ArrayQue: The comprehensive transcriptome data analysis tool

백동엽,유진호,이영복,조윤주,신지영,정호상,안준익,김양석 한국바이오칩학회 2012 BioChip Journal Vol.6 No.4

We have developed microarray analysis pipeline software for covering the entire process of transcriptome data analysis. This software, part of the Korea Toxicogenomics Integrated System (KOTIS), is freely distributed to users who upload their microarray data to the KOTIS database, which is operated under the server system of the National Institute of Toxicological Research (NITR). The uploaded microarray data can be downloaded by users through a web search interface within KOTIS and are used as input data of the analysis software. The software, which consists of four major analysis modules and one meta-analysis module, is connected to a gene-related annotation database through the web. Major analysis modules consist of (1) data import and preprocessing, (2) differentially expressed gene finding, (3) clustering analysis, and (4) classification analysis. A gene-related annotation database provides the biological meanings of the analysis results. A highly standardized analysis flow, from data import to differentially expressed gene finding, can be easily implemented using the interface series of a run wizard. The KOTIS system and analysis software are accessible at ttp://kotis.nitr.go.kr.

Transcriptome Analysis Identifies Altered Biological Processes and Novel Markers in Human Immunodeficiency Virus-1 Long-Term Non-Progressors

Lee Dayeon,Yoon Cheol-Hee,Choi Sin Young,Kim Jung-Eun,조영걸,Choi Byeong-Sun,Park Jihwan 대한감염학회 2021 Infection and Chemotherapy Vol.53 No.3

Background: The latent reservoir of Human Immunodificiency Virus-1 (HIV-1) has been a major barrier to the complete eradication of HIV-1 and the development of HIV therapy. Longterm non-progressors (LTNPs) are a rare group of patients with HIV-1 who can spontaneously control HIV-1 replication without antiretroviral therapy. Transcriptome analysis is necessary to predict the pathways involved in the natural control of HIV-1, elucidate the mechanisms involved in LTNPs, and find biomarkers for HIV-1 reservoir therapy. Materials and Methods: In this study, we obtained peripheral blood mononuclear cells from two LTNP subjects at multiple time points and performed RNA-sequencing analyses. Results: We found that LTNPs and normal subjects had different transcriptome profiles. Functional annotation analysis identified that differentially expressed genes in LTNPs were enriched in several biological pathways such as cell cycle-related pathways and the transforming growth factor-beta signaling pathway. However, genes that were downregulated in LTNPs were associated with immune responses such as the interferon response and IL2- STAT5 signaling. Protein-protein interaction network analysis showed that CD8A, KLRD1, ASGR1, and MLKL, whose gene expression was upregulated in LTNPs, directly interacted with HIV-1 proteins. The network analysis also found that viral proteins potentially regulated host genes that were associated with immune system processes, metabolic processes, and gene expression regulation. Conclusion: Our longitudinal transcriptome analysis of the LTNPs identified multiple previously undescribed pathways and genes that may be useful in the discovery of novel therapeutic targets and biomarkers.

Transcriptome analysis reveals synergistic modulation of E-cadherin/N-cadherin in hMSC aggregates chondrogenesis

Wang Xueping,Zhang Yan,Yang Jun 한국유전학회 2023 Genes & Genomics Vol.45 No.5

Background N-cadherin-mediated cell adhesion is a vital inductor for mesenchymal condensation in chondrogenesis. Recent studies have revealed the involvement of E-cadherin in enhancing the multipotency of mesenchymal stem cells (MSCs) and limb development; however, the signaling crosstalk of E/N-cadherin remains unclear. Objective This study aimed to explore the synergistic modulation of E/N-cadherin in the chondrogenic differentiation of MSC aggregates. Methods Human E/N-cadherin-functionalized (hE/N-cad-Fc) poly (lactic-co-glycolic acid) (PLGA) microparticles (hE/N-cad-PLGA) were incorporated into the human MSC (hMSC) aggregates to upregulate the expression of the corresponding endogenous cadherin. The chondrogenic differentiation of the hMSC aggregates was initiated by hE/N-cad-PLGA, controlling the release of transforming growth factor-β (TGF-β). A transcriptome analysis was used to assess differentially expressed genes (DEGs) modulated by hE/N-cad-Fc in hMSC aggregate chondrogenesis. Gene functions and signaling pathways were assessed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The associated biological pathways were assessed by a protein–protein interaction (PPI) network analysis, and the results were further confirmed by real-time quantitative PCR (qPCR) and western blotting. Results A total of 1083 DEGs, comprising 111 upregulated and 972 downregulated genes, were discovered to be related to the enhanced chondrogenic differentiation modulated by hE/N-cad-Fc. The GO and KEGG functional enrichment analyses revealed that hE/N-cad-Fc synergistically regulated the p53-related survival signaling pathway. PPI analysis revealed that mitogen-activated protein kinases (MAPK) caspase regulation is a core aspect of the chondrogenic differentiation process, confirmed by western blotting. Conclusion To the best of our knowledge, our study is the first to reveal that the synergistic modulation of E/N-cadherin enhances the chondrogenic differentiation of hMSCs via the ERK1/2-p53 signaling axis.

Transcriptomic profiles and their correlations in saliva and gingival tissue biopsy samples from periodontitis and healthy patients

Jeon, Yoon-Sun,Cha, Jae-Kook,Choi, Seong-Ho,Lee, Ji-Hyun,Lee, Jung-Seok Korean Academy of Periodontology 2020 Journal of Periodontal & Implant Science Vol.50 No.5

Purpose: This study was conducted to analyze specific RNA expression profiles in gingival tissue and saliva samples in periodontitis patients and healthy individuals, and to determine their correlations in light of the potential use of microarray-based analyses of saliva samples as a periodontal monitoring tool. Methods: Gingival tissue biopsies and saliva samples from 22 patients (12 with severe periodontitis and 10 with a healthy periodontium) were analyzed using transcriptomic microarray analysis. Differential gene expression was assessed, and pathway and clustering analyses were conducted for the samples. The correlations between the results for the gingival tissue and saliva samples were analyzed at both the gene and pathway levels. Results: There were 621 differentially expressed genes (DEGs; 320 upregulated and 301 downregulated) in the gingival tissue samples of the periodontitis group, and 154 DEGs (44 upregulated and 110 downregulated) in the saliva samples. Nine of these genes overlapped between the sample types. The periodontitis patients formed a distinct cluster group based on gene expression profiles for both the tissue and saliva samples. Database for Annotation, Visualization and Integrated Discovery analysis revealed 159 enriched pathways from the tissue samples of the periodontitis patients, as well as 110 enriched pathways In the saliva samples. Thirty-four pathways overlapped between the sample types. Conclusions: The present results indicate the possibility of using the salivary transcriptome to distinguish periodontitis patients from healthy individuals. Further work is required to enhance the extraction of available RNA from saliva samples.

Transcriptome analysis of Panax ginseng response to high light stress

Je Hyeong Jung,Ho-Youn Kim,Hyoung Seok Kim,Sang Hoon Jung 고려인삼학회 2020 Journal of Ginseng Research Vol.44 No.2

Background: Ginseng (Panax ginseng Meyer) is an essential source of pharmaceuticals and functionalfoods. Ginseng productivity has been compromised by high light (HL) stress, which is one of the majorabiotic stresses during the ginseng cultivation period. The genetic improvement for HL tolerance inginseng could be facilitated by analyzing its genetic and molecular characteristics associated with HLstress. Methods: Genome-wide analysis of gene expression was performed under HL and recovery conditions in1-year-old Korean ginseng (P. ginseng cv. Chunpoong) using the Illumina HiSeq platform. After de novoassembly of transcripts, we performed expression profiling and identified differentially expressed genes(DEGs). Furthermore, putative functions of identified DEGs were explored using Gene Ontology termsand Kyoto Encyclopedia of Genes and Genome pathway enrichment analysis. Results: A total of 438 highly expressed DEGs in response to HL stress were identified and selected from29,184 representative transcripts. Among the DEGs, 326 and 114 transcripts were upregulated anddownregulated, respectively. Based on the functional analysis, most upregulated and a significantnumber of downregulated transcripts were related to stress responses and cellular metabolic processes,respectively. Conclusion: Transcriptome profiling could be a strategy to comprehensively elucidate the genetic andmolecular mechanisms of HL tolerance and susceptibility. This study would provide a foundation fordeveloping breeding and metabolic engineering strategies to improve the environmental stress toleranceof ginseng.

Transcriptome analysis of Panax ginseng response to high light stress

Jung, Je Hyeong,Kim, Ho-Youn,Kim, Hyoung Seok,Jung, Sang Hoon The Korean Society of Ginseng 2020 Journal of Ginseng Research Vol.44 No.2

Background: Ginseng (Panax ginseng Meyer) is an essential source of pharmaceuticals and functional foods. Ginseng productivity has been compromised by high light (HL) stress, which is one of the major abiotic stresses during the ginseng cultivation period. The genetic improvement for HL tolerance in ginseng could be facilitated by analyzing its genetic and molecular characteristics associated with HL stress. Methods: Genome-wide analysis of gene expression was performed under HL and recovery conditions in 1-year-old Korean ginseng (P. ginseng cv. Chunpoong) using the Illumina HiSeq platform. After de novo assembly of transcripts, we performed expression profiling and identified differentially expressed genes (DEGs). Furthermore, putative functions of identified DEGs were explored using Gene Ontology terms and Kyoto Encyclopedia of Genes and Genome pathway enrichment analysis. Results: A total of 438 highly expressed DEGs in response to HL stress were identified and selected from 29,184 representative transcripts. Among the DEGs, 326 and 114 transcripts were upregulated and downregulated, respectively. Based on the functional analysis, most upregulated and a significant number of downregulated transcripts were related to stress responses and cellular metabolic processes, respectively. Conclusion: Transcriptome profiling could be a strategy to comprehensively elucidate the genetic and molecular mechanisms of HL tolerance and susceptibility. This study would provide a foundation for developing breeding and metabolic engineering strategies to improve the environmental stress tolerance of ginseng.

Transcriptome profiling and genomic atlas study for endocrine disrupting chemicals in whole body system of animals

Yejee Park,Min-Jae Jang,김준모 한국동물유전육종학회 2022 한국동물유전육종학회지 Vol.6 No.4

Understanding the biological phenomena encoded through the genome is important. Therefore, it is possible to identify the genes of each organism and infer the characteristics and similarities of each other through the genomic analysis. RNA-seq is a representative method among methods for comparing gene expression levels through transcriptome analysis. It is accompanied by next generation sequencing (NGS) and enables highly quantitative and wide-range precise measurement. A representative research method that includes whole genome contents is to construct a biological map. Using the atlas, it is possible to conduct research that includes all comprehensive genetic information to identify specific locations where genes are expressed through gene location mapping. In addition, by identifying the correlation between the gene and the biomarker in the network, select a significant biomarker and functional analysis could be performed. Endocrine disruptors cause diseases by disrupting endocrine function in the body. Bisphenol A, a representative endocrine disruptor, is most permeated in daily life, threatening human health, obesity and spermatogenesis. This review focuses on transcriptome profiling and genomic atlas construction that can provide comprehensive biological insights in animal genetics studies and information of endocrine disrupting chemicals.

Genome-wide analysis of root hair-preferential genes in rice

Moon, Sunok,Chandran, Anil Kumar Nalini,An, Gynheung,Lee, Chanhui,Jung, Ki-Hong Springer US 2018 Rice Vol.11 No.-

<P><B>Background</B></P><P>Root hairs are valuable in taking up nutrients and water from the rhizosphere and serving as sites of interactions with soil microorganisms. By increasing the external surface area of the roots or interacting with rhizobacteria, root hairs directly and indirectly promote plant growth and yield. Transcriptome data can be used to understand root-hair development in rice.</P><P><B>Result</B></P><P>We performed Agilent 44 K microarray experiments with enriched root-hair samples and identified 409 root hair-preferential genes in rice. The expression patterns of six genes were confirmed using a <I>GUS</I> reporter system and quantitative RT-PCR analysis. Gene Ontology (GO) analysis demonstrated that 13 GO terms, including oxygen transport and cell wall generation, were highly over-represented in those genes. Although comparative analysis between rice and <I>Arabidopsis</I> revealed a large proportion of orthologous pairs, their spatial expression patterns were not conserved. To investigate the molecular network associated with root hair-preferential genes in rice, we analyzed the PPI network as well as coexpression data. Subsequently, we developed a refined network consisting of 24 interactions between 10 genes and 18 of their interactors.</P><P><B>Conclusion</B></P><P>Identification of root hair-preferential genes and in depth analysis of those genes will be a useful reference to accelerate the understanding of root-hair development in rice.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1186/s12284-018-0241-2) contains supplementary material, which is available to authorized users.</P>

Identification of the transcriptome profile of Miamiensis avidus after mebendazole treatment

김현수,이아름,전경윤,고은지,Cha Hee-Jae,옥미선 고신대학교(의대) 고신대학교 의과대학 학술지 2022 고신대학교 의과대학 학술지 Vol.37 No.3

Background: The scuticociliate <i>Miamiensis avidus</i> is a major pathogenic agent that causes significant economic losses in the flounder aquaculture industry. Many different types of drugs are being tested to control this disease, including mebendazole, which is a broad-spectrum antiprotozoal agent. The purpose of this study was to determine whether mebendazole worked <i>in vitro</i> against <i>M. avidus</i> and to explore its mechanism of action. Methods: Transcriptome and gene ontology analyses were conducted to investigate the specifically expressed gene profile. We confirmed the cytotoxic effect of mebendazole against <i>M. avidus</i> when it was applied intermittently for a total of three times. We also identified differentially expressed genes using transcriptome analysis. Results: Most of the upregulated genes were membrane transport-related genes, including Na⁺/K⁺-ATPase. Most of the downregulated genes were categorized into three groups: tubulin-related, metabolism-related, and transport-related genes. The expression levels of glucose uptake-related genes decreased due to the inhibition of tubulin polymerization, but this was not statistically significant.Conclusions: Our results demonstrate that intermittent treatment with mebendazole has a significant cytotoxic effect on <i>M. avidus</i>. Furthermore, mebendazole induces downregulation of the tubulin-alpha chain and metabolism-related genes. It is presumed that this leads to a glucose shortage and the death of <i>M. avidus</i>. Transcriptome analysis will provide useful clues for further studies on mebendazole applications for scutica control.

Dissecting Metabolic Regulation in Mycelial Growth and Fruiting Body Developmental Stages of Cordyceps militaris through Integrative Transcriptome Analysis

Roypim Thananusak,Kobkul Laoteng,Nachon Raethong,Mattheos Koffas,Wanwipa Vongsangnak 한국생물공학회 2023 Biotechnology and Bioprocess Engineering Vol.28 No.3

Dissecting the cellular metabolism of Cordyceps militaris is important for the efficient production of bioactive compounds of a target with medicinal and industrial applications. However, the metabolic functions during developmental stages in this fungus at a system level are still unexplored. In this study, we aimed to reveal the metabolic functions and regulation of C. militaris TBRC6039 relevant to its developmental stages, including mycelial growth (MY) and fruiting body (FB) stages through integrative transcriptome analysis. The transcriptome analysis showed that 9,256 genes of C. militaris were expressed in both stages. Of them, 1,877 genes, residing primarily in the cell division cycle and amino acid, carbohydrate, and lipid metabolisms, exhibited significant differences in transcript levels between the MY and FB stages. Through integration with genome-scale networks analysis, the unique reporter metabolites (e.g., α-D-glucose, β-D-glucose, D-galactose, triacylglycerol, and diacylglycerol) and key regulators (e.g., AtfA, Atf2, and Yap1 transcription factors) were identified in C. militaris when grown at FB stage, linking to up-regulation of the metabolic genes involved in galactose and polysaccharide metabolisms, as well as glycerolipid and glycerophospholipid biosynthesis. Moreover, the high cordycepin content is related to the upregulated genes in lipid metabolism during the FB stage. Our findings suggest that the transcriptional regulation of these metabolic pathways played a crucial role in specific developmental stages of C. militaris. This study serves for cultivation process improvement for overproduction of valuable metabolites in C. militaris through an emerging systems and synthetic biology approach.