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prognosis and molecular characteristics of clear-cell renal cell carcinoma: a multi-center integrated analysisof microbiome, metabolome, and transcriptome data

《医学前沿(英文)》 doi: 10.1007/s11684-023-1029-3

摘要: Microbiome subsets determine tumor prognosis and molecular characteristics of clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptome data

关键词: tumor prognosis molecular     Microbiome subsets determine     center analysis microbiome     transcriptome data    

METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN

《农业科学与工程前沿(英文)》 2021年 第8卷 第2期

摘要:

Metabolites, especially secondary metabolites, are very important in the adaption of tea plants and the quality of tea products. Here, we focus on the seasonal variation in metabolites of fresh tea shoots and their regulatory mechanism at the transcriptional level. The metabolic profiles of fresh tea shoots of 10 tea accessions collected in spring, summer, and autumn were analyzed using ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry. We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome analysis. Multivariate statistical analysis indicates that metabolites were distinctly different with seasonal alternation. Flavonoids, amino acids, organic acids and alkaloids were the predominant metabolites. Levels of most key genes and downstream compounds in the flavonoid pathway were lowest in spring but the catechin quality index was highest in spring. The regulatory pathway was explored by constructing a metabolite correlation network and a weighted gene co-expression network.

 

Comparative transcriptome analysis of purple-fleshed sweet potato provides insights into the molecular

Hongyuan ZHAO, Shanshan ZHANG, Feibing WANG, Ning ZHAO, Shaozhen HE, Qingchang LIU, Hong ZHAI

《农业科学与工程前沿(英文)》 2018年 第5卷 第2期   页码 214-225 doi: 10.15302/J-FASE-2018219

摘要: Sweet potato, , is a globally important food crop. The purple-fleshed sweet potato, rich in anthocyanins, has great potential for both nutritional and pharmaceutical uses. In this study, we characterized the root transcriptomes of the purple-fleshed sweet potato cv. Jingshu 6 and its mutant JS6-5 with high anthocyanin content by high-throughput RNA sequencing. A total of 22873364 and 27955097 high quality reads were obtained from Jingshu 6 and JS6-5, respectively, and assembled into 35592 unigenes. In all, we obtained 1566 differentially expressed genes (DEGs). Among them, 994 were upregulated and 572 were downregulated in JS6-5 compared to the expression in Jingshu 6. A total of 1436 DEGs were annotated, in which 847 DEGs had gene ontology (GO) terms and 329 DEGs were assigned to 84 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most importantly, 23 differentially expressed genes and 24 transcription factors were identified as candidate genes involved in anthocyanin biosynthesis. In addition, 2349 SSRs were detected. This study not only provides the candidate genes but also provides insights into the molecular mechanism of anthocyanin biosynthesis in sweet potato.

关键词: anthocyanin     gene expression     mutant     purple-fleshed sweet potato     transcriptome    

Transcriptome analysis of wheat grain using RNA-Seq

Liu WEI,Zhihui WU,Yufeng ZHANG,Dandan GUO,Yuzhou XU,Weixia CHEN,Haiying ZHOU,Mingshan YOU,Baoyun LI

《农业科学与工程前沿(英文)》 2014年 第1卷 第3期   页码 214-222 doi: 10.15302/J-FASE-2014024

摘要: With the increase in consumer demand, wheat grain quality improvement has become a focus in China and worldwide. Transcriptome analysis is a powerful approach to research grain traits and elucidate their genetic regulation. In this study, two cDNA libraries from the developing grain and leaf-stem components of bread wheat cultivar, Nongda211, were sequenced using Roche/454 technology. There were 1061274 and 1516564 clean reads generated from grain and leaf-stem, respectively. A total of 61393 high-quality unigenes were obtained with an average length of 1456 bp after assembly. The analysis of the 61393 unigenes involved in the biological processes of the grain showed that there were 7355 differentially expressed genes upregulated in the grain library. Gene ontology enrichment and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that many transcription products and transcription factors associated with carbohydrate and protein metabolism were abundantly expressed in the grain. These results contribute to excavate genes associated with wheat quality and further study how they interact.

关键词: transcriptome analysis     wheat grain     differentially expressed genes     enrichment analysis    

Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during

null

《医学前沿(英文)》 2016年 第10卷 第3期   页码 297-310 doi: 10.1007/s11684-016-0452-0

摘要:

Studies on coding genes, miRNAs, and lncRNAs during erythroid development have been performed in recent years. However, analysis focusing on the integration of the three RNA types has yet to be done. In the present study, we compared the dynamics of coding genes, miRNA, and lncRNA expression profiles. To explore dynamic changes in erythropoiesis and potential mechanisms that control these changes in the transcriptome level, we took advantage of high throughput sequencing technologies to obtain transcriptome data from cord blood hematopoietic stem cells and the following four erythroid differentiation stages, as well as from mature red blood cells. Results indicated that lncRNAs were promising cell marker candidates for erythroid differentiation. Clustering analysis classified the differentially expressed genes into four subtypes that corresponded to dynamic changes during stemness maintenance, mid-differentiation, and maturation. Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation, and especially associated with heme metabolism and responses to oxygen species and DNA damage. These regulatory interactions were displayed in a comprehensive network, thereby inferring correlations between RNAs and their associated functions. These data provided a substantial resource for the study of normal erythropoiesis, which will permit further investigation and understanding of erythroid development and acquired erythroid disorders.

关键词: erythroid differentiation     hematopoietic stem cell     RNA-seq     miRNA     lncRNA    

METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN

Chen-Kai JIANG, De-Jiang NI, Ming-Zhe YAO, Jian-Qiang MA, Liang CHEN

《农业科学与工程前沿(英文)》   页码 215-230 doi: 10.15302/J-FASE-2021382

摘要: Metabolites, especially secondary metabolites, are very important in the adaption of tea plants and the quality of tea products. Here, we focus on the seasonal variation in metabolites of fresh tea shoots and their regulatory mechanism at the transcriptional level. The metabolic profiles of fresh tea shoots of 10 tea accessions collected in spring, summer, and autumn were analyzed using ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry. We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome analysis. Multivariate statistical analysis indicates that metabolites were distinctly different with seasonal alternation. Flavonoids, amino acids, organic acids and alkaloids were the predominant metabolites. Levels of most key genes and downstream compounds in the flavonoid pathway were lowest in spring but the catechin quality index was highest in spring. The regulatory pathway was explored by constructing a metabolite correlation network and a weighted gene co-expression network.

关键词: harvest season     metabolites     tea shoots     transcriptomics     untargeted metabolomics    

Transcriptome resources and genome-wide marker development for Japanese larch (

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

《农业科学与工程前沿(英文)》 2014年 第1卷 第1期   页码 77-84 doi: 10.15302/J-FASE-2014010

摘要: While the differential responses of trees to changes in climatic and environmental conditions have been demonstrated as they age, the underlying mechanisms and age control of tree growth and development are complex and poorly understood particularly at a molecular level. In this paper, we present a transcriptome analysis of , a deciduous conifer that is widely-grown in the northern hemisphere and of significant ecological and economic value. Using high-throughput RNA sequencing, we obtained about 26 million reads from the stems of 1-, 2-, 5-, 10-, 25- and 50-year-old trees. Combining these with the published Roche 454 sequencing reads and the expressed sequence tags (both mainly from embryogenic cell cultures), we assembled 26670549 reads into 146786 transcripts, of which we annotated 79182 to support investigations of the molecular basis of tree aging and adaption, somatic embryogenesis and wood formation. Using these sequences we also identified many single-nucleotide polymorphisms, simple sequence repeats, and insertion and deletion markers to assist breeding and genetic diversity studies of .

关键词: Larix     transcriptome     age     wood formation     somatic embryogenesis     molecular marker    

TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

null

《医学前沿(英文)》 2015年 第9卷 第3期   页码 322-330 doi: 10.1007/s11684-015-0408-9

摘要:

This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma (HCC) by comparing the global gene expression profiles between tumors and their corresponding non-tumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated (CENPF and FOXM1) and downregulated (CLEC4GCRHBP, and CLEC1B) genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs. Further examination for the mechanistic overview by subjecting significantly upregulated and downregulated genes to gene set enrichment analysis showed that different cellular pathways were involved. This study provides useful information on the transcriptomic landscape and molecular mechanism of hepatocarcinogenesis for development of new biomarkers and further in-depth characterization.

关键词: TCGA     whole-transcriptome sequencing     HCC     liver cancer    

Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome

null

《医学前沿(英文)》 2016年 第10卷 第1期   页码 61-75 doi: 10.1007/s11684-016-0436-0

摘要:

The latent expression pattern of Epstein-Barr Virus (EBV) genes in nasopharyngeal carcinoma (NPC) has been extensively investigated, and the expression of several lytic genes in NPC has been reported. However, comprehensive information through EBV transcriptome analysis in NPC is limited. We performed paired-end RNA-seq to systematically and comprehensively characterize the expression of EBV genes in NPC tissue and C666-1 NPC cell line, which consistently carries EBV. In addition to the transcripts restricted to type II latency infection, the type III latency EBNA3s genes and a substantial number of lytic genes, such as BZLF1, BRLF1, and BMRF1, were detected through RNA-seq and were further verified in C666-1 cells and NPC tissue through real-time PCR. We also performed clustering analysis to classify NPC patient groups in terms of EBV gene expression, which presented two subtypes of NPC samples. Results revealed interesting patterns of EBV gene expression in NPC patients. This clustering was correlated with many signaling pathways, such as those related to heterotrimeric G-protein signaling, inflammation mediated by chemokine and cytokine signaling, ribosomes, protein metabolism, influenza infection, and ECM-receptor interaction. Our combined findings suggested that the expression of EBV genes in NPC is restricted not only to type II latency genes but also to type III latency and lytic genes. This study provided further insights into the potential role of EBV in the development of NPC.

关键词: Epstein-Barr virus     paired-end transcriptome sequencing     latency genes     lytic genes     nasopharyngeal carcinoma    

Exploring the cancer genome in the era of next-generation sequencing

null

《医学前沿(英文)》 2012年 第6卷 第1期   页码 48-55 doi: 10.1007/s11684-012-0182-x

摘要:

The emergence of next-generation sequencing technologies has led to dramatic advances in cancer genome studies. The increased efficiency and resolution of next-generation sequencing greatly facilitate the detection of genetic, genomic, and epigenomic alterations, such as single nucleotide mutations, small insertions and deletions, chromosomal rearrangements, copy number variations, and DNA methylation. Comprehensive analysis of cancer genomes through approaches of whole genome, exome, and transcriptome sequencing has significantly improved the understanding of cancer biology, diagnosis, and therapy. The present study briefly reviews the recent pioneering studies on cancer genome sequencing and provides an unprecedented insight into the landscape of genomic alterations in human sporadic cancers.

关键词: next-generation sequencing     cancer genome     whole genome sequencing     exome     transcriptome    

大鼠脊髓发育过程中时序转录组的发育时间模式和分子网络特征 Article

杨建, 赵莉莉, 易晟, 丁斐, 杨宇民, 刘炎, 王勇军, 刘梅, 薛成斌, 许莲, 龚蕾蕾, 王星辉, 张愉, 于彬, 明国丽, 顾晓松

《工程(英文)》 2021年 第7卷 第11期   页码 1592-1602 doi: 10.1016/j.eng.2021.10.001

摘要:

目前对胎盘哺乳动物脊髓发育的分子网络特征我们知之甚少。这些特征对深入理解与再生相关的重要生物过程和组织工程研究非常必要。现在,借助于从胚胎期到成年期大鼠脊髓的大规模时序转录组分析取得了一些新的进展。研究发现发育早期波动的RNA表达水平反映了脊髓活跃的转录调控并可能启动了脊髓的早期模式发育。脊髓发育过程中由microRNA (miRNA)和转录因子(TF)构成的宏观调控网络在新生期前后存在切换现象(即“镶嵌模型”)。差异可变剪接事件提示了可变剪接可能是郎飞结发育的驱动力之一。我们的研究也支持了脊髓中先天免疫的发育与其内在生长能力之间存在负相关性。发育过程中的一些表观遗传学修饰很可能在不同发育阶段发挥各自的调控功能。G蛋白偶联受体(包括嗅觉受体)可能在发育的轴突生长中发挥多效性作用。该研究为脊髓发育领域提供了有价值的资源,并与越来越多的单细胞数据形成互补,也为开发新的脊髓损伤组织工程策略提供了组学基础。

关键词: 发育     基因表达模式     先天免疫     脊髓     转录组    

极地动物基因资源研究现状与发展战略

陈松林,徐文腾,陈张帆

《中国工程科学》 2019年 第21卷 第6期   页码 39-47 doi: 10.15302/J-SSCAE-2019.06.007

摘要:

本文主要从基因组和转录组层面分析了极地动物基因资源的研究现状,梳理了本领域研究中存在的问题,并提出了未来发展战略。极地动物基因组测序起步较晚,迄今只完成了 13种极地动物的全基因组测序。在转录组研究方面,人们对极地的 31个物种进行了转录组测序,并在以下四个方向重点开展了研究:环境适应性研究;污染物应激反应的分子机制研究;不同发育阶段或不同组织中的转录组分析;功能基因挖掘。本领域研究由于起步晚,研究广度和深度都有待加强,但极地动物的基因资源研究具有战略意义。建议国家设立“极地动物基因资源发掘与应用”重点研发计划专项,围绕极地渔业动物特殊性状遗传解析、特有基因功能分析和基因工程产品研发等开展研究。

关键词: 极地动物     基因组,转录组,基因资源    

Transcriptomic basis of neutrophil ratio variation induced by poly I:C stimulation in porcine peripheral blood

Haiyan WANG, Qiaoxia ZHANG, Lilin YIN, Xiangdong LIU, Shuhong ZHAO, Mengjin ZHU, Changchun LI

《农业科学与工程前沿(英文)》 2017年 第4卷 第3期   页码 342-352 doi: 10.15302/J-FASE-2017162

摘要: Neutrophils are vital components of defense mechanisms against invading pathogens and are closely linked with the individual antiviral capacity of pigs and other mammals. Neutrophilia is a well-known clinical characteristic of viral and bacterial infections. Using Affymetrix porcine genome microarrays, we investigated the gene expression profiles associated with neutrophil variation in porcine peripheral blood before and after polyriboinosinic-polyribocytidylic acid stimulation. Transcriptomic analysis showed 796 differentially expressed genes (DEGs) in extreme response (ER) pigs and 192 DEGs in moderate response (MR) pigs. Most DEGs were related to immune responses, included , , , , , , , and . Gene ontology analysis indicated that the DEGs of both ER and MR pigs were involved in common biological processes, such as cell proliferation, growth regulation, immune response, inflammatory response and cell activation. The ER and MR groups also showed differences in DEGs involved in biological processes. DEGs involved in cell division and cell cycle were specifically found in the ER pigs, whereas DEGs involved in cell migration were specifically found in the MR pigs. The study provides a basic understanding of the molecular basis for the antiviral capacity of pigs and other mammals.

关键词: neutrophil     peripheral blood     pig     poly I:C     transcriptome    

单细胞转录组测序鉴定COVID-19外周血重症疾病特异性单核细胞 Article

张研, 王淑婷, 夏鹤, 郭静, 何康信, 黄晨杰, 罗瑞, 陈燕飞, 徐凯进, 高海女, 盛吉芳, 李兰娟

《工程(英文)》 2022年 第17卷 第10期   页码 161-169 doi: 10.1016/j.eng.2021.05.009

摘要:

了解重症新型冠状病毒肺炎(COVID-19)患者单核细胞的免疫学特征(包括与纤维化相关的特征)对了解疾病的重症化机制和阻止疾病恶化至关重要。本研究共纳入7名COVID-19患者(包括3名重症/危重症患者和4名普通型患者)和6名健康对照者。采集7名COVID-19患者不同疾病时期外周血样本,包括重症/危重症时期血样3例,轻症时期血样4例,康复期血样7例。将以上血样和6例健康对照者血样进行单细胞转录组测序分析。本研究发现在COVID-19重症/危重症时期,单核细胞发生显著变化。单核细胞在外周血单个核细胞中占比增加,多样性却显著降低。同时本研究发现两个新的COVID-19重症疾病特异性单核细胞亚群:Mono 0和Mono 5。这两个亚群表达amphiregulin(AREG)、epiregulin(EREG)和细胞因子基因IL-18,KEGG分析显示富集的ErbB信号通路,这两个亚群可能具有促纤维化和促炎的特征。进一步分析发现Mono 0和Mono 5发生代谢改变,包括糖酵解/糖异生的增加和HIF-1信号通路的增加。本研究同时发现一个疾病重症前期取得的样本显示出与重症/危重症时期样本相似的单核细胞UMAP图谱。本研究发现了两种新的COVID-19重症疾病特异性单核细胞亚群,可作为重症COVID-19的潜在预测因子和治疗靶点。

关键词: COVID-19     重症感染     危重症     单核细胞     纤维化    

Decomposition analysis applied to energy and emissions: A literature review

《工程管理前沿(英文)》   页码 625-639 doi: 10.1007/s42524-023-0270-4

摘要: Decomposition analysis has been widely used to assess the determinants of energy and CO2 emissions in academic research and policy studies. Both the methodology and application of decomposition analysis have been largely improved in the past decades. After more than 50 years’ developments, decomposition studies have become increasingly sophisticated and diversified, and tend to converge internally and integrate with other analytical approaches externally. A good understanding of the literature and state of the art is critical to identify knowledge gaps and formulate future research agenda. To this end, this study presents a literature survey for decomposition analysis applied to energy and emission issues, with a focus on the period of 2016–2021. A review for three individual decomposition techniques is first conducted, followed by a synthesis of emerging trends and features for the decomposition analysis literature as a whole. The findings are expected to direct future research in decomposition analysis.

关键词: index decomposition analysis     structural decomposition analysis     production decomposition analysis     energy     CO2 emissions    

标题 作者 时间 类型 操作

prognosis and molecular characteristics of clear-cell renal cell carcinoma: a multi-center integrated analysisof microbiome, metabolome, and transcriptome data

期刊论文

METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN

期刊论文

Comparative transcriptome analysis of purple-fleshed sweet potato provides insights into the molecular

Hongyuan ZHAO, Shanshan ZHANG, Feibing WANG, Ning ZHAO, Shaozhen HE, Qingchang LIU, Hong ZHAI

期刊论文

Transcriptome analysis of wheat grain using RNA-Seq

Liu WEI,Zhihui WU,Yufeng ZHANG,Dandan GUO,Yuzhou XU,Weixia CHEN,Haiying ZHOU,Mingshan YOU,Baoyun LI

期刊论文

Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during

null

期刊论文

METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN

Chen-Kai JIANG, De-Jiang NI, Ming-Zhe YAO, Jian-Qiang MA, Liang CHEN

期刊论文

Transcriptome resources and genome-wide marker development for Japanese larch (

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

期刊论文

TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

null

期刊论文

Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome

null

期刊论文

Exploring the cancer genome in the era of next-generation sequencing

null

期刊论文

大鼠脊髓发育过程中时序转录组的发育时间模式和分子网络特征

杨建, 赵莉莉, 易晟, 丁斐, 杨宇民, 刘炎, 王勇军, 刘梅, 薛成斌, 许莲, 龚蕾蕾, 王星辉, 张愉, 于彬, 明国丽, 顾晓松

期刊论文

极地动物基因资源研究现状与发展战略

陈松林,徐文腾,陈张帆

期刊论文

Transcriptomic basis of neutrophil ratio variation induced by poly I:C stimulation in porcine peripheral blood

Haiyan WANG, Qiaoxia ZHANG, Lilin YIN, Xiangdong LIU, Shuhong ZHAO, Mengjin ZHU, Changchun LI

期刊论文

单细胞转录组测序鉴定COVID-19外周血重症疾病特异性单核细胞

张研, 王淑婷, 夏鹤, 郭静, 何康信, 黄晨杰, 罗瑞, 陈燕飞, 徐凯进, 高海女, 盛吉芳, 李兰娟

期刊论文

Decomposition analysis applied to energy and emissions: A literature review

期刊论文