Extending the Interpretation of Gene Profiling Microarray Experiments to Pathway Analysis Through the Use of Gene Ontology Terms

ICCS 2007 ◽  
2007 ◽  
pp. 55-61
Author(s):  
Aristotelis Chatziioannou ◽  
Panagiotis Moulos
Keyword(s):  
Gene Ontology ◽  
Pathway Analysis ◽  
Gene Profiling ◽  
Microarray Experiments

scholarly journals Digital Gene Expression Profiling Analysis of Aged Mice under Moxibustion Treatment

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Nan Liu ◽  
Yunyao Jiang ◽  
Min Xing ◽  
Baixiao Zhao ◽  
Jincai Hou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Gene Expression Profiling ◽  
Differentially Expressed Genes ◽  
Pathway Analysis ◽  
Expression Profiling ◽  
Digital Gene Expression ◽  
Differentially Expressed ◽  
Aged Mice ◽  
Digital Gene Expression Profiling

Aging is closely connected with death, progressive physiological decline, and increased risk of diseases, such as cancer, arteriosclerosis, heart disease, hypertension, and neurodegenerative diseases. It is reported that moxibustion can treat more than 300 kinds of diseases including aging related problems and can improve immune function and physiological functions. The digital gene expression profiling of aged mice with or without moxibustion treatment was investigated and the mechanisms of moxibustion in aged mice were speculated by gene ontology and pathway analysis in the study. Almost 145 million raw reads were obtained by digital gene expression analysis and about 140 million (96.55%) were clean reads. Five differentially expressed genes with an adjusted P value < 0.05 and |log⁡2(fold  change)| > 1 were identified between the control and moxibustion groups. They were Gm6563, Gm8116, Rps26-ps1, Nat8f4, and Igkv3-12. Gene ontology analysis was carried out by the GOseq R package and functional annotations of the differentially expressed genes related to translation, mRNA export from nucleus, mRNA transport, nuclear body, acetyltransferase activity, and so on. Kyoto Encyclopedia of Genes and Genomes database was used for pathway analysis and ribosome was the most significantly enriched pathway term.

scholarly journals Fast Gene Ontology based clustering for microarray experiments

2008 ◽  
Vol 1 (1) ◽  
Author(s):  
Kristian Ovaska ◽  
Marko Laakso ◽  
Sampsa Hautaniemi
Keyword(s):  
Gene Ontology ◽  
Microarray Experiments

scholarly journals IL-21 Enhances the Immune Protection Induced by the Vibrio Vulnificus Hemolysin A Protein

2021 ◽  
Author(s):  
Ke-Na Sun ◽  
Fei Huang ◽  
Ming-Yi Wang ◽  
Jing Wu ◽  
Cheng-Jin Hu ◽  
...  
Keyword(s):  
Gene Ontology ◽  
B Cell ◽  
Pathway Analysis ◽  
Germinal Center ◽  
Cell Response ◽  
Vibrio Vulnificus ◽  
Immune Protection ◽  
Rna Seq ◽  
Protection Effect ◽  
Novel Strategy

Abstract We previously reported that the Vibrio vulnificus hemolysin A (VvhA) protein elicited good immune protection and could effectively control V. vulnificus infection in mice. However, its molecular mechanism remains unknown. In this study, we found that IL-21 enhances immune protection by inducing a Tfh-cell and germinal center (GC) B-cell response. We used RNA-seq and identified 10 upregulated and 30 downregulated genes that were involved in IL-21-upregulated protection. We also performed Gene Ontology (GO) analysis and pathway analysis of these differentially expressed genes. Our findings indicate that IL-21 can enhance the immune protection effect of VvhA protein and may serve as a novel strategy for enhancing the immune protection effect of protein vaccines.

scholarly journals Screening differentially expressed genes of pancreatic cancer between Mongolian and Han people using bioinformatics technology

2019 ◽  
Author(s):  
Jiasheng Xu ◽  
Kaili Liao ◽  
ZHONGHUA FU ◽  
ZHENFANG XIONG
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Gene Ontology ◽  
Differentially Expressed Genes ◽  
Pathway Analysis ◽  
Differentially Expressed ◽  
Cancer Tissue ◽  
Pancreatic Cancer Tissue ◽  
Tissue Samples ◽  
Multiple Difference

Abstract Objective To screen and analyze differentially expressed genes in pancreatic carcinoma tissues taken from Mongolian and Han patients by Affymetrix Genechip. Methods: Pancreatic ductal cell carcinoma tissues were collected from the Mongolian and Han patients undergoing resection in the Second Affiliated Hospital of Nanchang University during March 2015 to May 2018 and the total RNA was extracted. Differentially expressed genes were selected from the total RNA qualified by Nanodrop 2000 and Agilent 2100 using Affymetrix and a cartogram was drawn; The gene ontology (GO) analysis and Pathway analysis were used for the collection and analysis of biological information of these differentially expressed genes. Finally, some differentially expressed genes were verified by real-time PCR. Results Through the microarray analysis of gene expression, 970 differentially expressed genes were detected by comparing pancreatic cancer tissue samples between Mongolian and Han patients. A total of 257 genes were significantly up-regulated in pancreatic cancer tissue samples in Mongolian patients;while a total of 713 genes were down-regulated. In the Gene Ontology database, 815 differentially expressed genes were identified with clear GO classification, and CPB1 gene had the highest multiple of differential expression (difference multiple: 31.76). The Pathway analysis detected 28 signaling pathways that included these differentially expressed genes, involving a total of 178 genes. Among these pathways, the enrichment of differentially expressed genes in the FAK signaling pathway was the highest and COL11A1 gene had the highest multiple difference (multiple difference: 5.02). The expressions of differentially expressed genes CPB1, COL11A1、ITGA4、BIRC3、PAK4、CPA1、CLPS、PIK3CG and HLA-DPA1 determined by real-time PCR were consistent with the results of gene chip analysis. Conclusions The results of microarray analysis of gene expression profiles showed that there are a large number of differentially expressed genes in pancreatic cancer tissue samples compared between Mongolian and Han populations. These genes are closely related to the proliferation, differentiation, invasion and metastasis and multi-drug resistance of pancreatic cancer and are involved in the regulation of multiple important signaling pathways in organisms.

Abstract 1195: A Genomic Signature of Atherosclerosis among Individuals with Low Framingham Risk Score: The Multi-Ethnic Study of Atherosclerosis (MESA)

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Chiang-Ching Huang ◽  
kiang Liu ◽  
Nalini Rajamannan ◽  
Pan Du ◽  
Simon Lin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Pathway Analysis ◽  
Framingham Risk Score ◽  
Subclinical Atherosclerosis ◽  
Innate Immune ◽  
Low Risk ◽  
Classification Model ◽  
Tlr Signaling ◽  
Framingham Risk

Background : The Framingham risk score (FRS) predicts low 10-year risks for the majority of women, even in the face of substantial burden of subclinical atherosclerosis (SA). However, many individuals predicted to be at low risk will still experience cardiovascular disease (CVD) events in the short term. We hypothesized that gene expression signatures in peripheral blood leukocytes (PBLs) could improve risk stratification among low-risk individuals, by identifying those with significant SA burden. Methods : We performed a case-control study of gene expression profiles among healthy women with low FRS (<10%) and no diabetes; we selected 49 cases with subclinical atherosclerosis (SA; defined as coronary artery calcification (CAC) >100 and carotid intima-media thickness (IMT) >1.0) and 72 age and race matched controls with CAC=0 and carotid IMT <0.65 from the MESA cohort. Microarray data were generated from Illumina BeadArray chips. Multiple cross-validation and gene ontology/pathway analysis were used to construct a classification model and identify genetic pathways involved in atherosclerosis. Results : A total of 2,462 genes with coefficient of variation >0.03 were used for data analysis. A gene signature composed of 40 to 60 genes in a support vector machine classification model was associated with an odds ratio of 3.5 for SA (p=0.002), resulting in a 71% specificity and 59% sensitivity for SA. For the 251 most differentially expressed genes (p = 10 −8 ~ 0.0004, false discovery rate (FDR) <0.2%) between those with and without SA, Ingenuity Pathway Analysis and Panther gene ontology analysis revealed this set of genes is enriched in innate immune function (p<10 −7 ). Notably, the majority of the top 30 genes (p<10 −6 , FDR<10 −6 ) were involved in toll-like receptor (TLR) signaling and hypoxia signaling. Conclusion : The results of functional genomic analysis suggest the activation of innate immune system through TLR signaling is associated with high burden of SA that can be detected in PBLs of healthy women predicted to be at low risk for CVD events. Our findings merit validation in a larger cohort.

scholarly journals Distinct Expression Profiles of lncRNAs Between Regressive and Mature Scars

2015 ◽  
Vol 35 (2) ◽  
pp. 663-675 ◽  
Author(s):  
Jingyun Li ◽  
Wei Long ◽  
Qian Li ◽  
Qing Zhou ◽  
Yu Wang ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Immune System ◽  
Differential Expression ◽  
Pathway Analysis ◽  
Expression Profiles ◽  
Molecular Targets ◽  
Differentially Expressed ◽  
Altered Expression ◽  
Qrt Pcr ◽  
Non Coding Rnas

Background: Recent studies suggest that long non-coding RNAs (lncRNAs) play crucial roles in human diseases. The function of lncRNAs in abnormal scar pathogenesis remains poorly understood. Methods: In this study, we examined the lncRNAs expression profiles among regressive and mature scars following caesarean sections. A total of 30,586 lncRNAs and 26,109 mRNAs were analyzed by microarrays (Human LncRNA Array v3.0, Arraystar, Inc.). Results: In total, we identified 1,871 lncRNAs and 817 mRNAs with differential expression between regressive and mature scar individuals (fold change≥3, p≤0.001). A set of differentially expressed lncRNA transcripts, in particular, lncRNA8975-1, AC097662.2 and RP11-586K2.1, were confirmed using qRT-PCR. Gene ontology and pathway analysis revealed that compared to mature scars, many processes over-represented in regressive scars are related to the immune system. Conclusion: Our results show significantly altered expression profiles of lncRNAs and mRNAs between regressive and mature scars. These transcripts are potential molecular targets for inhibiting abnormal scar formation following caesarean sections.

scholarly journals Identification and Characterization of Circular RNA Profiling in Kahin-Beck Disease

2021 ◽  
Author(s):  
Peilin Li ◽  
Ying Wang ◽  
Xiaodong Yang ◽  
Dalong Gao ◽  
Sijia Tan ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Pathway Analysis ◽  
Expression Profile ◽  
Nervous System Development ◽  
Normal Group ◽  
Differentially Expressed ◽  
Regulation Mechanism ◽  
Human Cartilage ◽  
Aberrant Expression ◽  
Beck Disease

Abstract Objective. Circular RNAs (circRNAs) have been manifested as novel regulatory molecules involved in various diseases processes, but their role in Kashin-Beck disease (KBD) has not been investigated. The aim of this study was to identify their expression profile and functions in KBD.Methods. Primary chondrocytes were isolated from human cartilage and cultured in vitro. The circRNA expression of chondrocytes was performed by microarray analysis. The differentially expressed circRNAs were further characterized by chromosome distribution, circRNA-miRNA correlation analysis, gene ontology (GO) and pathway analysis. Miranda was used to predict the target miRNAs of specific circRNAs. Cytoscape software was used to visualize the circRNA-miRNA interaction network to reveal the gene regulation mechanism of specific circRNAs.Results. In total, 886 circRNAs were discovered to be differentially expressed between the two groups, and of these, 348 were upregulated and 538 were downregulated in the KBD group (≥2-fold change). Gene ontology and pathway analysis revealed that compared to normal group, many processes that were over-represented in KBD group were related to nervous system development, cell periphery, laminin interactions, focal adhesion, extracellular matrix (ECM)-receptor interaction. Conclusion. The study revealed the aberrant expression profile of circRNA between KBD group and normal group, the outcomes may have potential significance in the pathogenesis and diagnostic markers of KBD.

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