scholarly journals Significance tests for comparing digital gene expression profiles

2008 ◽  
Author(s):  
Leonardo Varuzza ◽  
Arthur Gruber ◽  
Carlos Pereira
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Digital Gene Expression ◽  
Significance Tests

scholarly journals The Significance of Digital Gene Expression Profiles

1997 ◽  
Vol 7 (10) ◽  
pp. 986-995 ◽  
Author(s):  
Stéphane Audic ◽  
Jean-Michel Claverie
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Digital Gene Expression

scholarly journals De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening

2017 ◽  
Vol 69 (1) ◽  
pp. 181-190 ◽  
Author(s):  
Yong Peng ◽  
Huiqin Ma ◽  
Shangwu Chen
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Digital Gene Expression ◽  
Orthologous Group ◽  
Functional Studies ◽  
Lycium Ruthenicum

Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L. ruthenicum fruit at different stages of ripening, and a de novo assembly of its sequence was performed. Approximately 52.45 million 100-bp paired-end raw reads were generated from the samples by deep RNA-seq analysis. These short reads were assembled to obtain 164814 contigs, and the contigs were assembled into 84968 non-redundant unigenes using the Trinity method. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group and KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway terms. Digital gene expression analysis was applied to compare gene-expression patterns at different fruit developmental stages. These results contribute to existing sequence resources for Lycium spp. during the fruit-ripening stages, which is valuable for further functional studies of genes involved in L. ruthenicum fruit nutraceutical quality.

Transcriptome profiling of muscle by RNA-Seq reveals significant differences in digital gene expression profiling between Angus and Luxi cattle

2015 ◽  
Vol 55 (9) ◽  
pp. 1172 ◽  
Author(s):  
G. F. Liu ◽  
H. J. Cheng ◽  
W. You ◽  
E. L. Song ◽  
X. M. Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Beef Cattle ◽  
Growth And Development ◽  
Massively Parallel Sequencing ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Digital Gene Expression ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Angus Cattle

The development of massively parallel sequencing technologies enables the sequencing of total cDNA to identify unigene expression and to discover novel regions of transcription. Here, we report the first use of RNA sequencing (RNA-Seq) to find the digital gene expression profiles (DGEs) associated with the growth and development of muscle in Chinese Luxi and Angus beef cattle. More than 9 243 921 clean reads were found in samples of muscle tissue. We found 232 DGEs between Luxi cattle and Angus cattle (false discovery ratio ≤0.001 and |log2 ratio| ≥1). Among the DGEs, we determined that 147 genes were downregulated and 85 genes were upregulated. Gene Ontology and KEGG Pathway analyses were performed to analyse the biological role of the DGEs and determine their contribution to the differences seen in muscle growth and development between local Chinese Luxi cattle and the introduced Angus cattle. The results suggest that RNA-Seq is a useful tool for predicting differences in gene expression between Luxi and Angus beef cattle; moreover, our results provides unprecedented resolution of mRNAs that are expressed across the two breeds.

Digital gene expression profiles of Arabidopsis thaliana under salt stress

2017 ◽  
Vol 34 (6) ◽  
pp. 631
Author(s):  
Hua Cheng ◽  
Meiyan Yang ◽  
Jiahui Wu ◽  
Nan Sun ◽  
Jianzi Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Salt Stress ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Digital Gene Expression
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