A novel method to prioritize RNAseq data for post-hoc analysis based on absolute changes in transcript abundance

2015 ◽  
Vol 14 (3) ◽  
Author(s):  
Patrick McNutt ◽  
Ian Gut ◽  
Kyle Hubbard ◽  
Phil Beske
Keyword(s):  
Differentially Expressed Genes ◽  
Transcript Abundance ◽  
Fold Change ◽  
Differentially Expressed ◽  
Post Hoc Analysis ◽  
Rnaseq Data ◽  
Novel Method ◽  
Post Hoc

AbstractThe use of fold-change (FC) to prioritize differentially expressed genes (DEGs) for

scholarly journals A red herring in zebrafish genetics: allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants

2021 ◽  
Author(s):  
Richard J White ◽  
Eirinn Mackay ◽  
Stephen W Wilson ◽  
Elisabeth M Busch-Nentwich
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed Gene ◽  
Transcript Abundance ◽  
Differentially Expressed ◽  
Model Organisms ◽  
Specific Gene ◽  
Wild Type ◽  
Specific Expression ◽  
Genomic Location ◽  
Allele Specific

In model organisms, RNA sequencing is frequently used to assess the effect of genetic mutations on cellular and developmental processes. Typically, animals heterozygous for a mutation are crossed to produce offspring with different genotypes. Resultant embryos are grouped by genotype to compare homozygous mutant embryos to heterozygous and wild-type siblings. Genes that are differentially expressed between the groups are assumed to reveal insights into the pathways affected by the mutation. Here we show that in zebrafish, differentially expressed genes are often overrepresented on the same chromosome as the mutation due to different levels of expression of alleles from different genetic backgrounds. Using an incross of haplotype-resolved wild-type fish, we found evidence of widespread allele-specific expression, which appears as differential expression when comparing embryos homozygous for a region of the genome to their siblings. When analysing mutant transcriptomes, this means that differentially expressed genes on the same chromosome as a mutation of interest may not be caused by that mutation. Typically, the genomic location of a differentially expressed gene is not considered when interpreting its importance with respect to the phenotype. This could lead to pathways being erroneously implicated or overlooked due to the noise of spurious differentially expressed genes on the same chromosome as the mutation. These observations have implications for the interpretation of RNA-seq experiments involving outbred animals and non-inbred model organisms.

scholarly journals The synergistic interaction of thermal stress coupled with overstocking strongly modulates the transcriptomic activity and immune capacity of rainbow trout (Oncorhynchus mykiss)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Alexander Rebl ◽  
Tomáš Korytář ◽  
Andreas Borchel ◽  
Ralf Bochert ◽  
Joanna Ewa Strzelczyk ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
High Temperature ◽  
Critical Temperature ◽  
Differentially Expressed Genes ◽  
Reference Group ◽  
Synergistic Effects ◽  
Stocking Density ◽  
Transcript Abundance ◽  
Condition Index ◽  
Differentially Expressed

Abstract The objective of the present study is to identify and evaluate informative indicators for the welfare of rainbow trout exposed to (A) a water temperature of 27 °C and (B) a stocking density of 100 kg/m3 combined with a temperature of 27 °C. The spleen-somatic and condition index, haematocrit and the concentrations of haemoglobin, plasma cortisol and glucose revealed non-significant differences between the two stress groups and the reference group 8 days after the onset of the experiments. The transcript abundance of almost 1,500 genes was modulated at least twofold in in the spleen of rainbow trout exposed to a critical temperature alone or a critical temperature combined with crowding as compared to the reference fish. The number of differentially expressed genes was four times higher in trout that were simultaneously challenged with high temperature and crowding, compared to trout challenged with high temperature alone. Based on these sets of differentially expressed genes, we identified unique and common tissue- and stress type-specific pathways. Furthermore, our subsequent immunologic analyses revealed reduced bactericidal and inflammatory activity and a significantly altered blood-cell composition in challenged versus non-challenged rainbow trout. Altogether, our data demonstrate that heat and overstocking exert synergistic effects on the rainbow trout’s physiology, especially on the immune system.

Identification of Differentially Expressed and Spliced Genes with RNA Sequencing Analysis of CLL Specimens

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4582-4582
Author(s):  
Wei Liao ◽  
Gwen Jordaan ◽  
Artur Jaroszewicz ◽  
Matteo Pellegrini ◽  
Sanjai Sharma
Keyword(s):  
B Cells ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Fold Change ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Mrna Isoforms ◽  
Core Set

Abstract Abstract 4582 High throughput sequencing of cellular mRNA provides a comprehensive analysis of the transcriptome. Besides identifying differentially expressed genes in different cell types, it also provides information of mRNA isoforms and splicing alterations. We have analyzed two CLL specimens and a normal peripheral blood B cells mRNA by this approach and performed data analysis to identify differentially expressed and spliced genes. The result showed CLLs specimens express approximately 40% more transcripts compared to normal B cells. The FPKM data (fragment per kilobase of exon per million) revealed a higher transcript expression on chromosome 12 in CLL#1 indicating the presence of trisomy 12, which was confirmed by fluorescent in-situ hybridization assay. With a two-fold change in FPKM as a cutoff and a p value cutoff of 0.05 as compared to the normal B cell control, 415 genes and 174 genes in CLL#1 and 676 and 235 genes in CLL#2 were up and downregulated or differentially expressed. In these two CLL specimens, 45% to 75% of differentially expressed genes are common to both the CLL specimens indicating that genetically disparate CLL specimens have a high percentage of a core set of genes that are potentially important for CLL biology. Selected differentially expressed genes with increased expression (selectin P ligand, SELPLG, and adhesion molecule interacts with CXADR antigen 1, AMICA) and decreased (Fos, Jun, CD69 and Rhob) expression based on the FPKM from RNA-sequencing data were also analyzed in additional CLL specimens by real time PCR analysis. The expression data from RNA-seq closely matches the fold-change in expression as measured by RT-PCR analysis and confirms the validity of the RNA-seq analysis. Interestingly, Fos was identified as one of the most downregulated gene in CLL. Using the Cufflinks and Cuffdiff software, the splicing patterns of genes in CLL specimens and normal B cells were analyzed. Approximately, 1100 to 1250 genes in the two CLL specimens were significantly differentially spliced as compared to normal B cells. In this analysis as well, there is a core set of 800 common genes which are differentially spliced in the two CLL specimens. The RNA-sequencing analysis accurately identifies differentially expressed novel genes and splicing variations that will help us understand the biology of CLL. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Explicating anti-amyloidogenic role of curcumin and piperine via amyloid beta (Aβ) explicit pathway: recovery and reversal paradigm effects

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10003
Author(s):  
Aimi Syamima Abdul Manap ◽  
Priya Madhavan ◽  
Shantini Vijayabalan ◽  
Adeline Chia ◽  
Koji Fukui
Keyword(s):  
Differentially Expressed Genes ◽  
Cell Model ◽  
Synergistic Effects ◽  
Expression Profiles ◽  
Combined Treatment ◽  
Neuronal Cell ◽  
Treated Group ◽  
Fold Change ◽  
Differentially Expressed ◽  
Microarray Profiling

Previously, we reported the synergistic effects of curcumin and piperine in cell cultures as potential anti-cholinesterase and anti-amyloidogenic agents. Due to limited findings on the enrolment of these compounds on epigenetic events in AD, we aimed at elucidating the expression profiles of Aβ42-induced SH-SY5Y cells using microarray profiling. In this study, an optimized concentration of 35 µM of curcumin and piperine in combination was used to treat Aβ42 fibril and high-throughput microarray profiling was performed on the extracted RNA. This was then compared to curcumin and piperine used singularly at 49.11 µM and 25 µM, respectively. Our results demonstrated that in the curcumin treated group, from the top 10 upregulated and top 10 downregulated significantly differentially expressed genes (p < 0.05; fold change ≥ 2 or ≤ −2), there were five upregulated and three downregulated genes involved in the amyloidogenic pathway. While from top 10 upregulated and top 10 downregulated significantly differentially expressed genes (p < 0.05; fold change ≥ 2 or ≤ − 2) in the piperine treated group, there were four upregulated and three downregulated genes involved in the same pathway, whereas there were five upregulated and two downregulated genes involved (p < 0.05; fold change ≥ 2 or ≤ − 2) in the curcumin-piperine combined group. Four genes namely GABARAPL1, CTSB, RAB5 and AK5 were expressed significantly in all groups. Other genes such as ITPR1, GSK3B, PPP3CC, ERN1, APH1A, CYCS and CALM2 were novel putative genes that are involved in the pathogenesis of AD. We revealed that curcumin and piperine have displayed their actions against Aβ via the modulation of various mechanistic pathways. Alterations in expression profiles of genes in the neuronal cell model may explain Aβ pathology post-treatment and provide new insights for remedial approaches of a combined treatment using curcumin and piperine.

scholarly journals Transcriptome based analysis of apoptosis genes in chickens co-infected with avian infectious bronchitis virus and pathogenic Escherichia coli

2021 ◽  
Author(s):  
Shabnam Hashemi ◽  
Seyed Masoud Hosseini ◽  
Arash Ghalyanchilangeroudi ◽  
Nariman Sheikhi
Keyword(s):  
Escherichia Coli ◽  
Cell Death ◽  
Differentially Expressed Genes ◽  
Infectious Bronchitis Virus ◽  
Fold Change ◽  
Differentially Expressed ◽  
Control Group ◽  
Infectious Bronchitis ◽  
Pathogenic Escherichia Coli ◽  
Apoptotic Genes

Background and Objectives: Infection with Infectious bronchitis virus (IBV) and avian pathogenic Escherichia coli (APEC) is an important respiratory infection worldwide. Apoptosis is a physiological process of cell death that occurs as part of normal development and responds to a variety of physiological and pathophysiological stimuli. The identification of molecular mechanisms of action or inaction of key apoptotic proteins is important. This study aimed to investigate apoptotic related genes in the trachea tissue of infected (IBV variant 2, and APEC serotype O78: K80) SPF chickens group compared to the control group. Materials and Methods: Forty SPF chickens was divided into 2 groups. Differential transcriptional profile in the infected SPF chickens trachea tissue was compared to those of control group in the early stage of infection by Illumina RNA-seq technique paired-end and strand-specific sequencing. Differentially expressed genes (DEGs) of transcriptome profiling of the trachea from the infected group were identified. Gene ontology category, KEGG pathway, and STRING analysis were analyzed to identify relationships among differentially expressed genes. Results: Twenty-eight apoptotic genes were identified. They consisted of six pathways related to cell death: the extrinsic pathway, intrinsic pathway, endoplasmic reticulum stress pathway, MAPK signaling pathway, and cell death by NFkB and activates mTOR pathway and some regulator and apoptosis inhibitors. Conclusion: All of the apoptotic genes in our study were up-regulated. Among these genes, the more fold change value was for TRADD and BCL2A1 genes, and the less fold change value was for MAP3K14, NFKB1, PIK3CB, and ITPR2 genes.

Integrated analysis of the physiology, RNA, and microRNA involved in black locust (Robinia pseudoacacia) rejuvenation

2019 ◽  
Author(s):  
Zijie Zhang ◽  
Yuhan Sun ◽  
Chao Han ◽  
Li Dong ◽  
Qi Guo ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
High Throughput ◽  
Woody Plants ◽  
Black Locust ◽  
Robinia Pseudoacacia ◽  
Fold Change ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Physiological Differences

Abstract Background Rejuvenation is a key process that enables perennial woody plants to regain growth potential. In Robinia pseudoacacia plantations, natural root sprouting individuals provide good material for studying the rejuvenation of woody plants. However, the physiological differences and molecular mechanisms underlying black locust rejuvenation remain unclear. In this study, we compared the physiological conditions and molecular responses of rejuvenated individuals and mother trees. Results Our analysis of leaf structures and physiological indices showed that the epidermis thickness, leaf thickness and leaf-tissue tightness of rejuvenated individuals were less than those of mother trees. The soluble-sugar content and total SOD activity of rejuvenated individuals were also lower than those of mother trees. The younger the rejuvenated individuals were, the lower the ABA content, ABA/ZT and GA3/ZT in the leaves. The ZT content increased with decreasing age of rejuvenated individuals. Using high-throughput sequencing strategies, the mRNA and miRNA involved in the rejuvenation of black locust were identified. RNA-seq identified 175,862 unigenes by de novo transcript assembly. Of those, 4,727 differentially expressed genes were identified based on clean reads mapped to the assembled transcriptome for gene expression analysis(fold change≥2 or ≤0.5 and q-value≤0.05). These genes were enriched to 53 gene ontology(GO) terms and 20 KEGG pathways (FDR≤0.01). Among these were a major pathway related to flavone and flavonol biosynthesis. High-throughput miRNA sequencing identified a total of 991 miRNAs, including 671 novel miRNAs. Furthermore, 262 known and 625 novel differentially expressed miRNAs were identified(fold change≥1.5 or ≤0.67 and p≤0.05). The main functions identified in the GO analysis of the target predictions overlapped with differentially expressed genes derived from RNA-seq. KEGG pathway enrichment showed that circadian rhythm-fly and signaling pathways regulating pluripotency of stem cells attracted considerable attention during rejuvenation. Conclusion Our study revealed physiological differences between rejuvenated individuals and mother trees of R. pseudoacacia. Differential genes between mother trees and rejuvenated individuals may vary according to the tree ages, but miRNAs may play a key regulatory role in rejuvenation. The same genotype system composed of root germinating individuals and mother-tree individuals provides a solid starting point for further elucidation of the rejuvenation of woody plants.

scholarly journals GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

2012 ◽  
Vol 28 (21) ◽  
pp. 2782-2788 ◽  
Author(s):  
Jianxing Feng ◽  
Clifford A. Meyer ◽  
Qian Wang ◽  
Jun S. Liu ◽  
X. Shirley Liu ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Fold Change ◽  
Differentially Expressed ◽  
Rna Seq

scholarly journals Response to comments on our article (Yin YL et al., Parasit Vectors, 10.1186/s13071-021-04739-w) by Yuqing Wang and colleagues

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yan-Ling Yin ◽  
Xin Yang ◽  
Guang-Hui Zhao
Keyword(s):  
Differentially Expressed Genes ◽  
Microarray Analysis ◽  
Cryptosporidium Parvum ◽  
Microarray Data ◽  
R Package ◽  
Fold Change ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Statistical Procedures

AbstractThis letter responds to comments on our article (Yin YL et al., Parasit Vectors, 10.1186/s13071-021-04739-w) by Yuqing Wang and colleagues, who wrote a letter entitled “Microarray analysis of circular RNAs in HCT-8 cells infected with Cryptosporidium parvum” and discussed statistical procedures for microarray analysis during C. parvum infection. To further confirm our data, in this letter, a common R package for analyses of differentially expressed genes, namely DESeq2, with Benjamini-Hochberg correction, was used to analyze our microarray data and identified 26 significantly differentially expressed circRNAs using adjusted P value < 0.05 and | Log2 (fold change [FC]) | ≥ 1.0, including our circRNA ciRS-7 of interest. Therefore, the protocol for selecting circRNAs of interest for further study in our article is acceptable and did not affect the subsequent scientific findings in our article.

scholarly journals Exhaustive Capture of Ovarian Cancer Transcriptional and Genomic Variant Integrating Canonical and Mapping-Free Protocols

2020 ◽  
Author(s):  
Zhiqin Fu ◽  
Chao Lu ◽  
Chao Ding ◽  
Chengxi Zhou ◽  
Tingting Yu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Gynecologic Malignancies ◽  
Canonical Mapping ◽  
Survival Prognosis ◽  
Rnaseq Data ◽  
Cause Of Deaths ◽  
Genomic Variant ◽  
Independent Cohort

Ovarian cancer is the most frequent cause of deaths in gynecologic malignancies. Many possible mechanisms have been proposed via RNAseq and DNAseq technique recently. However, the driving factors are still obscure. The possible reasons are attributed to the incomplete human reference. This study integrated the canonical mapping-based and mapping-free protocols to extract reliable variations and novel events. We eventually obtained 450 reliable SNVs from the WES data and novel events from the RNAseq data, including 154 SNVs, 462 intron events, two repeats and six splice events. We identified six differentially expressed genes and six contigs that are significantly related to survival prognosis. The recurrent SNVs in significantly differentially expressed genes can be validated in an independent cohort of 20 Chinese ovarian cancer patients.

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