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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 (CLEC4G, CRHBP, 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    

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clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptomedata

《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    

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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    

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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.

 

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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    

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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    

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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    

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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    

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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    

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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    

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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    

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A review of systematic evaluation and improvement in the big data environment

Feng YANG, Manman WANG

《工程管理前沿（英文）》 2020年 第7卷 第1期   页码 27-46 doi: 10.1007/s42524-020-0092-6

摘要： The era of big data brings unprecedented opportunities and challenges to management research. As one of the important functions of management decision-making, evaluation has been given more functions and application space. Exploring the applicable evaluation methods in the big data environment has become an important subject of research. The purpose of this paper is to provide an overview and discussion of systematic evaluation and improvement in the big data environment. We first review the evaluation methods based on the main analytic techniques of big data such as data mining, statistical methods, optimization and simulation, and deep learning. Focused on the characteristics of big data (association feature, data loss, data noise, and visualization), the relevant evaluation methods are given. Furthermore, we explore the systematic improvement studies and application fields. Finally, we analyze the new application areas of evaluation methods and give the future directions of evaluation method research in a big data environment from six aspects. We hope our research could provide meaningful insights for subsequent research.

关键词： big data     evaluation methods     systematic improvement     big data analytic techniques     data mining    

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Data quality assessment for studies investigating microplastics and nanoplastics in food products: Arecurrent data reliable?

《环境科学与工程前沿（英文）》 2023年 第17卷 第8期 doi: 10.1007/s11783-023-1694-0

摘要：

● Data quality assessment criteria for MP/NPs in food products were developed.

关键词： Microplastic     Nanoplastic     Food products     Data quality     Human health risk    

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Blockchain application in healthcare service mode based on Health Data Bank

Jianxia GONG, Lindu ZHAO

《工程管理前沿（英文）》 2020年 第7卷 第4期   页码 605-614 doi: 10.1007/s42524-020-0138-9

摘要： Blockchain is commonly considered a potential disruptive technology. Moreover, the healthcare industry has experienced rapid growth in the adoption of health information technology, such as electronic health records and electronic medical records. To guarantee data privacy and data security as well as to harness the value of health data, the concept of Health Data Bank (HDB) is proposed. In this study, HDB is defined as an integrated health data service institution, which bears no “ownership” of health data and operates health data under the principal–agent model. This study first comprehensively reviews the main characters of blockchain and identifies the blockchain-based healthcare industry projects and startups in the areas of health insurance, pharmacy, and medical treatment. Then, we analyze the fundamental principles of HDB and point out four challenges faced by HDB’s sustainable development: (1) privacy protection and interoperability of health data; (2) data rights; (3) health data supervision; (4) and willingness to share health data. We also analyze the important benefits of blockchain adoption in HDB. Furthermore, three application scenarios including distributed storage of health data, smart-contract-based healthcare service mode, and consensus-algorithm-based incentive policy are proposed to shed light on HDB-based healthcare service mode. In the end, this study offers insights into potential research directions and challenges.

关键词： Health Data Bank     blockchain     data assets     smart contract     incentive mechanism    

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Challenges to Engineering Management in the Big Data Era

Yong Shi

《工程管理前沿（英文）》 2015年 第2卷 第3期   页码 293-303 doi: 10.15302/J-FEM-2015042

摘要： This paper presents a review of the challenges to engineering management in the Big Data Era as well as the Big Data applications. First, it outlines the definitions of big data, data science and intelligent knowledge and the history of big data. Second, the paper reviews the academic activities about big data in China. Then, it elaborates a number of challenging big data problems, including transforming semi-structured and non-structured data into “structured format” and explores the relationship of data heterogeneity, knowledge heterogeneity and decision heterogeneity. Furthermore, the paper reports various real-life applications of big data, such as financial and petroleum engineering and internet business.

关键词： big data     data science     intelligent knowledge     engineering management     real-life applications    

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标题 作者 时间 类型 操作

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

null

期刊论文

clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptomedata

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

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

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

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

null

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

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

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

A review of systematic evaluation and improvement in the big data environment

Feng YANG, Manman WANG

期刊论文

Data quality assessment for studies investigating microplastics and nanoplastics in food products: Arecurrent data reliable?

期刊论文

Blockchain application in healthcare service mode based on Health Data Bank

Jianxia GONG, Lindu ZHAO

期刊论文

Challenges to Engineering Management in the Big Data Era

Yong Shi

期刊论文