scholarly journals Transcriptome Analysis Reveals a Potential Role of Benzoxazinoid in Regulating Stem Elongation in the Wheat Mutant qd

2021 ◽  
Vol 12 ◽  
Author(s):  
Daxing Xu ◽  
Yongdun Xie ◽  
Huijun Guo ◽  
Weiwei Zeng ◽  
Hongchun Xiong ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Stem Elongation ◽  
Ion Beam ◽  
Heavy Ion ◽  
Differentially Expressed ◽  
Transcriptome Data ◽  
Expression Levels ◽  
Subunit Organization ◽  
Dna Complex ◽  
Wheat Mutant

The stems of cereal crops provide both mechanical support for lodging resistance and a nutrient supply for reproductive organs. Elongation, which is considered a critical phase for yield determination in winter wheat (Triticum aestivum L.), begins from the first node detectable to anthesis. Previously, we characterized a heavy ion beam triggered wheat mutant qd, which exhibited an altered stem elongation pattern without affecting mature plant height. In this study, we further analyzed mutant stem developmental characteristics by using transcriptome data. More than 40.87 Mb of clean reads including at least 36.61 Mb of unique mapped reads were obtained for each biological sample in this project. We utilized our transcriptome data to identify 124,971 genes. Among these genes, 4,340 differentially expressed genes (DEG) were identified between the qd and wild-type (WT) plants. Compared to their WT counterparts, qd plants expressed 2,462 DEGs with downregulated expression levels and 1878 DEGs with upregulated expression levels. Using DEXSeq, we identified 2,391 counting bins corresponding to 1,148 genes, and 289 of them were also found in the DEG analysis, demonstrating differences between qd and WT. The 5,199 differentially expressed genes between qd and WT were employed for GO and KEGG analyses. Biological processes, including protein-DNA complex subunit organization, protein-DNA complex assembly, nucleosome organization, nucleosome assembly, and chromatin assembly, were significantly enriched by GO analysis. However, only benzoxazinoid biosynthesis pathway-associated genes were enriched by KEGG analysis. Genes encoding the benzoxazinoid biosynthesis enzymes Bx1, Bx3, Bx4, Bx5, and Bx8_9 were confirmed to be differentially expressed between qd and WT. Our results suggest that benzoxazinoids could play critical roles in regulating the stem elongation phenotype of qd.

scholarly journals Prediction of molecular markers of bovine mastitis by meta-analysis of differentially expressed genes using combined p-value and robust rank aggregation

2021 ◽  
Author(s):  
Anushri Umesh ◽  
Praveen Kumar Guttula ◽  
Mukesh Kumar Gupta
Keyword(s):  
Molecular Markers ◽  
Differentially Expressed Genes ◽  
Meta Analysis ◽  
Mirna Gene ◽  
Bovine Mastitis ◽  
Rank Aggregation ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
P Value ◽  
Expression Levels

Bovine mastitis causes significant economic loss to the dairy industry by affecting milk quality and quantity. E.coli and S.aureus are the two common mastitis-causing bacteria among the consortia of mastitis pathogens, wherein E.coli is an opportunistic environmental pathogen, and S.aureus is a contagious pathogen. This study was designed to predict molecular markers of bovine mastitis by meta-analysis of differentially expressed genes (DEG) in E.coli or S.aureus infected mammary epithelial cells (MECs) using p-value combination and robust rank aggregation (RRA) methods. High throughput transcriptome of bovine (MECs, infected with E.coli or S.aureus, were analyzed, and correlation of z-scores were computed for the expression datasets to identify the lineage profile and functional ontology of DEGs. Key pathways enriched in infected MECs were deciphered by Gene Set Enrichment Analysis (GSEA), following which combined p-value and RRA were used to perform DEG meta-analysis to limit type I error in the analysis. The miRNA-Gene networks were then built to uncover potential molecular markers of mastitis. Lineage profiling of MECs showed that the gene expression levels were associated with mammary tissue lineage. The up-regulated genes were enriched in immune-related pathways whereas down-regulated genes influenced the cellular processes. GSEA analysis of DEGs deciphered the involvement of Toll-like receptor (TLR), and NF- Kappa B signalling pathway during infection. Comparison after meta-analysis yielded with genes ZC3H12A, RND1 and MAP3K8 having significant expression levels in both E.coli and S.aureus dataset and on evaluating miRNA-Gene network 7 pairs were common to both sets identifying them as potential molecular markers.

scholarly journals C3aR1 Correlates With Immune Cell Infiltration and Serves as Prognostic and Therapeutic Biomarker in Gastric Cancer

2021 ◽  
Author(s):  
weifeng liu ◽  
Zhijie Chu ◽  
Cheng Yang ◽  
Tianbao Yang ◽  
Yanhui Yang ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
T Cell ◽  
Differentially Expressed Genes ◽  
Tumor Tissue ◽  
Immune Cell ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Expression Levels

Abstract As the fourth most common malignancy worldwide, gastric cancer can lead more than 720 000 patient death every year. Precisely therapeutic intervention can significantly improve patients’ survival status underlying the precise clarification by molecular indexes. Identifying the biomarkers highly associated with disease prognosis will be helpful to guide the clinical therapy. C3ar1 is an essential receptor in the complement system, and participates in various biological processes associated with immunological responses. To identify the crucial roles of C3AR1 in gastric cancer tmorigenesis, we determined the mRNA profile, protein expression levels and the clinicopathological indexes using cBioportal, Kaplan-Meier plotter and the Human Protein Atlas databases. To identify the molecular network in C3AR1-expressed gastric cancer, we obtained the differentially expressed genes using the GEPIA database compared with normal stomach tissues. Furthermore, we analyzed the biological impact of these differentially expressed genes using protein-protein interaction network and gene set enrichment analysis, in which we identified the hub genes and critical pathways influenced by over-expressed C3AR1 in gastric cancer. Finally, we evaluated the correlation between the C3AR1 expression levels and immune cell infiltration levels utilizing the Tumor Immunoassay Resource database. Our results revealed that the higher expression level of C3AR1 can lead higher infiltration of T cell CD8+, T cell CD4+, macrophage, neutrophil, B cell and myeloid dendritic cells into tumor tissue. Moreover, we also found that higher infiltration of macrophage cells into tumor tissue can worsen the survival of patients with gastric cancer, which may be highly associated with the polarization states of macrophages (TAM and M2 status). Our investigation suggest that C3AR1 can be as an efficient diagnostic biomarkers for gastric cancer therapy.

scholarly journals Estimating the False Discovery Rate Using Mixed Normal Distribution for Identifying Differentially Expressed Genes in Microarray Data Analysis

2007 ◽  
Vol 3 ◽  
pp. 117693510700300
Author(s):  
Akihiro Hirakawa ◽  
Yasunori Sato ◽  
Takashi Sozu ◽  
Chikuma Hamada ◽  
Isao Yoshimura
Keyword(s):  
False Discovery Rate ◽  
Normal Distribution ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Microarray Data Analysis ◽  
Test Statistic ◽  
Experimental Conditions ◽  
Expression Levels ◽  
False Discovery ◽  
Mixed Normal Distribution

The recent development of DNA microarray technology allows us to measure simultaneously the expression levels of thousands of genes and to identify truly correlated genes with anticancer drug response (differentially expressed genes) from many candidate genes. Significance Analysis of Microarray (SAM) is often used to estimate the false discovery rate (FDR), which is an index for optimizing the identifiability of differentially expressed genes, while the accuracy of the estimated FDR by SAM is not necessarily confirmed. We propose a new method for estimating the FDR assuming a mixed normal distribution on the test statistic and examine the performance of the proposed method and SAM using simulated data. The simulation results indicate that the accuracy of the estimated FDR by the proposed method and SAM, varied depending on the experimental conditions. We applied both methods to actual data comprised of expression levels of 12,625 genes of 10 responders and 14 non-responders to docetaxel for breast cancer. The proposed method identified 280 differentially expressed genes correlated with docetaxel response using a cut-off value for achieving FDR <0.01 to prevent false-positive genes, although 92 genes were previously thought to be correlated with docetaxel response ones.

Haploinsufficiency of RPS14 and Deregulation of Ribosomal- and Translation-Related Genes in MDS Patients with Del(5q)

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 3641-3641
Author(s):  
Andrea Pellagatti ◽  
Eva Hellström-Lindberg ◽  
Aristoteles Giagounidis ◽  
Janet Perry ◽  
Luca Malcovati ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Hierarchical Clustering ◽  
Ribosome Biogenesis ◽  
De Novo ◽  
Bone Marrow Cells ◽  
Expression Profiles ◽  
Ribosomal Subunit ◽  
Differentially Expressed ◽  
Expression Levels ◽  
Lower Expression

Abstract The del(5q) is the most commonly reported deletion in de novo MDS and is found in 10–15% of all patients. Our group demonstrated haploinsufficiency for the ribosomal gene RPS14, which is required for the maturation of 40S ribosomal subunits and maps to the commonly deleted region in patients with the 5q- syndrome (Boultwood et al, Br J Haematol2007, 139:578–89). Haploinsufficiency of RPS14 has been shown to be the mechanism underlying the erythroid defect in this disorder (Ebert et al, Nature2008, 451:335–9). We have recently shown that haploinsufficiency of RPS14 in patients with the 5q- syndrome is associated with deregulated expression of ribosomal- and translation-related genes, suggesting that the 5q- syndrome represents a disorder of aberrant ribosome biogenesis (Pellagatti et al, Br J Haematol2008, 142:57–64). The del(5q) in the 5q-syndrome is cytogenetically indistinguishable from the del(5q) found in other MDS and in the vast majority of these patients the CDR of the 5q- syndrome will be deleted (and therefore one allele of RPS14 will be lost). We are investigating the hypothesis that haploinsufficiency of RPS14 and consequent deregulated ribosome biogenesis may also play a role in the pathogenesis of non-5q- syndrome MDS patients with del(5q). Using Affymetrix U133 Plus2.0 arrays, we have studied the expression profiles of a group of 579 ribosomal- and translation-related genes in the CD34+ cells of 21 non-5q- syndrome MDS patients with del(5q) and 95 MDS patients without del(5q). 168 of 579 ribosomal-and translation-related probe sets were found to be significantly differentially expressed between these two groups, with approximately 90% of these showing lower expression levels in patients with del(5q). Hierarchical clustering using this set of 168 genes gave a good separation between patients with and without the del(5q). RPS14 was one of the most significant differentially expressed genes, with lower expression levels in patients with del(5q) confirming its haploinsufficient status in these patients. Other significant differentially expressed genes include the ribosomal protein RPL22L1, and the translation initiation factors EIF4EBP3 and EIF4B. Interestingly, when samples from 16 patients with 5q- syndrome were included in the analysis, hierarchical clustering using significantly differentially expressed ribosomal- and translation-related genes showed that most patients with 5q- syndrome and most patients with del(5q) clustered together. We are currently using polysome profile analysis on bone marrow cells to examine the levels of the 40S ribosomal subunit in patients with del(5q) and without del(5q). Our results support the hypothesis that haploinsufficiency of RPS14 and deregulation of ribosomal- and translation-related genes contribute to disease pathogenesis in MDS patients with del(5q). An exciting possibility is that other MDS with the del(5q) and the 5q- syndrome share a related molecular basis in that they are all disorders of defective ribosomal biogenesis.

scholarly journals 0020 Differentially Expressed Genes Using Saliva Samples from Nurses Rotating Shifts

SLEEP ◽  
2020 ◽  
Vol 43 (Supplement_1) ◽  
pp. A8-A8
Author(s):  
C C Imes ◽  
M A Monica ◽  
E R Chasens ◽  
Y P Conley
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Shift Work ◽  
Repeated Measures ◽  
Night Shift ◽  
Differentially Expressed ◽  
Study Program ◽  
Expression Levels ◽  
Increased Risk ◽  
Female Nurses

Abstract Introduction Globally, millions of people work night or rotating shifts (i.e., shift work), including nurses and other healthcare providers. Shift work can cause insufficient and mistimed sleep which disrupts the normal circadian rhythm. Shift work is associated with an increased risk for cardio-metabolic disorders and certain cancers. This descriptive, single group, within-subject, repeated-measures study explored the effect of shift work on gene expression levels in a sample of female nurses engaged in rotating shifts. Methods Saliva samples were collected from ten nurses without sleep or alertness medication use or a sleep disorder. The samples were collected using DNA Genotek RNA stabilizing saliva kits after participants worked at least 3 consecutive day shifts (~ 7:30 pm) and 3 consecutive night shifts (~7:30 am). Takara Smarter Stranded Total RNA Seq Kit was used following manufacturer’s instructions on an Illumina NextSeq500. CLC Genomic Workbench 12 (Qiagen) was used for quality control, aligning the sequence reads, normalization, and differential expression analyses. Genes with log2 fold changes of ± 2.0 were included in gene set enrichment and pathway analyses using Ingenuity Pathway Analysis (IPA; Qiagen). Results Participants were all female, white, and mostly healthy with a mean ± SD age of 27.2 ± 4.5 years. Compared to the post-day shift samples, a total of 287 genes were differentially expressed at a log2 fold change of ± 2.0 in the post-night shift samples. The genes with the greatest increase in expression levels were: PRDX5, SLC7A5, FCGR1A, DNAJC7, PSMD4, and PER1. The genes with the greatest decrease in expression levels were: PPIP5K2, SCART1, CASP10, SLC24A4, and OSBP. Based on the IPA analyses, the differentially expressed genes play a role in gene expression, cell signaling, cell death and survival, and RNA damage and repair. Conclusion Significant differential gene expression in pathways associated with poor health were observed among female nurses engaged in rotating shifts. Potential molecular and cellular functions were identified that may be the mechanisms resulting in the increased health risks associated with shift work. Support University of Pittsburgh School of Nursing Center for Research and Evaluation Pilot/Feasibility Study Program

scholarly journals Intraspecific transcriptome variation and sex-biased expression in Anopheles arabiensis

2021 ◽  
Author(s):  
Vivek Jayaswal ◽  
Cyrille Ndo ◽  
Hsiu-Ching Ma ◽  
Bryan Clifton ◽  
Marco Pombi ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
X Chromosome ◽  
Anopheles Arabiensis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Variable Component ◽  
Sample Type ◽  
Expression Ratio ◽  
Expression Levels ◽  
Transcriptional Variation

Abstract The magnitude and functional patterns of intraspecific transcriptional variation in the anophelines, including those of sex-biased genes underlying sex-specific traits relevant for malaria transmission, remain understudied. As a result, how changes in expression levels drive adaptation in these species is poorly understood. We sequenced the female, male, and larval transcriptomes of three populations of Anopheles arabiensis from Burkina Faso. One-third of the genes were differentially expressed between populations, often involving insecticide resistance-related genes in a sample type-specific manner, and with the females showing the largest number of differentially expressed genes. At the genomic level, the X chromosome appears depleted of differentially expressed genes compared to the autosomes, chromosomes harbouring inversions do not exhibit evidence for enrichment of such genes, and genes that are top contributors to functional enrichment patterns of population differentiation tend to be clustered in the genome. Further, the magnitude of variation for the sex expression ratio across populations did not substantially differ between male- and female-biased genes, except for some populations in which male-limited expressed genes showed more variation than their female counterparts. In fact, female-biased genes exhibited a larger level of interpopulation variation than male-biased genes, both when assayed in males and females. Beyond uncovering extensive adaptive potential of transcriptional variation in An. arabiensis, our findings suggest that the evolutionary rate of changes in expression levels on the X chromosome exceeds that on the autosomes, while pointing to female-biased genes as the most variable component of the An. arabiensis transcriptome.

scholarly journals Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells

2017 ◽  
Author(s):  
John D. Blischak ◽  
Ludovic Tailleux ◽  
Marsha Myrthil ◽  
Cécile Charlois ◽  
Emmanuel Bergot ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dendritic Cells ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Healthy Individuals ◽  
Data Set ◽  
Expression Levels ◽  
Infected Cells ◽  
Latent Tb ◽  
Gene Expression Levels

ABSTRACTTuberculosis (TB) is a deadly infectious disease, which kills millions of people every year. The causative pathogen, Mycobac-terium tuberculosis (MTB), is estimated to have infected up to a third of the world’s population; however, only approximately 10% of infected healthy individuals progress to active TB. Despite evidence for heritability, it is not currently possible to predict who may develop TB. To explore approaches to classify susceptibility to TB, we infected with MTB dendritic cells (DCs) from putatively resistant individuals diagnosed with latent TB, and from susceptible individuals that had recovered from active TB. We measured gene expression levels in infected and non-infected cells and found hundreds of differentially expressed genes between susceptible and resistant individuals in the non-infected cells. We further found that genetic polymorphisms nearby the differentially expressed genes between susceptible and resistant individuals are more likely to be associated with TB susceptibility in published GWAS data. Lastly, we trained a classifier based on the gene expression levels in the non-infected cells, and demonstrated decent performance on our data and an independent data set. Overall, our promising results from this small study suggest that training a classifier on a larger cohort may enable us to accurately predict TB susceptibility.

scholarly journals Screening and Identification of Differentially Expressed Genes Expressed among Left and Right Colon Adenocarcinoma

2020 ◽  
Vol 2020 ◽  
pp. 1-16
Author(s):  
Jing Han ◽  
Xue Zhang ◽  
Yang Yang ◽  
Li Feng ◽  
Gui-Ying Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Kinase Inhibitor ◽  
Colon Adenocarcinoma ◽  
Interaction Network ◽  
Differentially Expressed ◽  
Right Colon ◽  
Hub Genes ◽  
Expression Levels ◽  
Public Data

Purpose. Colon adenocarcinoma (COAD) is the third most common malignancy globally and is further categorized as left colon adenocarcinoma (LCOAD) or right colon adenocarcinoma (RCOAD) depending on the location of the primary tumor. The therapeutic outcome and long-term prognosis for patients with COAD are less than satisfactory, and this may be associated with tumor location. Therefore, it is important to investigate the genetic differences in COAD at different sites. Patients and Methods. Public data associated with COAD were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified using R software (version 3.5.3), and functional annotation of DEGs was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. A protein-protein interaction network was constructed, hub genes were identified and analyzed, and data mining using Gene Expression Profiling Interactive Analysis (GEPIA) was conducted. Results. A total of 286 DEGs were identified between LCOAD and RCOAD. Additionally, 10 hub genes associated with COAD at different locations were screened, namely, CDKN2A, IGF1R, MDM2, SMAD3, SLC2A1, GRM5, PLCB4, FGFR1, UBE2V2, and TNFRSF10B. The expression of cyclin-dependent kinase inhibitor 2A (CDKN2A) and solute carrier family 2 member 1 (SLC2A1) was significantly associated with pathological stage P<0.05. COAD patients with high expression levels of CDKN2A exhibited poorer overall survival (OS) times than those with low expression levels P<0.05. Conclusion. CDKN2A expression was significantly different between LCOAD and RCOAD and was closely related to the prognosis of COAD. It is of great value for further understanding of the pathogenesis of LCOAD and RCOAD.

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