Bioinformatics analyses of gene expression profile identify key genes and functional pathways involved in cutaneous lupus erythematosus

2021 ◽  
Author(s):  
Zhen-yu Gao ◽  
Lin-chong Su ◽  
Qing-chao Wu ◽  
Jiao-e Sheng ◽  
Yun-long Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Lupus Erythematosus ◽  
Cutaneous Lupus Erythematosus ◽  
Bioinformatics Analyses ◽  
Functional Pathways ◽  
Key Genes ◽  
Cutaneous Lupus

scholarly journals Application of Serial Analysis of Gene Expression to the Study of the Gene Expression Profile ofLeishmania infantum chagasiPromastigote

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Adelino Soares Lima Neto ◽  
Osvaldo Pompílio de Melo Neto ◽  
Carlos Henrique Nery Costa
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Leishmania Infantum ◽  
Open Reading Frames ◽  
Genomic Sequences ◽  
Coding Sequences ◽  
Key Genes ◽  
Reading Frames

This study describes the application of the LongSAGE methodology to study the gene expression profile in promastigotes ofLeishmania infantum chagasi. A tag library was created using the LongSAGE method and consisted of 14,208 tags of 17 bases. Of these, 8,427 (59.3%) were distinct. BLAST research of the 1,645 most abundant tags showed that 12.8% of them identified the coding sequences of genes, while 82% (1,349/1,645) identified one or more genomic sequences that did not correspond with open reading frames. Only 5.2% (84/1,645) of the tags were not aligned to any position in theL. infantum genome. The UTR size ofLeishmaniaand the lack of CATG sites in some transcripts were decisive for the generation of tags in these regions. Additional analysis will allow a better understanding of the expression profile and discovering the key genes in this life cycle.

Integration of Single-Cell RNA- and CAGE-seq Reveals Tooth-Enriched Genes

2021 ◽  
pp. 002203452110497
Author(s):  
Y. Chiba ◽  
K. Yoshizaki ◽  
T. Tian ◽  
K. Miyazaki ◽  
D. Martin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Tooth Development ◽  
Expression Profiles ◽  
Cell Type ◽  
Bioinformatics Analyses ◽  
Data Set ◽  
Cell Type Specific

Organ development is dictated by the regulation of genes preferentially expressed in tissues or cell types. Gene expression profiling and identification of specific genes in organs can provide insights into organogenesis. Therefore, genome-wide analysis is a powerful tool for clarifying the mechanisms of development during organogenesis as well as tooth development. Single-cell RNA sequencing (scRNA-seq) is a suitable tool for unraveling the gene expression profile of dental cells. Using scRNA-seq, we can obtain a large pool of information on gene expression; however, identification of functional genes, which are key molecules for tooth development, via this approach remains challenging. In the present study, we performed cap analysis of gene expression sequence (CAGE-seq) using mouse tooth germ to identify the genes preferentially expressed in teeth. The CAGE-seq counts short reads at the 5′-end of transcripts; therefore, this method can quantify the amount of transcripts without bias related to the transcript length. We hypothesized that this CAGE data set would be of great help for further understanding a gene expression profile through scRNA-seq. We aimed to identify the important genes involved in tooth development via bioinformatics analyses, using a combination of scRNA-seq and CAGE-seq. We obtained the scRNA-seq data set of 12,212 cells from postnatal day 1 mouse molars and the CAGE-seq data set from postnatal day 1 molars. scRNA-seq analysis revealed the spatiotemporal expression of cell type–specific genes, and CAGE-seq helped determine whether these genes are preferentially expressed in tooth or ubiquitously. Furthermore, we identified candidate genes as novel tooth-enriched and dental cell type–specific markers. Our results show that the integration of scRNA-seq and CAGE-seq highlights the genes important for tooth development among numerous gene expression profiles. These findings should contribute to resolving the mechanism of tooth development and establishing the basis for tooth regeneration in the future.

scholarly journals Identification of potential key genes associated with glioblastoma based on the gene expression profile

2017 ◽  
Vol 14 (2) ◽  
pp. 2045-2052 ◽  
Author(s):  
Lijuan Bo ◽  
Bo Wei ◽  
Chaohui Li ◽  
Zhanfeng Wang ◽  
Zheng Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Key Genes

scholarly journals A study on linking of clinical phenotype and gene expression profile in systemic lupus erythematosus

2020 ◽  
Author(s):  
Jian-Ruei Ciou ◽  
Pu-Wei Ho ◽  
Po-Chang Wu ◽  
Shu-I Chen ◽  
Ching-Mao Chang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Systemic Lupus Erythematosus ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Lupus Erythematosus ◽  
Transcriptome Sequencing ◽  
Clinical Phenotype ◽  
Differentially Expressed ◽  
Systemic Lupus ◽  
Malar Rash

Abstract Objectives: Malar rash is one of clinical phenotypes seen in systemic lupus erythematosus (SLE). However, the pathogenesis of malar rash is not clear for each case of SLE patients. In this paper we endeavored to investigate the linking of clinical phenotype from the gene expression profiles between both patients with malar rash and without malar rash. Therefore we might perform better evaluation of the possible prognosis for different SLE patients in the future.Methods: This study utilizes transcriptome sequencing (RNA-Seq) technologies to discover underlying gene expression profile for systemic lupus erythematosus patients. We performed transcriptome sequencing experiments and analyzed differentially expressed genes (DEGs) and associated pathways.Results: From the analysis of gene expression profiling, we identified the gene DAAM2 is the most differentially expressed gene for patients with malar rash. Using a gene set enrichment analysis, we discuss the linkage between DAAM2 and the possible pathways for systemic lupus erythematosus with malar rash. Conclusions: We identified DAAM2 as a candidate biomarker for the clinical phenotype of malar rash for systemic lupus erythematosus.

scholarly journals AB006. A modular analysis approach to studying gene expression in cutaneous lupus erythematosus

2021 ◽  
Vol 9 (5) ◽  
pp. AB006-AB006
Author(s):  
Jane Zhu ◽  
Ly Tran ◽  
Frank Zheng ◽  
Judith James ◽  
Joel Guthridge ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lupus Erythematosus ◽  
Cutaneous Lupus Erythematosus ◽  
Analysis Approach ◽  
Modular Analysis ◽  
Cutaneous Lupus

scholarly journals Quercetin inhibits the proliferation of multiple myeloma cells by upregulating PTPRR expression

2021 ◽  
Author(s):  
Houcai Wang ◽  
Dandan Yu ◽  
Hui Zhang ◽  
Ruye Ma ◽  
Huiqun Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Cell Proliferation ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Plasma Cells ◽  
Tyrosine Phosphatase ◽  
Underlying Mechanism ◽  
Bioinformatics Analyses ◽  
Important Approach

Abstract Multiple myeloma (MM) is an incurable disease characterized by malignant plasma cell clonal expansion in the bone marrow; therefore, inhibiting the proliferation of plasma cells is an important approach to overcome the progression of MM. Quercetin (Que) is a promising flavonoid with broad-spectrum anti-tumor activity against various cancers, including MM; however, the underlying mechanism is not yet understood. The present study aimed to reveal the gene expression profile of Que-treated MM cells and clarify its potential mechanism. The 30% inhibitory concentration (IC30) of Que against MM cells was calculated, and the proliferation rate was significantly reduced after Que treatment. Next, 495 dysregulated genes were identified via RNA sequencing in Que-treated MM cells. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses indicated that the dysregulated genes were enriched in various apoptosis-related GO terms and amino acid metabolism-related pathways. qPCR validation showed that protein tyrosine phosphatase receptor-type R (PTPRR) had the highest verified log2 FC (abs) among the top 15 dysregulated genes. Overexpression of PTPRR increased the sensitivity of MM cells against Que, significantly inhibiting their proliferation and colony formation ability; silencing of PTPRR showed the opposite results. Furthermore, bioinformatics analyses and PPI network construction of PTPRR indicated that dephosphorylation of ERK might be the potential pathway for the PTPRR-induced inhibition of MM cell proliferation. In summary, our study identified the gene expression profile in Que-treated MM cells and demonstrated that the upregulation of PTPRR was one of the important mechanisms for the Que-induced inhibition of MM cell proliferation.

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