scholarly journals Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome

RNA ◽  
2019 ◽  
Vol 25 (6) ◽  
pp. 669-684 ◽  
Author(s):  
Erin Slabaugh ◽  
Jigar S. Desai ◽  
Ryan C. Sartor ◽  
Lovely Mae F. Lawas ◽  
S.V. Krishna Jagadish ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Differential Gene Expression ◽  
Reference Genome ◽  
Differential Gene

scholarly journals Differential gene expression and alternative splicing in insect immune specificity

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 1031 ◽  
Author(s):  
Carolyn E Riddell ◽  
Juan D Lobaton Garces ◽  
Sally Adams ◽  
Seth M Barribeau ◽  
David Twell ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Differential Gene Expression ◽  
Differential Gene

scholarly journals Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

BMC Genomics ◽  
2006 ◽  
Vol 7 (1) ◽  
Author(s):  
Paul J Gardina ◽  
Tyson A Clark ◽  
Brian Shimada ◽  
Michelle K Staples ◽  
Qing Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colon Cancer ◽  
Alternative Splicing ◽  
Differential Gene Expression ◽  
Exon Array ◽  
Whole Genome ◽  
Differential Gene

scholarly journals Evaluating Methods for Differential Gene Expression And Alternative Splicing Using Internal Synthetic Controls

2020 ◽  
Author(s):  
Sudeep Mehrotra ◽  
Revital Bronstein ◽  
Daniel Navarro-Gomez ◽  
Ayellet V. Segrè ◽  
Eric A. Pierce
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Differential Gene Expression ◽  
Internal Control ◽  
Accurate Determination ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Specificity And Sensitivity ◽  
Differential Gene ◽  
Synthetic Controls

AbstractHigh-throughput transcriptome sequencing has become a powerful tool in the study of human diseases. Identification of causal mechanisms may entail analysis of differential gene expression (DGE), differential transcript/isoform expression (DTE) and identification, classification and quantification of alternative splicing (AS) and/or detection of novel AS events. For such a global transcriptome profiling execution of multi-level data analysis methodologies is required. Each level presents its own unique challenges and the questions about their performance remains. In this work we present results from systematic and consistent assessing and comparing a number of widely used methods for detecting DGE, DTE and AS using internal control “spike-in” sequences (Sequins) in RNA-seq data. We demonstrated that inclusion of internal controls in RNA-seq experiments allows accurate determination of lower bounds detection levels, and better assessment of DGE, DTE and AS accuracy and sensitivity. Tools for RNA-seq read alignment and detection of DGE performed reasonably. More efforts are needed to improve specificity and sensitivity of DTE and AS detection. Low expression of isoforms accompanied with sequencing depth does impact sensitivity and specificity of DTE and AS tools.

scholarly journals Differential gene expression and alternative splicing between diploid and tetraploid watermelon

2014 ◽  
Vol 66 (5) ◽  
pp. 1369-1385 ◽  
Author(s):  
Thangasamy Saminathan ◽  
Padma Nimmakayala ◽  
Sumanth Manohar ◽  
Sridhar Malkaram ◽  
Aldo Almeida ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Differential Gene Expression ◽  
Differential Gene

scholarly journals Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish

2020 ◽  
Author(s):  
Arne Jacobs ◽  
Kathryn R. Elmer
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Differential Gene Expression ◽  
Differentially Expressed Genes ◽  
Adaptive Evolution ◽  
Salmonid Fish ◽  
Differentially Expressed ◽  
Molecular Processes ◽  
Regulatory Regions ◽  
Differential Gene

AbstractUnderstanding the contribution of different molecular processes to the evolution and development of divergent phenotypes is crucial for identifying the molecular routes of rapid adaptation. Here, we used RNA-seq data to compare patterns of alternative splicing and differential gene expression in a case of parallel adaptive evolution, the replicated postglacial divergence of the salmonid fish Arctic charr (Salvelinus alpinus) into benthic and pelagic ecotypes across multiple independent lakes.We found that genes that were differentially spliced and differentially expressed between the benthic and pelagic ecotypes were mostly independent (<6% overlap) and were involved in different processes. Differentially spliced genes were primarily enriched for muscle development and functioning, while differentially expressed genes were mostly involved in energy metabolism, immunity and growth. Together, these likely explain different axes of divergence between ecotypes in swimming performance and activity. Furthermore, we found that alternative splicing and gene expression are mostly controlled by independent cis-regulatory quantitative trait loci (<3.4% overlap). Cis-regulatory regions were associated with the parallel divergence in splicing (16.5% of intron clusters) and expression (6.7 - 10.1% of differentially expressed genes), indicating shared regulatory variation across ecotype pairs. Contrary to theoretical expectation, we found that differentially spliced genes tended to be highly central in regulatory networks (‘hub genes’) and were annotated to significantly more gene ontology terms compared to non-differentially spliced genes, consistent with a higher level of connectivity and pleiotropy.Together, our results suggest that the concerted regulation of alternative splicing and differential gene expression through different regulatory regions leads to the divergence of complementary phenotypes important for local adaptation. This study provides novel insights into the importance of contrasting but putatively complementary molecular processes for rapid and parallel adaptive evolution.

scholarly journals The Role of Alternative Splicing and Differential Gene Expression in Cichlid Adaptive Radiation

2017 ◽  
Vol 9 (10) ◽  
pp. 2764-2781 ◽  
Author(s):  
Pooja Singh ◽  
Christine Börger ◽  
Heather More ◽  
Christian Sturmbauer
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Differential Gene Expression ◽  
Adaptive Radiation ◽  
Differential Gene

scholarly journals Differential gene expression and alternative splicing in insect immune specificity

2014 ◽  
Author(s):  
Carolyn Riddell ◽  
Juan David Lobaton Garces ◽  
Sally Adams ◽  
Seth M Barribeau ◽  
David Twell ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Differential Gene Expression ◽  
Bombus Terrestris ◽  
Peritrophic Membrane ◽  
Parasite Genotype ◽  
Crithidia Bombi ◽  
Genotype Interaction ◽  
Differential Gene ◽  
Host Parasite

Ecological studies routinely show genotype-genotype interactions between insects and their parasites. The mechanisms behind these interactions are not clearly understood. Using the bumblebee Bombus terrestris / trypanosome Crithidia bombi model system, we have carried out a transcriptome-wide analysis of gene expression and alternative splicing in bees during C. bombi infection. We have performed four analyses, 1) comparing gene expression in infected and non-infected bees 24 hours after infection by Crithidia bombi, 2) comparing expression at 24 and 48 hours after C.bombi infection, 3) searching for differential gene expression associated with the host-parasite genotype-genotype interaction at 24 hours after infection and 4) searching for alternative splicing associated with the host-parasite genotype-genotype interaction at 24 hours post infection. We found a large number of genes differentially regulated related to numerous canonical immune pathways. These genes include receptors, signaling pathways and effectors. We discovered a possible interaction between the peritrophic membrane and the insect immune system in defense against Crithidia. Most interestingly we found differential expression and alternative splicing of Dscam related transcripts and a novel immunoglobulin related gene Twitchin depends on the genotype-genotype interactions of the given bumblebee colony and Crithidia strain.

scholarly journals Differential gene expression and alternative splicing of survivin following mouse sciatic nerve injury

Spinal Cord ◽  
2009 ◽  
Vol 47 (10) ◽  
pp. 739-744 ◽  
Author(s):  
S Amiri ◽  
M Movahedin ◽  
S J Mowla ◽  
Z Hajebrahimi ◽  
M Tavallaei
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Sciatic Nerve ◽  
Nerve Injury ◽  
Differential Gene Expression ◽  
Sciatic Nerve Injury ◽  
Differential Gene
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