scholarly journals Analysis of allele-specific expression using RNA-seq of the Korean native pig and Landrace reciprocal cross

2019 ◽  
Vol 32 (12) ◽  
pp. 1816-1825
Author(s):  
Byeongyong Ahn ◽  
Min-Kyeung Choi ◽  
Joori Yum ◽  
In-Cheol Cho ◽  
Jin-Hoi Kim ◽  
...  
Keyword(s):  
Reciprocal Cross ◽  
Rna Seq ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Korean Native Pig ◽  
Allele Specific

scholarly journals Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Joseph Tomlinson ◽  
Shawn W. Polson ◽  
Jing Qiu ◽  
Juniper A. Lake ◽  
William Lee ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Specific Expression ◽  
Single Nucleotide ◽  
Allele Specific Expression ◽  
Detection Tool ◽  
Commercial Broiler ◽  
Significant Phenomenon ◽  
Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

scholarly journals Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis-eQTL Identified Using Genetic Linkage

Genetics ◽  
2013 ◽  
Vol 195 (3) ◽  
pp. 1157-1166 ◽  
Author(s):  
Sandrine Lagarrigue ◽  
Lisa Martin ◽  
Farhad Hormozdiari ◽  
Pierre-François Roux ◽  
Calvin Pan ◽  
...  
Keyword(s):  
Mouse Liver ◽  
Genetic Linkage ◽  
Rna Seq ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

Variant calling from RNA-seq data of the brain transcriptome of pigs and its application for allele-specific expression and imprinting analysis

Gene ◽  
2018 ◽  
Vol 641 ◽  
pp. 367-375 ◽  
Author(s):  
Maria Oczkowicz ◽  
Tomasz Szmatoła ◽  
Katarzyna Piórkowska ◽  
Katarzyna Ropka-Molik
Keyword(s):  
Variant Calling ◽  
Rna Seq ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Brain Transcriptome ◽  
Allele Specific ◽  
The Brain

scholarly journals Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression

2018 ◽  
Vol 34 (13) ◽  
pp. 2177-2184 ◽  
Author(s):  
Narayanan Raghupathy ◽  
Kwangbom Choi ◽  
Matthew J Vincent ◽  
Glen L Beane ◽  
Keith S Sheppard ◽  
...  
Keyword(s):  
Hierarchical Analysis ◽  
Rna Seq ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

RNA-Seq Analysis of Allele-Specific Expression in the Mouse Cochlea

2014 ◽  
Vol 151 (1_suppl) ◽  
pp. P226-P226
Author(s):  
Maria K. L. Ho ◽  
Yehudit Hasin ◽  
Aldons J. Lusis ◽  
Rick A. Friedman
Keyword(s):  
Rna Seq ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

scholarly journals Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0126911 ◽  
Author(s):  
David L. A. Wood ◽  
Katia Nones ◽  
Anita Steptoe ◽  
Angelika Christ ◽  
Ivon Harliwong ◽  
...  
Keyword(s):  
Rna Seq ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

scholarly journals GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Daniel Edsgärd ◽  
Maria Jesus Iglesias ◽  
Sarah-Jayne Reilly ◽  
Anders Hamsten ◽  
Per Tornvall ◽  
...  
Keyword(s):  
Rna Seq ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific ◽  
Haplotype Information
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