reveal groups of genes sharing common functional attributes. Biologists frequently face the problem of choosing an appro...Background Clustering is a useful exploratory technique for interpreting gene expression data to reveal groups of genes sharing common functional attributes. Biologists frequently face the problem of choosing an appropriate algorithm. We aimed to provide a standalone, easily accessible and biologically oriented criterion for expression data clustering evaluation. Methods An external criterion utilizing annotation based similarities between genes is proposed in this work. Gene ontology information is employed as the annotation source. Comparisons among six widely used clustering algorithms over various types of gene expression data sets were carried out based on the criterion proposed. Results The rank of these algorithms given by the criterion coincides with our common knowledge. Single-linkage has significantly poorer performance, even worse than the random algorithm. Ward＇s method archives the best performance in most cases. Conclusions The criterion proposed has a strong ability to distinguish among different clustering algorithms with different distance measurements. It is also demonstrated that analyzing main contributors of the criterion may offer some guidelines in finding local compact clusters. As an addition, we suggest using Ward＇s algorithm for gene expression data analysis.展开更多
To better know FM （Fusarium moniliforme） induced genes in maize ear rot, GO （gene ontology） method was performed to analyze detail physiological functions in the defensive response after pathogen infection. This g...To better know FM （Fusarium moniliforme） induced genes in maize ear rot, GO （gene ontology） method was performed to analyze detail physiological functions in the defensive response after pathogen infection. This gene annotation system was widely used to investigate large numbers of genes involving in real active role or regulator in cell response. First of all, differentially expressed genes were isolated by using genechip platform at 96 h post-inoculation with FM in maize inbred Bt-1. In total, 482 differentially expressed unique genes were screened out in inbred Bt-1 when compared to mock-inoculated bract tissues. Then, each gene was annotated to define functional class by GO method. Finally, these large FM-responsive genes with significant differentially change were sorted into cellular component, molecular function and biological process with complicated network by molecular annotation system. The demonstrated information in the GO analysis could provide another view for understanding the molecular mechanism and indicate a deeply complicated network with gene function underlying disease development in the host tissue. The findings in this study provide important bases to probe the molecular processes, the alteration of metabolism and the immune mechanism upon the FM infection in maize.展开更多
Background Although biomedical ontologies have standardized the representation of gene products across species and databases, a method for determining the functional similarities of gene products has not yet been deve...Background Although biomedical ontologies have standardized the representation of gene products across species and databases, a method for determining the functional similarities of gene products has not yet been developed. Methods We proposed a new semantic similarity measure based on Gene Ontology that considers the semantic influences from all of the ancestor terms in a graph. Our measure was compared with Resnik＇s measure in two applications, which were based on the association of the measure used with the gene co-expression and the protein- protein interactions. Results The results showed a considerable association between the semantic similarity and the expression correlation and between the semantic similarity and the protein-protein interactions, and our measure performed the best overall. Conclusion These results revealed the potential value of our newly proposed semantic similarity measure in studying the functional relevance of gene products.展开更多
Clustering is perhaps one of the most widely used tools for microarray data analysis. Proposed roles for genes of unknown function are inferred from clusters of genes similarity expressed across many biological condit...Clustering is perhaps one of the most widely used tools for microarray data analysis. Proposed roles for genes of unknown function are inferred from clusters of genes similarity expressed across many biological conditions. However, whether function annotation by similarity metrics is reliable or not and to what extent the similarity in gene expression patterns is useful for annotation of gene functions, has not been evaluated. This paper made a comprehensive research on the correlation between the similarity of expression data and of gene functions using Gene Ontology. It has been found that although the similarity in expression patterns and the similarity in gene functions are significantly dependent on each other, this association is rather weak. In addition, among the three categories of Gene Ontology, the similarity of expression data is more useful for cellular component annotation than for biological process and molecular function. The results presented are interesting for the gene functions prediction research area.展开更多
Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive...Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive thyroid-related cell lines cultured under simulated microgravity.Methods:Five thyroid-related cell lines—normal thyrocytes(Nthy-ori 3-1),papillary thyroid cancer(PTC)cells(SNU-790,TPC-1),poorly differentiated thyroid cancer cell(BCPAP),and anaplastic thyroid cancer cell(SNU-80)—were cultured under simulated microgravity(10-3 g)using a clinostat.Differentially expressed genes(DEGs)were analyzed using cDNA microarray,followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.Results:DEG analysis under simulated microgravity revealed distinct gene expression profiles by gravity condition,with 2980 DEGs in SNU-790,1033 in BCPAP,562 in TPC-1,477 in Nthy-ori 3-1,and 246 in SNU-80,as confirmed by hierarchical clustering.In PTC cell lines(SNU-790,TPC-1),G2–M phase–related genes were upregulated.In non-PTC cell lines(BCPAP,SNU-80),genes associated with innate immune response,Toll-like receptor signaling,were upregulated,whereas Hypoxia-Inducible Factor 1-alpha(HIF-1α)signaling-related genes were downregulated.Additionally,under simulated microgravity,significant migration was observed in SNU-790(3×104 cells)and BCPAP(2×104 and 3×104),while significant invasion occurred in SNU-790,Nthy-ori 3-1,and BCPAP at a seeding density of 2×104.Other conditions showed no significant differences.Conclusion:This study comprehensively evaluates the effects of simulated microgravity using a diverse panel of thyroid-related cell lines.Thesefindings provide valuable insight into how microgravity could influence cancer biology,emphasizing the importance of further research on cancer behavior in space environments and its implications for human health during long-term space missions.展开更多
The exact mechanisms associated with secondary brain damage following traumatic brain injury(TBI)remain unclear;therefore,identifying the critical molecular mechanisms involved in TBI is essential.The m RNA expression...The exact mechanisms associated with secondary brain damage following traumatic brain injury(TBI)remain unclear;therefore,identifying the critical molecular mechanisms involved in TBI is essential.The m RNA expression microarray GSE2871 was downloaded from the Gene Expression Omnibus(GEO)repository.GSE2871 comprises a total of 31 cerebral cortex samples,including two post-TBI time points.The microarray features eight control and seven TBI samples,from 4 hours post-TBI,and eight control and eight TBI samples from 24 hours post-TBI.In this bioinformatics-based study,109 and 66 differentially expressed genes(DEGs)were identified in a Sprague-Dawley(SD)rat TBI model,4 and 24 hours post-TBI,respectively.Functional enrichment analysis showed that the identified DEGs were significantly enriched in several terms,such as positive regulation of nuclear factor-κB transcription factor activity,mitogen-activated protein kinase signaling pathway,negative regulation of apoptotic process,and tumor necrosis factor signaling pathway.Moreover,the hub genes with high connectivity degrees were primarily related to inflammatory mediators.To validate the top five hub genes,a rat model of TBI was established using the weight-drop method,and real-time quantitative polymerase chain reaction analysis of the cerebral cortex was performed.The results showed that compared with control rats,Tnf-α,c-Myc,Spp1,Cxcl10,Ptprc,Egf,Mmp9,and Lcn2 were upregulated,and Fn1 was downregulated in TBI rats.Among these hub genes,Fn1,c-Myc,and Ptprc may represent novel biomarkers or therapeutic targets for TBI.These identified pathways and key genes may provide insights into the molecular mechanisms of TBI and provide potential treatment targets for patients with TBI.This study was approved by the Experimental Animal Ethics Committee of the First Affiliated Hospital of Nanchang University,China(approval No.003)in January 2016.展开更多
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 lev...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.展开更多
Soybean cyst nematode （SCN） is one of the most devastating pathogen for soybean. Therefore, identiifcation of resistant germplasm resources and resistant genes is needed to improve SCN resistance for soybean. Soybea...Soybean cyst nematode （SCN） is one of the most devastating pathogen for soybean. Therefore, identiifcation of resistant germplasm resources and resistant genes is needed to improve SCN resistance for soybean. Soybean varieties Huipizhiheidou and Wuzhaiheidou were distributed in China and exhibited broad spectrums of resistance to various SCN races. In this study, these two resistant varieties, combined with standard susceptible varieties （Lee and Essex）, were utilized to identify the differentially expressed transcripts after infection with SCN race 4 between resistant and susceptible reactions by using the Affymetrix Soybean Genome GeneChip. Comparative analyses indicated that 21 common genes changed signiifcantly in the resistant group, of which 16 increased and 5 decreased. However, 12 common genes changed signiifcantly in the susceptible group, of which 9 increased and 3 decreased. Additionally, 27 genes were found in common between resistant and susceptible reactions. The 21 signiifcantly changed genes in resistant reaction were associated with disease and defense, cell structure, transcription, metabolism, and signal transduction. The fold induction of 4 from the 21 genes was conifrmed by quantitative RT-PCR （qRT-PCR） analysis. Moreover, the gene ontology （GO） enrichment analyses demonstrated the serine family amino acid metabolic process and arginine metabolic process may play important roles in SCN resistance. This study provided a new insight on the genetic basis of soybean resistance to SCN race 4, and the identiifed resistant or resistant-related genes are potentially useful for SCN-resistance breeding in soybean.展开更多
Exosomes exhibit complex biological functions and mediate a variety of biological processes,such as promoting axonal regeneration and functional recove ry after injury.Long non-coding RNAs(IncRNAs)have been reported t...Exosomes exhibit complex biological functions and mediate a variety of biological processes,such as promoting axonal regeneration and functional recove ry after injury.Long non-coding RNAs(IncRNAs)have been reported to play a crucial role in axonal regeneration.Howeve r,the role of the IncRNA-microRNAmessenger RNA(mRNA)-competitive endogenous RNA(ceRNA)network in exosome-mediated axonal regeneration remains unclear.In this study,we performed RNA transcriptome sequencing analysis to assess mRNA expression patterns in exosomes produced by cultured fibroblasts(FC-EXOs)and Schwann cells(SCEXOs).Diffe rential gene expression analysis,Gene Ontology analysis,Kyoto Encyclopedia of Genes and Genomes analysis,and protein-protein intera ction network analysis were used to explo re the functions and related pathways of RNAs isolated from FC-EXOs and SC-EXOs.We found that the ribosome-related central gene Rps5 was enriched in FC-EXOs and SC-EXOs,which suggests that it may promote axonal regeneration.In addition,using the miRWalk and Starbase prediction databases,we constructed a regulatory network of ceRNAs targeting Rps5,including 27 microRNAs and five IncRNAs.The ceRNA regulatory network,which included Ftx and Miat,revealed that exsosome-derived Rps5 inhibits scar formation and promotes axonal regeneration and functional recovery after nerve injury.Our findings suggest that exosomes derived from fibro blast and Schwann cells could be used to treat injuries of peripheral nervous system.展开更多
While the peripheral nervous system has regenerative ability,restoration of sufficient function remains a challenge.Vimentin has been shown to be localized in axonal growth fronts and associated with nerve regeneratio...While the peripheral nervous system has regenerative ability,restoration of sufficient function remains a challenge.Vimentin has been shown to be localized in axonal growth fronts and associated with nerve regeneration,including myelination,neuroplasticity,kinase signaling in nerve axoplasm,and cell migration;however,the mechanisms regulating its expression within Schwann cell（SC） remain unexplored.The aim of this study was to profile the spatial and temporal expression profile of micro RNA（mi RNA） in a regenerating rat sciatic nerve after transection,and explore the potential role of mi R-138-5 p targeting vimentin in SC proliferation and migration.A rat sciatic nerve transection model,utilizing a polyethylene nerve guide,was used to investigate mi RNA expression at 7,14,30,60,and 90 days during nerve regeneration.Relative levels of mi RNA expression were determined using microarray analysis and subsequently validated with quantitative real-time polymerase chain reaction.In vitro assays were conducted with cultured Schwann cells transfected with mi RNA mimics and assessed for migratory and proliferative potential.The top seven dysregulated mi RNAs reported in this study have been implicated in cell migration elsewhere,and GO and KEGG analyses predicted activities essential to wound healing.Transfection of one of these,mi RNA-138-5 p,into SCs reduced cell migration and proliferation.mi R-138-5 p has been shown to directly target vimentin in cancer cells,and the luciferase assay performed here in rat Schwann cells confirmed it.These results detail a role of mi R-138-5 p in rat peripheral nerve regeneration and expand on reports of it as an important regulator in the peripheral nervous system.展开更多
Molluscan shell color has received persistent attention for its distinctive diversity and complexity. In the present study, six transcriptome libraries obtained from two developmental stages, pre-pigmentation and post...Molluscan shell color has received persistent attention for its distinctive diversity and complexity. In the present study, six transcriptome libraries obtained from two developmental stages, pre-pigmentation and post-pigmentation, were used for paired-end sequencing in the bay scallop Argopecten irradians. In total, 289 839 646 paired-end reads were assembled into 70 929 transcripts. Using BLASTX and BLASTN, 30 896 unigenes were successfully annotated against the SWISS-PROT, NR, and KOG database. Gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes classification identified numbers of unigenes involved in biomineralization and pigmentation. Digital gene expression analysis revealed that melanin, trace metal elements and porphyrins are potentially involved in shell coloration of A. irradians.展开更多
Olfactory ensheathing cells(OECs) from the olfactory bulb(OB) and the olfactory mucosa(OM) have the capacity to repair nerve injury. However, the difference in the therapeutic effect between OB-derived OECs and OM-der...Olfactory ensheathing cells(OECs) from the olfactory bulb(OB) and the olfactory mucosa(OM) have the capacity to repair nerve injury. However, the difference in the therapeutic effect between OB-derived OECs and OM-derived OECs remains unclear. In this study, we extracted OECs from OB and OM and compared the gene and protein expression profiles of the cells using transcriptomics and non-quantitative proteomics techniques. The results revealed that both OB-derived OECs and OM-derived OECs highly expressed genes and proteins that regulate cell growth, proliferation, apoptosis and vascular endothelial cell regeneration. The differentially expressed genes and proteins of OB-derived OECs play a key role in regulation of nerve regeneration and axon regeneration and extension, transmission of nerve impulses and response to axon injury. The differentially expressed genes and proteins of OM-derived OECs mainly participate in the positive regulation of inflammatory response, defense response, cytokine binding, cell migration and wound healing. These findings suggest that differentially expressed genes and proteins may explain why OB-derived OECs and OM-derived OECs exhibit different therapeutic roles. This study was approved by the Animal Ethics Committee of the General Hospital of Ningxia Medical University(approval No. 2017-073) on February 13, 2017.展开更多
Soybean is a major cash crop in the world, and its oil content was one of the very important traits. Therefore, the study of gene mapping for oil content in soybean is very important for breeding application. At prese...Soybean is a major cash crop in the world, and its oil content was one of the very important traits. Therefore, the study of gene mapping for oil content in soybean is very important for breeding application. At present, at least 130 QTL loci for soybean oil content have been published; however, the mapping results of oil content were dispersed and a coalescent public map should be established to integrate the published QTLs, and to more efficiently mine genes based on the meta- analysis method of the bioinformatics tools. This study was to construct an integrated map of QTLs for soybean oil content and accelerate the application of bioinformation resource related to oil content improvement in the practice of soybean breeding. We collected information of 130 QTLs reported over the past 20 yr for soybean oil content and used the Software BioMercator 2.1 to project QTLs from their own maps onto a reference map, which was an early-integrated map constructed by Song （2004） for oil-content quantitative trait loci （QTLs） in soybean. Gene mining was performed based on the meta-analysis by running the local ver. GENSCAN and InterProScan. The confidence interval of QTLs was efficaciously narrowed using the meta-analysis method, and 25 consensus QTLs were mapped on the reference map. Using a local version of GENSCAN, 12 805 sequences in the consensus QTL intervals were predicted. With BLAST, these predicted sequences were aligned to gene sequences from the International Protein Index database using InterProScan locally. Thirteen predicted genes were in the class of the geme ontology （GO） accession （0006631）, which were involved in the fatty acid metabolic process. These genes were analyzed using BLAST at the NCBI website to examine whether they were related to oil content. Six genes were found in the oil-synthesis pathway. Twenty-five consensus QTLs and six genes were found in the oil-synthesis pathway. These results would lay the foundation for marker-assisted selection and mapping QTL precisely, and these genes will facilitate the researches on the gene mining of oil synthesis and molecular breeding in soybean.展开更多
AIM:To identify metastatic genes and mi RNAs and to investigate the metastatic mechanism of uveal melanoma(UVM).METHODS:GSE27831,GSE39717,and GSE73652 gene expression profiles were downloaded from the Gene Expression ...AIM:To identify metastatic genes and mi RNAs and to investigate the metastatic mechanism of uveal melanoma(UVM).METHODS:GSE27831,GSE39717,and GSE73652 gene expression profiles were downloaded from the Gene Expression Omnibus(GEO)database,and the limma R package was used to identify differentially expressed genes(DEGs).Gene Ontology(GO)term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis were performed using the DAVID online tool.A comprehensive list of interacting DEGs was constructed using the Search Tool for the Retrieval of Interacting Genes(STRING)database and Cytoscape software.The Cytoscape MCODE plug-in was used to identify clustered sub-networks and modules of hub genes from the proteinprotein interaction network.GEPIA online software was used for survival analysis of UVM patients(n=80)from the The Cancer Genome Atlas(TCGA)cohort.Oncomi R online software was used to find that the mi RNAs were associated with UVM prognosis from the TCGA cohort.Target Scan Human 7.2 software was then used to identify the mi RNAs targeting the genes.RESULTS:There were 1600 up-regulated genes and 1399 down-regulated genes.The up-regulated genes were mainly involved in protein translation in the cytosol,whereas the down-regulated genes were correlated with extracellular matrix organization and cell adhesion in the extracellular space.Among the 2999 DEGs,five genes,Znf391,Mrps11,Htra3,Sulf2,and Smarcd3 were potential predictors of UVM prognosis.Otherwise,three mi RNAs,hsa-mi R-509-3-5 p,hsa-mi R-513 a-5 p,and hsa-mi R-1269 a were associated with UVM prognosis.CONCLUSION:After analyzing the metastasis-related enriched terms and signaling pathways,the up-regulated DEGs are mainly involved in protein synthesis and cell proliferation by ribosome and mitogen-activated protein kinase(MAPK)pathways.However,the down-regulated DEGs are mainly involved in processes that reduced cell-cell adhesion and promoted cell migration in the extracellular matrix through PI3 K-Akt signaling pathway,focal adhesion,and extracellular matrix-receptor interactions.Bioinformatics and interaction analysis may provide new insights on the events leading up to the development and progression of UVM.展开更多
The differential expression of genes in HepG2 cells caused by UC001 kfo RNAi was investigated using RNA-seq. HepG2 cells were infected by Lenti-sh UC001 kfo lentivirus particles. The expression of UC001 kfo m RNA in t...The differential expression of genes in HepG2 cells caused by UC001 kfo RNAi was investigated using RNA-seq. HepG2 cells were infected by Lenti-sh UC001 kfo lentivirus particles. The expression of UC001 kfo m RNA in the HepG2-sh UC001 kfo cell line was detected by real-time PCR. RNA-seq technology was used to identify the difference in the expression of genes regulated by lnc RNA UC001 kfo in the HepG2 cell line. Gene ontology and signaling pathway analysis were performed to reveal the biological functions of the genes encoding of significantly different m RNAs. The results showed that m RNAs were differentially expressed between the HepG2-sh UC001 kfo cell line and the HepG2 cell line. The UC001 kfo m RNA was significantly down-regulated in the stable cell line HepG2-sh UC001kfo（P〈0.001）. Additionally, we found 19 signaling pathways or functional classifications encompassing 30 genes that played a role in cancer characteristics, cell adhesion, invasion and migration. The results also showed that the expression of many genes associated with cancer cell invasion and metastasis was decreased with the down-regulation of the lnc RNA UC001 kfo. Lnc RNA UC001 kfo may play a role in regulating cancer cell invasion and metastasis. It was suggested that m RNAs were differentially expressed in the HepG2 cell line after the down-regulation of lnc RNA-UC001 kfo. Some took part in the extracellular matrix, cell adhesion, motility, growth, and localization. The genes encoding of differentially expressed m RNAs may participate in cell invasion and metastasis.展开更多
Oral clefts, the most frequent congenital birth defects in humans, are multifactorial disorders caused by genetic and environmental factors. Epidemiological studies point to different etiologies underlying the oral cl...Oral clefts, the most frequent congenital birth defects in humans, are multifactorial disorders caused by genetic and environmental factors. Epidemiological studies point to different etiologies underlying the oral cleft phenotypes, cleft lip(CL),CL and/or palate(CL/P) and cleft palate(CP). More than 350 genes have syndromic and/or nonsyndromic oral cleft associations in humans. Although genes related to genetic disorders associated with oral cleft phenotypes are known, a gap between detecting these associations and interpretation of their biological importance has remained. Here, using a gene ontology analysis approach, we grouped these candidate genes on the basis of different functional categories to gain insight into the genetic etiology of oral clefts. We identified different genetic profiles and found correlations between the functions of gene products and oral cleft phenotypes. Our results indicate inherent differences in the genetic etiologies that underlie oral cleft phenotypes and support epidemiological evidence that genes associated with CL/P are both developmentally and genetically different from CP only, incomplete CP, and submucous CP. The epidemiological differences among cleft phenotypes may reflect differences in the underlying genetic causes. Understanding the different causative etiologies of oral clefts is important as it may lead to improvements in diagnosis, counseling, and prevention.展开更多
The initial mechanical damage of a spinal cord injury(SCI)triggers a progressive secondary injury cascade,which is a complicated process integrating multiple systems and cells.It is crucial to explore the molecular an...The initial mechanical damage of a spinal cord injury(SCI)triggers a progressive secondary injury cascade,which is a complicated process integrating multiple systems and cells.It is crucial to explore the molecular and biological process alterations that occur after SCI for therapy development.The differences between the rostral and caudal regions around an SCI lesion have received little attention.Here,we analyzed the differentially expressed genes between rostral and caudal sites after injury to determine the biological processes in these two segments after SCI.We identified a set of differentially expressed genes,including Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1,between rostral and caudal regions at different time points following SCI.Functional enrichment analysis indicated that these genes were involved in response to mechanical stimulus,blood vessel development,and brain development.We then chose Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1 for quantitative real-time PCR and Fn1 for immunostaining validation.Our results indicate alterations in different biological events enriched in the rostral and caudal lesion areas,providing new insights into the pathology of SCI.展开更多
Common aquaculture practices subject fish to a variety of acute and chronic stressors.Such stressors are inherent in aquaculture production but can adversely affect survival,growth,immune response,reproductive capacit...Common aquaculture practices subject fish to a variety of acute and chronic stressors.Such stressors are inherent in aquaculture production but can adversely affect survival,growth,immune response,reproductive capacity,and behavior.Understanding the biological mechanisms underlying stress responses helps with methods to alleviate the negative effects through better aquaculture practices,resulting in improved animal welfare and production efficiency.In the present study,transcriptome sequencing of liver and kidney was performed in silver pomfret(Pampus argenteus)subjected to handling stress versus controls.A total of 162.19 million clean reads were assembled to 30339 unigenes.The quality of the assembly was high,with an N50 length of 2472 bases.For function classification and pathway assignment,the unigenes were categorized into three GO(gene ontology)categories,twenty-six clusters of egg NOG(evolutionary genealogy of genes:non-supervised orthologous groups)function categories,and thirty-eight KEGG(Kyoto Encyclopedia of Genes and Genomes)pathways.Stress affected different functional groups of genes in the tissues studied.Differentially expressed genes were mainly involved in metabolic pathways(carbohydrate metabolism,lipid metabolism,amino-acid metabolism,uptake of cofactors and vitamins,and biosynthesis of other secondary metabolites),environmental information processing(signaling molecules and their interactions),organismal systems(endocrine system,digestive system),and disease(immune,neurodegenerative,endocrine and metabolic diseases).This is the first reported analysis of genome-wide transcriptome in P.argenteus,and the findings expand our understanding of the silver pomfret genome and gene expression in association with stress.The results will be useful to future analyses of functional genes and studies of healthy artificial breeding in P.argenteus and other related fish species.展开更多
基金The National Basic Research Program of China (973Program) (No.2005CB321802)Program for New Century Excellent Talents in University (No.NCET-06-0926)the National Natural Science Foundation of China (No.60873097,90612009)
文摘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.
文摘A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology(GO)annotations together.The operation system was based on Debian Linux 3.1,with Apache as the web server and Mysql database as the data storage system.FASTA files with GO annotations were taken as the sequence source for blast alignment,which were formatted by wu-formatdb program.The GoBlast system includes three Bioperl modules in Perl:a data input module,a data process module and a data output module.A GoBlast query starts with an amino acid or nucleotide sequence.It ends with an output in an html page,presenting high scoring gene products which are of a high homology to the queried sequence and listing associated GO terms beside respective gene poducts.A simple click on a GO term leads to the detailed explanation of the specific gene function.This avails gene function prediction by Blast.GoBlast can be a very useful tool for functional genome research and is available for free at http://bioq.org/goblast.
文摘Background Clustering is a useful exploratory technique for interpreting gene expression data to reveal groups of genes sharing common functional attributes. Biologists frequently face the problem of choosing an appropriate algorithm. We aimed to provide a standalone, easily accessible and biologically oriented criterion for expression data clustering evaluation. Methods An external criterion utilizing annotation based similarities between genes is proposed in this work. Gene ontology information is employed as the annotation source. Comparisons among six widely used clustering algorithms over various types of gene expression data sets were carried out based on the criterion proposed. Results The rank of these algorithms given by the criterion coincides with our common knowledge. Single-linkage has significantly poorer performance, even worse than the random algorithm. Ward＇s method archives the best performance in most cases. Conclusions The criterion proposed has a strong ability to distinguish among different clustering algorithms with different distance measurements. It is also demonstrated that analyzing main contributors of the criterion may offer some guidelines in finding local compact clusters. As an addition, we suggest using Ward＇s algorithm for gene expression data analysis.
基金Acknowledgments This research was supported by the Natural National Science Foundation of China （No. 30571173, No. 31201274）, National High Technology Research and Development Program of China （863 Program） （No. 2012AA10A307）.
文摘To better know FM （Fusarium moniliforme） induced genes in maize ear rot, GO （gene ontology） method was performed to analyze detail physiological functions in the defensive response after pathogen infection. This gene annotation system was widely used to investigate large numbers of genes involving in real active role or regulator in cell response. First of all, differentially expressed genes were isolated by using genechip platform at 96 h post-inoculation with FM in maize inbred Bt-1. In total, 482 differentially expressed unique genes were screened out in inbred Bt-1 when compared to mock-inoculated bract tissues. Then, each gene was annotated to define functional class by GO method. Finally, these large FM-responsive genes with significant differentially change were sorted into cellular component, molecular function and biological process with complicated network by molecular annotation system. The demonstrated information in the GO analysis could provide another view for understanding the molecular mechanism and indicate a deeply complicated network with gene function underlying disease development in the host tissue. The findings in this study provide important bases to probe the molecular processes, the alteration of metabolism and the immune mechanism upon the FM infection in maize.
文摘Background Although biomedical ontologies have standardized the representation of gene products across species and databases, a method for determining the functional similarities of gene products has not yet been developed. Methods We proposed a new semantic similarity measure based on Gene Ontology that considers the semantic influences from all of the ancestor terms in a graph. Our measure was compared with Resnik＇s measure in two applications, which were based on the association of the measure used with the gene co-expression and the protein- protein interactions. Results The results showed a considerable association between the semantic similarity and the expression correlation and between the semantic similarity and the protein-protein interactions, and our measure performed the best overall. Conclusion These results revealed the potential value of our newly proposed semantic similarity measure in studying the functional relevance of gene products.
基金Project supported by the Key Program of Basic Research of Science ＆ Technology Commission of Shanghai Municipality （No. 04dz14004） and the Shanghai Natural Science Foundation （No. 03ZR14065）. Dedicated to Professor Xikui Jiang on the occasion of his 80th birthday.
文摘Clustering is perhaps one of the most widely used tools for microarray data analysis. Proposed roles for genes of unknown function are inferred from clusters of genes similarity expressed across many biological conditions. However, whether function annotation by similarity metrics is reliable or not and to what extent the similarity in gene expression patterns is useful for annotation of gene functions, has not been evaluated. This paper made a comprehensive research on the correlation between the similarity of expression data and of gene functions using Gene Ontology. It has been found that although the similarity in expression patterns and the similarity in gene functions are significantly dependent on each other, this association is rather weak. In addition, among the three categories of Gene Ontology, the similarity of expression data is more useful for cellular component annotation than for biological process and molecular function. The results presented are interesting for the gene functions prediction research area.
文摘Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive thyroid-related cell lines cultured under simulated microgravity.Methods:Five thyroid-related cell lines—normal thyrocytes(Nthy-ori 3-1),papillary thyroid cancer(PTC)cells(SNU-790,TPC-1),poorly differentiated thyroid cancer cell(BCPAP),and anaplastic thyroid cancer cell(SNU-80)—were cultured under simulated microgravity(10-3 g)using a clinostat.Differentially expressed genes(DEGs)were analyzed using cDNA microarray,followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.Results:DEG analysis under simulated microgravity revealed distinct gene expression profiles by gravity condition,with 2980 DEGs in SNU-790,1033 in BCPAP,562 in TPC-1,477 in Nthy-ori 3-1,and 246 in SNU-80,as confirmed by hierarchical clustering.In PTC cell lines(SNU-790,TPC-1),G2–M phase–related genes were upregulated.In non-PTC cell lines(BCPAP,SNU-80),genes associated with innate immune response,Toll-like receptor signaling,were upregulated,whereas Hypoxia-Inducible Factor 1-alpha(HIF-1α)signaling-related genes were downregulated.Additionally,under simulated microgravity,significant migration was observed in SNU-790(3×104 cells)and BCPAP(2×104 and 3×104),while significant invasion occurred in SNU-790,Nthy-ori 3-1,and BCPAP at a seeding density of 2×104.Other conditions showed no significant differences.Conclusion:This study comprehensively evaluates the effects of simulated microgravity using a diverse panel of thyroid-related cell lines.Thesefindings provide valuable insight into how microgravity could influence cancer biology,emphasizing the importance of further research on cancer behavior in space environments and its implications for human health during long-term space missions.
基金supported by the National Natural Science Foundation of China,Nos.81860409(to ZF),81660382(to ZF)Graduate Students Innovation Fund Project in Jiangxi Province of China,No.YC2019-B036(to YLT)。
文摘The exact mechanisms associated with secondary brain damage following traumatic brain injury(TBI)remain unclear;therefore,identifying the critical molecular mechanisms involved in TBI is essential.The m RNA expression microarray GSE2871 was downloaded from the Gene Expression Omnibus(GEO)repository.GSE2871 comprises a total of 31 cerebral cortex samples,including two post-TBI time points.The microarray features eight control and seven TBI samples,from 4 hours post-TBI,and eight control and eight TBI samples from 24 hours post-TBI.In this bioinformatics-based study,109 and 66 differentially expressed genes(DEGs)were identified in a Sprague-Dawley(SD)rat TBI model,4 and 24 hours post-TBI,respectively.Functional enrichment analysis showed that the identified DEGs were significantly enriched in several terms,such as positive regulation of nuclear factor-κB transcription factor activity,mitogen-activated protein kinase signaling pathway,negative regulation of apoptotic process,and tumor necrosis factor signaling pathway.Moreover,the hub genes with high connectivity degrees were primarily related to inflammatory mediators.To validate the top five hub genes,a rat model of TBI was established using the weight-drop method,and real-time quantitative polymerase chain reaction analysis of the cerebral cortex was performed.The results showed that compared with control rats,Tnf-α,c-Myc,Spp1,Cxcl10,Ptprc,Egf,Mmp9,and Lcn2 were upregulated,and Fn1 was downregulated in TBI rats.Among these hub genes,Fn1,c-Myc,and Ptprc may represent novel biomarkers or therapeutic targets for TBI.These identified pathways and key genes may provide insights into the molecular mechanisms of TBI and provide potential treatment targets for patients with TBI.This study was approved by the Experimental Animal Ethics Committee of the First Affiliated Hospital of Nanchang University,China(approval No.003)in January 2016.
基金Supported by the National Natural Science Foundation of China(No.81271019No.61463046)Gansu Province Science Foundation for Youths(No.145RJYA282)
文摘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.
基金supported by the National Nature Science Foundation of China (31301345 and 31171576)the CAAS Innovation Project, the Genetically Modified Organisms Breeding Major Projects, China (2009ZX08004-003B and 2011ZX08004-003)the Key Technologies R&D Program of China during the 12th Five-Year Plan period (2011BAD35B06-3)
文摘Soybean cyst nematode （SCN） is one of the most devastating pathogen for soybean. Therefore, identiifcation of resistant germplasm resources and resistant genes is needed to improve SCN resistance for soybean. Soybean varieties Huipizhiheidou and Wuzhaiheidou were distributed in China and exhibited broad spectrums of resistance to various SCN races. In this study, these two resistant varieties, combined with standard susceptible varieties （Lee and Essex）, were utilized to identify the differentially expressed transcripts after infection with SCN race 4 between resistant and susceptible reactions by using the Affymetrix Soybean Genome GeneChip. Comparative analyses indicated that 21 common genes changed signiifcantly in the resistant group, of which 16 increased and 5 decreased. However, 12 common genes changed signiifcantly in the susceptible group, of which 9 increased and 3 decreased. Additionally, 27 genes were found in common between resistant and susceptible reactions. The 21 signiifcantly changed genes in resistant reaction were associated with disease and defense, cell structure, transcription, metabolism, and signal transduction. The fold induction of 4 from the 21 genes was conifrmed by quantitative RT-PCR （qRT-PCR） analysis. Moreover, the gene ontology （GO） enrichment analyses demonstrated the serine family amino acid metabolic process and arginine metabolic process may play important roles in SCN resistance. This study provided a new insight on the genetic basis of soybean resistance to SCN race 4, and the identiifed resistant or resistant-related genes are potentially useful for SCN-resistance breeding in soybean.
基金supported by the National Natural Science Foundation of China,No.81870975(to SZ)。
文摘Exosomes exhibit complex biological functions and mediate a variety of biological processes,such as promoting axonal regeneration and functional recove ry after injury.Long non-coding RNAs(IncRNAs)have been reported to play a crucial role in axonal regeneration.Howeve r,the role of the IncRNA-microRNAmessenger RNA(mRNA)-competitive endogenous RNA(ceRNA)network in exosome-mediated axonal regeneration remains unclear.In this study,we performed RNA transcriptome sequencing analysis to assess mRNA expression patterns in exosomes produced by cultured fibroblasts(FC-EXOs)and Schwann cells(SCEXOs).Diffe rential gene expression analysis,Gene Ontology analysis,Kyoto Encyclopedia of Genes and Genomes analysis,and protein-protein intera ction network analysis were used to explo re the functions and related pathways of RNAs isolated from FC-EXOs and SC-EXOs.We found that the ribosome-related central gene Rps5 was enriched in FC-EXOs and SC-EXOs,which suggests that it may promote axonal regeneration.In addition,using the miRWalk and Starbase prediction databases,we constructed a regulatory network of ceRNAs targeting Rps5,including 27 microRNAs and five IncRNAs.The ceRNA regulatory network,which included Ftx and Miat,revealed that exsosome-derived Rps5 inhibits scar formation and promotes axonal regeneration and functional recovery after nerve injury.Our findings suggest that exosomes derived from fibro blast and Schwann cells could be used to treat injuries of peripheral nervous system.
文摘While the peripheral nervous system has regenerative ability,restoration of sufficient function remains a challenge.Vimentin has been shown to be localized in axonal growth fronts and associated with nerve regeneration,including myelination,neuroplasticity,kinase signaling in nerve axoplasm,and cell migration;however,the mechanisms regulating its expression within Schwann cell（SC） remain unexplored.The aim of this study was to profile the spatial and temporal expression profile of micro RNA（mi RNA） in a regenerating rat sciatic nerve after transection,and explore the potential role of mi R-138-5 p targeting vimentin in SC proliferation and migration.A rat sciatic nerve transection model,utilizing a polyethylene nerve guide,was used to investigate mi RNA expression at 7,14,30,60,and 90 days during nerve regeneration.Relative levels of mi RNA expression were determined using microarray analysis and subsequently validated with quantitative real-time polymerase chain reaction.In vitro assays were conducted with cultured Schwann cells transfected with mi RNA mimics and assessed for migratory and proliferative potential.The top seven dysregulated mi RNAs reported in this study have been implicated in cell migration elsewhere,and GO and KEGG analyses predicted activities essential to wound healing.Transfection of one of these,mi RNA-138-5 p,into SCs reduced cell migration and proliferation.mi R-138-5 p has been shown to directly target vimentin in cancer cells,and the luciferase assay performed here in rat Schwann cells confirmed it.These results detail a role of mi R-138-5 p in rat peripheral nerve regeneration and expand on reports of it as an important regulator in the peripheral nervous system.
基金Supported by the China Agriculture Research System(No.CARS-49)the Science and Technology Service Network Initiative of Chinese Academy of Sciences
文摘Molluscan shell color has received persistent attention for its distinctive diversity and complexity. In the present study, six transcriptome libraries obtained from two developmental stages, pre-pigmentation and post-pigmentation, were used for paired-end sequencing in the bay scallop Argopecten irradians. In total, 289 839 646 paired-end reads were assembled into 70 929 transcripts. Using BLASTX and BLASTN, 30 896 unigenes were successfully annotated against the SWISS-PROT, NR, and KOG database. Gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes classification identified numbers of unigenes involved in biomineralization and pigmentation. Digital gene expression analysis revealed that melanin, trace metal elements and porphyrins are potentially involved in shell coloration of A. irradians.
基金supported by Key Research Projects of Ningxia Hui Autonomous Region of China,No.2018BCG01002(to HCX)the Natural Science Foundation of Ningxia Hui Autonomous Region of China,No.NZ17150(to PY)。
文摘Olfactory ensheathing cells(OECs) from the olfactory bulb(OB) and the olfactory mucosa(OM) have the capacity to repair nerve injury. However, the difference in the therapeutic effect between OB-derived OECs and OM-derived OECs remains unclear. In this study, we extracted OECs from OB and OM and compared the gene and protein expression profiles of the cells using transcriptomics and non-quantitative proteomics techniques. The results revealed that both OB-derived OECs and OM-derived OECs highly expressed genes and proteins that regulate cell growth, proliferation, apoptosis and vascular endothelial cell regeneration. The differentially expressed genes and proteins of OB-derived OECs play a key role in regulation of nerve regeneration and axon regeneration and extension, transmission of nerve impulses and response to axon injury. The differentially expressed genes and proteins of OM-derived OECs mainly participate in the positive regulation of inflammatory response, defense response, cytokine binding, cell migration and wound healing. These findings suggest that differentially expressed genes and proteins may explain why OB-derived OECs and OM-derived OECs exhibit different therapeutic roles. This study was approved by the Animal Ethics Committee of the General Hospital of Ningxia Medical University(approval No. 2017-073) on February 13, 2017.
基金supported by the Transgenic Specific Technology Programs,China (2009ZX08009-013B)
文摘Soybean is a major cash crop in the world, and its oil content was one of the very important traits. Therefore, the study of gene mapping for oil content in soybean is very important for breeding application. At present, at least 130 QTL loci for soybean oil content have been published; however, the mapping results of oil content were dispersed and a coalescent public map should be established to integrate the published QTLs, and to more efficiently mine genes based on the meta- analysis method of the bioinformatics tools. This study was to construct an integrated map of QTLs for soybean oil content and accelerate the application of bioinformation resource related to oil content improvement in the practice of soybean breeding. We collected information of 130 QTLs reported over the past 20 yr for soybean oil content and used the Software BioMercator 2.1 to project QTLs from their own maps onto a reference map, which was an early-integrated map constructed by Song （2004） for oil-content quantitative trait loci （QTLs） in soybean. Gene mining was performed based on the meta-analysis by running the local ver. GENSCAN and InterProScan. The confidence interval of QTLs was efficaciously narrowed using the meta-analysis method, and 25 consensus QTLs were mapped on the reference map. Using a local version of GENSCAN, 12 805 sequences in the consensus QTL intervals were predicted. With BLAST, these predicted sequences were aligned to gene sequences from the International Protein Index database using InterProScan locally. Thirteen predicted genes were in the class of the geme ontology （GO） accession （0006631）, which were involved in the fatty acid metabolic process. These genes were analyzed using BLAST at the NCBI website to examine whether they were related to oil content. Six genes were found in the oil-synthesis pathway. Twenty-five consensus QTLs and six genes were found in the oil-synthesis pathway. These results would lay the foundation for marker-assisted selection and mapping QTL precisely, and these genes will facilitate the researches on the gene mining of oil synthesis and molecular breeding in soybean.
基金Supported by the Natural Science Foundation for Young Scholars of Shanxi(No.201801D221256)the Science Foundation for Young Scholars of Shanxi Eye Hospital(No.Q201803)。
文摘AIM:To identify metastatic genes and mi RNAs and to investigate the metastatic mechanism of uveal melanoma(UVM).METHODS:GSE27831,GSE39717,and GSE73652 gene expression profiles were downloaded from the Gene Expression Omnibus(GEO)database,and the limma R package was used to identify differentially expressed genes(DEGs).Gene Ontology(GO)term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis were performed using the DAVID online tool.A comprehensive list of interacting DEGs was constructed using the Search Tool for the Retrieval of Interacting Genes(STRING)database and Cytoscape software.The Cytoscape MCODE plug-in was used to identify clustered sub-networks and modules of hub genes from the proteinprotein interaction network.GEPIA online software was used for survival analysis of UVM patients(n=80)from the The Cancer Genome Atlas(TCGA)cohort.Oncomi R online software was used to find that the mi RNAs were associated with UVM prognosis from the TCGA cohort.Target Scan Human 7.2 software was then used to identify the mi RNAs targeting the genes.RESULTS:There were 1600 up-regulated genes and 1399 down-regulated genes.The up-regulated genes were mainly involved in protein translation in the cytosol,whereas the down-regulated genes were correlated with extracellular matrix organization and cell adhesion in the extracellular space.Among the 2999 DEGs,five genes,Znf391,Mrps11,Htra3,Sulf2,and Smarcd3 were potential predictors of UVM prognosis.Otherwise,three mi RNAs,hsa-mi R-509-3-5 p,hsa-mi R-513 a-5 p,and hsa-mi R-1269 a were associated with UVM prognosis.CONCLUSION:After analyzing the metastasis-related enriched terms and signaling pathways,the up-regulated DEGs are mainly involved in protein synthesis and cell proliferation by ribosome and mitogen-activated protein kinase(MAPK)pathways.However,the down-regulated DEGs are mainly involved in processes that reduced cell-cell adhesion and promoted cell migration in the extracellular matrix through PI3 K-Akt signaling pathway,focal adhesion,and extracellular matrix-receptor interactions.Bioinformatics and interaction analysis may provide new insights on the events leading up to the development and progression of UVM.
基金supported by National Natural Science Foudation of China(No.U1404309)
文摘The differential expression of genes in HepG2 cells caused by UC001 kfo RNAi was investigated using RNA-seq. HepG2 cells were infected by Lenti-sh UC001 kfo lentivirus particles. The expression of UC001 kfo m RNA in the HepG2-sh UC001 kfo cell line was detected by real-time PCR. RNA-seq technology was used to identify the difference in the expression of genes regulated by lnc RNA UC001 kfo in the HepG2 cell line. Gene ontology and signaling pathway analysis were performed to reveal the biological functions of the genes encoding of significantly different m RNAs. The results showed that m RNAs were differentially expressed between the HepG2-sh UC001 kfo cell line and the HepG2 cell line. The UC001 kfo m RNA was significantly down-regulated in the stable cell line HepG2-sh UC001kfo（P〈0.001）. Additionally, we found 19 signaling pathways or functional classifications encompassing 30 genes that played a role in cancer characteristics, cell adhesion, invasion and migration. The results also showed that the expression of many genes associated with cancer cell invasion and metastasis was decreased with the down-regulation of the lnc RNA UC001 kfo. Lnc RNA UC001 kfo may play a role in regulating cancer cell invasion and metastasis. It was suggested that m RNAs were differentially expressed in the HepG2 cell line after the down-regulation of lnc RNA-UC001 kfo. Some took part in the extracellular matrix, cell adhesion, motility, growth, and localization. The genes encoding of differentially expressed m RNAs may participate in cell invasion and metastasis.
基金supported by the Japan Society for the Promotion of Science(JSPS)KAKENHI(grant numbers 25670774,15K11004)to NF
文摘Oral clefts, the most frequent congenital birth defects in humans, are multifactorial disorders caused by genetic and environmental factors. Epidemiological studies point to different etiologies underlying the oral cleft phenotypes, cleft lip(CL),CL and/or palate(CL/P) and cleft palate(CP). More than 350 genes have syndromic and/or nonsyndromic oral cleft associations in humans. Although genes related to genetic disorders associated with oral cleft phenotypes are known, a gap between detecting these associations and interpretation of their biological importance has remained. Here, using a gene ontology analysis approach, we grouped these candidate genes on the basis of different functional categories to gain insight into the genetic etiology of oral clefts. We identified different genetic profiles and found correlations between the functions of gene products and oral cleft phenotypes. Our results indicate inherent differences in the genetic etiologies that underlie oral cleft phenotypes and support epidemiological evidence that genes associated with CL/P are both developmentally and genetically different from CP only, incomplete CP, and submucous CP. The epidemiological differences among cleft phenotypes may reflect differences in the underlying genetic causes. Understanding the different causative etiologies of oral clefts is important as it may lead to improvements in diagnosis, counseling, and prevention.
基金supported by Postgraduate Research&Practice Innovation Program of Jiangsu Province,No.KYCX-2065(to XMC).
文摘The initial mechanical damage of a spinal cord injury(SCI)triggers a progressive secondary injury cascade,which is a complicated process integrating multiple systems and cells.It is crucial to explore the molecular and biological process alterations that occur after SCI for therapy development.The differences between the rostral and caudal regions around an SCI lesion have received little attention.Here,we analyzed the differentially expressed genes between rostral and caudal sites after injury to determine the biological processes in these two segments after SCI.We identified a set of differentially expressed genes,including Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1,between rostral and caudal regions at different time points following SCI.Functional enrichment analysis indicated that these genes were involved in response to mechanical stimulus,blood vessel development,and brain development.We then chose Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1 for quantitative real-time PCR and Fn1 for immunostaining validation.Our results indicate alterations in different biological events enriched in the rostral and caudal lesion areas,providing new insights into the pathology of SCI.
基金Supported by the Natural Science Foundation of Shanghai City(No.12ZR1455000)the Central Nonprofit Basic Scientific Research Project for the Scientific Research Institutes of China(No.East 2014Y01)
文摘Common aquaculture practices subject fish to a variety of acute and chronic stressors.Such stressors are inherent in aquaculture production but can adversely affect survival,growth,immune response,reproductive capacity,and behavior.Understanding the biological mechanisms underlying stress responses helps with methods to alleviate the negative effects through better aquaculture practices,resulting in improved animal welfare and production efficiency.In the present study,transcriptome sequencing of liver and kidney was performed in silver pomfret(Pampus argenteus)subjected to handling stress versus controls.A total of 162.19 million clean reads were assembled to 30339 unigenes.The quality of the assembly was high,with an N50 length of 2472 bases.For function classification and pathway assignment,the unigenes were categorized into three GO(gene ontology)categories,twenty-six clusters of egg NOG(evolutionary genealogy of genes:non-supervised orthologous groups)function categories,and thirty-eight KEGG(Kyoto Encyclopedia of Genes and Genomes)pathways.Stress affected different functional groups of genes in the tissues studied.Differentially expressed genes were mainly involved in metabolic pathways(carbohydrate metabolism,lipid metabolism,amino-acid metabolism,uptake of cofactors and vitamins,and biosynthesis of other secondary metabolites),environmental information processing(signaling molecules and their interactions),organismal systems(endocrine system,digestive system),and disease(immune,neurodegenerative,endocrine and metabolic diseases).This is the first reported analysis of genome-wide transcriptome in P.argenteus,and the findings expand our understanding of the silver pomfret genome and gene expression in association with stress.The results will be useful to future analyses of functional genes and studies of healthy artificial breeding in P.argenteus and other related fish species.
