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Your search keyword '"Liao, Yuan"' showing total 19 results
Start Over Author "Liao, Yuan" Publication Year Range Last 50 years Journal plos one
19 results on '"Liao, Yuan"'

2. Prediction of potential prognostic biomarkers in metastatic prostate cancer based on a circular RNA-mediated competing endogenous RNA regulatory network.

Author

Liang Luo, Lei-Lei Zhang, Wen Tao, Tao-Lin Xia, and Liao-Yuan Li

Subjects
Medicine, Science
Abstract

Recently, studies on competing endogenous RNA (ceRNA) networks have become prevalent, and circular RNAs (circRNAs) have crucial implications for the development and progression of carcinoma. However, studies relevant to metastatic prostate cancer (mPCa) are scant. This study aims to discover potential ceRNAs that may be related to the prognosis of mPCa. RNA-Seq data were obtained from the MiOncoCirc database and Gene Expression Omnibus (GEO). Differential expression patterns of RNAs were examined using R packages. Circular RNA Interactome, miRTarBase, miRDB and TargetScan were applied to predict the corresponding relation between circRNAs, miRNAs and mRNAs. The Gene Ontology (GO) annotations were performed to present related GO terms, and Gene Set Enrichment Analysis (GSEA) tools were applied for pathway annotations. Moreover, survival analysis was conducted for the hub genes. We found 820 circRNAs, 81 miRNAs and 179 mRNAs that were distinguishingly expressed between primary prostate cancer (PCa) and mPCa samples. A ceRNA network including 45 circRNAs, 24 miRNAs and 56 mRNAs was constructed. In addition, the protein-protein interaction (PPI) network was built, and 10 hub genes were selected by using the CytoHubba application. Among the 10 hub genes, survival analysis showed that ITGA1, LMOD1, MYH11, MYLK, SORBS1 and TGFBR3 were significantly connected with disease-free survival (DFS). The circRNA-mediated ceRNA network provides potential prognostic biomarkers for metastatic prostate cancer.

Published
2021
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4. Prediction of potential prognostic biomarkers in metastatic prostate cancer based on a circular RNA-mediated competing endogenous RNA regulatory network

Author

Tao-Lin Xia, Liao-Yuan Li, Wen Tao, Liang Luo, and Lei-Lei Zhang

Subjects
Proteomics, Male, Biochemistry, Interactome, Metastasis, Prostate cancer, Basic Cancer Research, Breast Tumors, Medicine and Health Sciences, Gene Regulatory Networks, Protein Interaction Maps, Neoplasm Metastasis, Multidisciplinary, MiRTarBase, Prostate Cancer, Liver Diseases, Gene Ontologies, Prostate Diseases, Genomics, Nucleic acids, Gene Expression Regulation, Neoplastic, Oncology, Medicine, Protein Interaction Networks, Network Analysis, Research Article, Computer and Information Sciences, Urology, Science, Gastroenterology and Hepatology, Computational biology, Biology, Circular RNA, Gastrointestinal Tumors, Breast Cancer, microRNA, Genetics, Biomarkers, Tumor, medicine, Humans, RNA, Messenger, Non-coding RNA, Gene, Colorectal Cancer, Natural antisense transcripts, Biology and life sciences, Competing endogenous RNA, Gene Expression Profiling, Carcinoma, Cancers and Neoplasms, Computational Biology, Prostatic Neoplasms, Molecular Sequence Annotation, MYLK, Hepatocellular Carcinoma, RNA, Circular, Genome Analysis, medicine.disease, Gene regulation, MicroRNAs, Genitourinary Tract Tumors, RNA, Gene expression
Abstract

Recently, studies on competing endogenous RNA (ceRNA) networks have become prevalent, and circular RNAs (circRNAs) have crucial implications for the development and progression of carcinoma. However, studies relevant to metastatic prostate cancer (mPCa) are scant. This study aims to discover potential ceRNAs that may be related to the prognosis of mPCa. RNA-Seq data were obtained from the MiOncoCirc database and Gene Expression Omnibus (GEO). Differential expression patterns of RNAs were examined using R packages. Circular RNA Interactome, miRTarBase, miRDB and TargetScan were applied to predict the corresponding relation between circRNAs, miRNAs and mRNAs. The Gene Ontology (GO) annotations were performed to present related GO terms, and Gene Set Enrichment Analysis (GSEA) tools were applied for pathway annotations. Moreover, survival analysis was conducted for the hub genes. We found 820 circRNAs, 81 miRNAs and 179 mRNAs that were distinguishingly expressed between primary prostate cancer (PCa) and mPCa samples. A ceRNA network including 45 circRNAs, 24 miRNAs and 56 mRNAs was constructed. In addition, the protein–protein interaction (PPI) network was built, and 10 hub genes were selected by using the CytoHubba application. Among the 10 hub genes, survival analysis showed that ITGA1, LMOD1, MYH11, MYLK, SORBS1 and TGFBR3 were significantly connected with disease-free survival (DFS). The circRNA-mediated ceRNA network provides potential prognostic biomarkers for metastatic prostate cancer.

Published
2021

18. Next-Generation Sequencing of the Chrysanthemum nankingense (Asteraceae) Transcriptome Permits Large-Scale Unigene Assembly and SSR Marker Discovery

Author

Fadi Chen, Jiafu Jiang, Zhiyong Guan, Pirui Li, Aiping Song, Liao Yuan, Weimin Fang, Sumei Chen, Haibin Wang, Xiangyu Qi, and Hui Peng

Subjects
DNA, Complementary, Marker-Assisted Selection, Agricultural Biotechnology, lcsh:Medicine, Sequence assembly, UniGene, Genomics, Plant Science, Asteraceae, Biology, Genetic analysis, DNA sequencing, Transcriptomes, Transcriptome, Genome Analysis Tools, Plant Genomics, lcsh:Science, Phylogeny, Flowering Plants, Expressed Sequence Tags, Genetics, Expressed sequence tag, Polymorphism, Genetic, Multidisciplinary, lcsh:R, Computational Biology, High-Throughput Nucleotide Sequencing, food and beverages, Molecular Sequence Annotation, Agriculture, Plants, Agronomy, Plant Breeding, Microsatellite, lcsh:Q, Plant Biotechnology, Sequence Analysis, Microsatellite Repeats, Research Article
Abstract

Background Simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST) sequences have been acquired to date, so the number of available EST-SSR markers is very low. Methodology/Principal Findings Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59%) unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all) of the assays were transferable across species and that they exposed a significant amount of allelic diversity. Conclusions/Significance SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera.

Published
2013

19. Next-Generation Sequencing of the Chrysanthemum nankingense (Asteraceae) Transcriptome Permits Large-Scale Unigene Assembly and SSR Marker Discovery.

Author

Wang, Haibin, Jiang, Jiafu, Chen, Sumei, Qi, Xiangyu, Peng, Hui, Li, Pirui, Song, Aiping, Guan, Zhiyong, Fang, Weimin, Liao, Yuan, and Chen, Fadi

Subjects
ASTERACEAE, GENETIC transcription in plants, MICROSATELLITE repeats in plants, NUCLEOTIDE sequence, EUKARYOTIC genomes, AGRICULTURAL biotechnology, PLANT breeding
Abstract

Background: Simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST) sequences have been acquired to date, so the number of available EST-SSR markers is very low. Methodology/Principal Findings: Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59%) unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all) of the assays were transferable across species and that they exposed a significant amount of allelic diversity. Conclusions/Significance: SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera. [ABSTRACT FROM AUTHOR]

Published
2013
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