scholarly journals Identifying differential expression genes and single nucleotide variations using RNA-seq in metastatic melanoma

2014 ◽  
Vol 13 (4) ◽  
pp. 8153-8162 ◽  
Author(s):  
D. Liu ◽  
Z.G. Zhao ◽  
Z.L. Jiao ◽  
H.J. Li
Keyword(s):  
Metastatic Melanoma ◽  
Differential Expression ◽  
Rna Seq ◽  
Single Nucleotide ◽  
Differential Expression Genes ◽  
Single Nucleotide Variations

scholarly journals Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq

2009 ◽  
Vol 37 (16) ◽  
pp. e106-e106 ◽  
Author(s):  
Iouri Chepelev ◽  
Gang Wei ◽  
Qingsong Tang ◽  
Keji Zhao
Keyword(s):  
Human Genome ◽  
Rna Seq ◽  
Single Nucleotide ◽  
Single Nucleotide Variations

scholarly journals Using Single Nucleotide Variations in Single-Cell RNA-Seq to Identify Subpopulations and Genotype-phenotype Linkage

2016 ◽  
Author(s):  
Olivier Poirion ◽  
Xun Zhu ◽  
Travers Ching ◽  
Lana X. Garmire
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Single Cells ◽  
Transcript Abundance ◽  
Rna Seq ◽  
Linear Modeling ◽  
Modeling Framework ◽  
Single Nucleotide ◽  
Single Nucleotide Variations

AbstractDespite its popularity, characterization of subpopulations with transcript abundance is subject to a significant amount of noise. We propose to use effective and expressed nucleotide variations (eeSNVs) from scRNA-seq as alternative features for tumor subpopulation identification. We developed a linear modeling framework, SSrGE, to link eeSNVs associated with gene expression. In all the datasets tested, eeSNVs achieve better accuracies than gene expression for identifying subpopulations. Previously validated cancer-relevant genes are also highly ranked, confirming the significance of the method. Moreover, SSrGE is capable of analyzing coupled DNA-seq and RNA-seq data from the same single cells, demonstrating its value in integrating multi-omics single cell techniques. In summary, SNV features from scRNA-seq data have merits for both subpopulation identification and linkage of genotype-phenotype relationship. The method SSrGE is available at https://github.com/lanagarmire/SSrGE.

scholarly journals Transcriptome analysis of flower color reveals the correlation between SNP and differential expression genes in Phalaenopsis

2021 ◽  
Author(s):  
Yu Ding ◽  
Ding-Hai Yang ◽  
Ma-Yin Wang ◽  
Dai-Cheng Hao ◽  
Wei-Shi Li ◽  
...  
Keyword(s):  
Differential Expression ◽  
Economic Value ◽  
Flower Color ◽  
Rna Seq ◽  
Transcription Level ◽  
Color Formation ◽  
Pathway Enrichment ◽  
Differential Expression Genes ◽  
Important Position ◽  
Transcriptome Level

Abstract Background Phalaenopsis is an important ornamental plant, which occupies an important position in the world flower market and has great economic value due to its rich and diverse flower colors. In order to investigate the flower color formation of Phalaenopsis at transcription level, the flower color formation involved genes were identified from RNA-seq in this study.Results White and purple petals of Phalaenopsis were collected in this study, and results were focused on two aspects: (1) the differential expression genes (DEGs) between white and purple flower color; and (2) association between SNP mutations and DEGs in transcriptome level. Results indicated that a total of 1,175 DEGs were identified, and the up- and down-regulation genes were 718 and 457, respectively. Gene Ontology (GO) and pathway enrichment showed that the biosynthesis of secondary metabolites pathway was key responsible for color formation and twelve crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase and E1.11.17) from them involved in the regulation of flower color in Phalaenopsis. Conclusion This study firstly reported that the SNP mutations strongly associated with DEGs in color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.

Comparison of differential expression genes in ovaries and testes of Pearlscale angelfish Centropyge vrolikii based on RNA-Seq analysis

2021 ◽  
Vol 47 (5) ◽  
pp. 1565-1583
Author(s):  
Zhaowei Zhong ◽  
Lulu Ao ◽  
Yilei Wang ◽  
Shuhong Wang ◽  
Liping Zhao ◽  
...  
Keyword(s):  
Differential Expression ◽  
Rna Seq ◽  
Differential Expression Genes

scholarly journals Full-length transcriptome sequencing and comparative transcriptomic analysis to uncover genes involved in early gametogenesis in the gonads of Amur sturgeon (Acipenser schrenckii)

2019 ◽  
Author(s):  
Xiujuan Zhang ◽  
Jiabin Zhou ◽  
Linmiao Li ◽  
Wenzhong Huang ◽  
Hafiz Ishfaq Ahmad ◽  
...  
Keyword(s):  
Differential Expression ◽  
Average Length ◽  
Full Length ◽  
Rna Seq ◽  
Genetic Characteristics ◽  
Kegg Pathways ◽  
Amur Sturgeon ◽  
Differential Expression Genes ◽  
Transcription Data ◽  
Development And Evolution

Abstract Background Sturgeons (Acipenseriformes) are polyploid chondrostean fish that constitute an important model species for studying development and evolution in vertebrates. To better understand the mechanisms of reproduction regulation in sturgeon, this study combined PacBio isoform sequencing (Iso-Seq) with Illumina short-read RNA-seq methods to discover full-length genes involved in early gametogenesis of the Amur sturgeon, Acipenser schrenckii .Results A total of 50.04 G subread bases were generated from two SMRT cells, and herein 164,618 nonredundant full-length transcripts (unigenes) were produced with an average length of 2,782 bp from gonad tissues (three testes and four ovaries) from seven 3-year-old A. schrenckii individuals. The number of ovary-specific expressed unigenes was greater than those of testis (19,716 vs. 3,028), and functional assignment indicated that 6 of 14 annotated KEGG pathways were directly ovary-related and had abundant transcripts and differential expression genes. Importantly, 60 early gametogenesis-related genes (involving 755 unigenes) were successfully identified, and exactly 50 percent (30/60) of those showed differential expression in testes and ovaries. The Amh and Gsdf with testis-biased expression, and Foxl2 and Cyp19a with ovary-biased expression strongly suggested the important regulatory roles in spermatogenesis and oogenesis of A. schrenckii , respectively. We also found the four novel Sox9 transcript variants, which increase the numbers of regulatory genes and imply function complexity of early gametogenesis. Finally, a total of 236,672 AS events (involving 36,522 unigenes) were detected, and 10,556 putative long noncoding RNAs (lncRNAs) and 4,339 predicted transcript factors (TFs) were also respectively identified, which all significantly associated with the early gametogenesis of A. schrenckii .Conclusions Overall, our results provide new genetic resources of full-length transcription data and information as a genomic-level reference for sturgeon. Crucially, we explored the comprehensive genetic characteristics that differ between the testes and ovaries of A. schrenckii in the early gametogenesis stage. These provide candidate genes and theoretical basis for further the mechanisms of reproduction regulation of sturgeon.

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