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

Daniel Wai-Hung Ho,Alan Ka-Lun Kai,Irene Oi-Lin Ng

Frontiers of Medicine 2015, Volume 9, Issue 3,   Pages 322-330 doi: 10.1007/s11684-015-0408-9

Abstract:

This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular

Keywords： 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

Frontiers of Medicine doi: 10.1007/s11684-023-1029-3

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

Keywords： 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

Frontiers of Agricultural Science and Engineering 2014, Volume 1, Issue 1,   Pages 77-84 doi: 10.15302/J-FASE-2014010

Abstract: In this paper, we present a transcriptome analysis of , a deciduous conifer that is widely-grown in

Keywords： 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

Frontiers of Agricultural Science and Engineering 2021, Volume 8, Issue 2,

Abstract: We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome
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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

Frontiers of Agricultural Science and Engineering 2018, Volume 5, Issue 2,   Pages 214-225 doi: 10.15302/J-FASE-2018219

Abstract: 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.

Keywords： 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

Lijuan Hu,Zhirui Lin,Yanheng Wu,Juqin Dong,Bo Zhao,Yanbing Cheng,Peiyu Huang,Lihua Xu,Tianliang Xia,Dan Xiong,Hongbo Wang,Manzhi Li,Ling Guo,Elliott Kieff,Yixin Zeng,Qian Zhong,Musheng Zeng

Frontiers of Medicine 2016, Volume 10, Issue 1,   Pages 61-75 doi: 10.1007/s11684-016-0436-0

Abstract: However, comprehensive information through EBV transcriptome analysis in NPC is limited.

Keywords： 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

Hui Dong, Shengyue Wang

Frontiers of Medicine 2012, Volume 6, Issue 1,   Pages 48-55 doi: 10.1007/s11684-012-0182-x

Abstract: Comprehensive analysis of cancer genomes through approaches of whole genome, exome, and transcriptome

Keywords： 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

Nan Ding,Jiafei Xi,Yanming Li,Xiaoyan Xie,Jian Shi,Zhaojun Zhang,Yanhua Li,Fang Fang,Sihan Wang,Wen Yue,Xuetao Pei,Xiangdong Fang

Frontiers of Medicine 2016, Volume 10, Issue 3,   Pages 297-310 doi: 10.1007/s11684-016-0452-0

Abstract: explore dynamic changes in erythropoiesis and potential mechanisms that control these changes in the transcriptomelevel, we took advantage of high throughput sequencing technologies to obtain transcriptome data fromThese data provided a substantial resource for the study of normal erythropoiesis, which will permit

Keywords： 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

Frontiers of Agricultural Science and Engineering 2014, Volume 1, Issue 3,   Pages 214-222 doi: 10.15302/J-FASE-2014024

Abstract: Transcriptome analysis is a powerful approach to research grain traits and elucidate their genetic regulation

Keywords： 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

Frontiers of Agricultural Science and Engineering   Pages 215-230 doi: 10.15302/J-FASE-2021382

Abstract: We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome

Keywords： harvest season     metabolites     tea shoots     transcriptomics     untargeted metabolomics    

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Developmental Temporal Patterns and Molecular Network Features in the Transcriptome of Rat Spinal Cord Article

Jian Yang, Lili Zhao, Sheng Yi, Fei Ding, Yumin Yang, Yan Liu, Yongjun Wang, Mei Liu, Chengbin Xue, Lian Xu, Leilei Gong, Xinghui Wang, Yu Zhang, Bin Yu, Guo-li Ming, Xiaosong Gu

Engineering 2021, Volume 7, Issue 11,   Pages 1592-1602 doi: 10.1016/j.eng.2021.10.001

Abstract:

The molecular network features of spinal cord development that are integral to tissue engineering remain poorly understood in placental mammals, especially in terms of their relationships with vital biological processes such as regeneration. Here, using a large-scale temporal transcriptomic analysis of rat spinal cord from the embryonic stage to adulthood, we show that fluctuating RNA expression levels reflect highly active transcriptional regulation, which may initiate spinal cord patterning. We also demonstrate that microRNAs (miRNAs) and transcriptional factors exhibit a mosaic profile based on their expression patterns, while differential alternative splicing events reveal that alternative splicing may be a driving force for the development of the node of Ranvier. Our study also supports the existence of a negative correlation between innate immunity and intrinsic growth capacity. Epigenetic modifications appear to perform their respective regulatory functions at different stages of development, while guanine nucleotide-binding protein (G protein)-coupled receptors (including olfactory receptors (ORs)) may perform pleiotropic roles in axonal growth. This study provides a valuable resource for investigating spinal cord development and complements the increasing number of single-cell datasets. These findings also provide a genetic basis for the development of novel tissue engineering strategies.

Keywords： Development     Gene expression pattern     Innate immunity     Spinal cord     Transcriptome    

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

Feng YANG, Manman WANG

Frontiers of Engineering Management 2020, Volume 7, Issue 1,   Pages 27-46 doi: 10.1007/s42524-020-0092-6

Abstract: The era of big data brings unprecedented opportunities and challenges to management research.Exploring the applicable evaluation methods in the big data environment has become an important subjectpaper is to provide an overview and discussion of systematic evaluation and improvement in the big dataWe first review the evaluation methods based on the main analytic techniques of big data such as dataFocused on the characteristics of big data (association feature, data loss, data noise, and visualization

Keywords： 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?

Frontiers of Environmental Science & Engineering 2023, Volume 17, Issue 8, doi: 10.1007/s11783-023-1694-0

Abstract:

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

Keywords： 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

Frontiers of Engineering Management 2020, Volume 7, Issue 4,   Pages 605-614 doi: 10.1007/s42524-020-0138-9

Abstract: To guarantee data privacy and data security as well as to harness the value of health data, the conceptof 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.; (2) data rights; (3) health data supervision; (4) and willingness to share health data.

Keywords： 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

Frontiers of Engineering Management 2015, Volume 2, Issue 3,   Pages 293-303 doi: 10.15302/J-FEM-2015042

Abstract: as the Big Data applications.First, it outlines the definitions of big data, data science and intelligent knowledge and the historyof big data.Second, the paper reviews the academic activities about big data in China.and non-structured data into “structured format” and explores the relationship of data heterogeneity

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

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Title Author Date Type Operation

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

Daniel Wai-Hung Ho,Alan Ka-Lun Kai,Irene Oi-Lin Ng

Journal Article

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

Journal Article

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

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

Journal Article

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

Journal Article

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

Journal Article

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

Lijuan Hu,Zhirui Lin,Yanheng Wu,Juqin Dong,Bo Zhao,Yanbing Cheng,Peiyu Huang,Lihua Xu,Tianliang Xia,Dan Xiong,Hongbo Wang,Manzhi Li,Ling Guo,Elliott Kieff,Yixin Zeng,Qian Zhong,Musheng Zeng

Journal Article

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

Hui Dong, Shengyue Wang

Journal Article

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

Nan Ding,Jiafei Xi,Yanming Li,Xiaoyan Xie,Jian Shi,Zhaojun Zhang,Yanhua Li,Fang Fang,Sihan Wang,Wen Yue,Xuetao Pei,Xiangdong Fang

Journal Article

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

Journal Article

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

Journal Article

Developmental Temporal Patterns and Molecular Network Features in the Transcriptome of Rat Spinal Cord

Jian Yang, Lili Zhao, Sheng Yi, Fei Ding, Yumin Yang, Yan Liu, Yongjun Wang, Mei Liu, Chengbin Xue, Lian Xu, Leilei Gong, Xinghui Wang, Yu Zhang, Bin Yu, Guo-li Ming, Xiaosong Gu

Journal Article

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

Feng YANG, Manman WANG

Journal Article

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

Journal Article

Blockchain application in healthcare service mode based on Health Data Bank

Jianxia GONG, Lindu ZHAO

Journal Article

Challenges to Engineering Management in the Big Data Era

Yong Shi

Journal Article