Gene expression profile analysis of colorectal cancer to investigate potential mechanisms using&amp;nbsp;bioinformatics

Kou, Yubin; Zhang, Suya; Chen, Xiaoping; Hu, Sanyuan

doi:10.2147/ott.s78974

Cited by 14 publications

(9 citation statements)

References 33 publications

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“…Calcium ions play a vital role in muscle contraction, neuronal transmission, cell motility, cell growth or proliferation [ 24 – 27 ]. It has been reported that calcium signaling pathway is related to progression and development of various cancers including lung adenocarcinoma [ 28 ], colorectal cancer [ 29 ], glioblastoma [ 30 ], breast cancer [ 31 ], and Burkitt lymphoma [ 32 ]. Calcium signaling pathway may play a key role in the progression and development of AML.…”

Section: Discussionmentioning

confidence: 99%

Identification of miRNA-mRNA Network Associated with Acute Myeloid Leukemia Survival

Zhang

Bai

Zhu³

et al. 2017

Med Sci Monit

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BackgroundAcute myeloid leukemia (AML) is a common hematologic malignancy of adults. The pathophysiological mechanism of AML is not well understood. The purpose of this study was to examine the crucial miRNAs and mRNAs associated with AML survival.Material/MethodsThe full clinical dataset of miRNA and mRNA expression profiling of AML patients was downloaded from The Cancer Genome Atlas database. Univariate Cox regression analysis was performed to obtain those miRNAs and mRNAs associated with AML survival. A miRNA-mRNA interaction network was constructed. The underlying functions of mRNAs were predicted through Kyoto Encyclopedia of Genes and Genomes (KEEG) pathway enrichment. The expression levels of miRNAs and mRNAs were detected by quantitative real-time polymerase chain reaction (qRT-PCR).ResultsFourteen miRNAs and 830 mRNAs associated with AML survival were identified. Of the 14 miRNAs, hsa-mir-425, hsa-mir-1201, and hsa-mir-1978 were identified as risk factors and the other 11 miRNAs were identified as protective factors of AML survival. For target-genes of miRNAs, GTSF1, RTN4R, and CD44 were the top risk factor target-genes associated with AML survival. An interaction network was constructed that including 607 miRNA-target gene pairs associated with AML survival. Target-genes associated with AML survival were significantly enriched in several pathways including pancreatic secretion, calcium signaling pathway, natural killer cell mediated cytotoxicity, and Alzheimer’s disease. The qRT-PCR results were consistent with our bioinformatics analyses.ConclusionsThe miRNA hsa-mir-425 was identified as the top risk factor miRNA of AML survival and CD44 was identified as one of the top three risk factor target-genes associated with AML survival. Both hsa-mir-425 and CD44 may play key roles in progression and development of AML through calcium signaling pathway and natural killer cell mediated cytotoxicity.

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Section: Discussionmentioning

confidence: 99%

Identification of miRNA-mRNA Network Associated with Acute Myeloid Leukemia Survival

Zhang

Bai

Zhu³

et al. 2017

Med Sci Monit

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“…To assist in visualizing the biological networks and integrating the data generated by the STRING database, the PPI networks were constructed and visualized using Cytoscape (version 3.3.0; ) ( 22 ). As the majority of the networks were scale-free, the hub genes were then selected with a connectivity degree >15 ( 23 ).…”

Section: Methodsmentioning

confidence: 99%

Gene expression profile analysis of the progression of carotid atherosclerotic plaques

Liu

Zhao

2018

Mol Med Report

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The present study aimed to examine the universal gene expression signature and the underlying molecular mechanisms involved in the progression of carotid atherosclerotic plaques. The gene expression dataset, GSE28829, containing 13 early and 16 advanced carotid atherosclerotic plaques was selected for analysis. The differentially expressed genes (DEGs) were identified and analyzed using bioinformatics analyses, including cluster analysis, Gene Ontology (GO) and pathway enrichment analyses. Finally, a protein-protein interaction (PPI) was constructed and analyzed. A total of 515 downregulated and 243 downregulated DEGs were identified. The cluster analysis revealed two separate two groups. In addition, the GO terms enriched by the upregulated DEGs were associated with immune response, and the downregulated DEGs were associated with cell adhesion. The upregulated DEGs were enriched in pathways associated with signaling in the immune system, and the downregulated DEGs were enriched in pathways associated with muscle contraction. In the PPI network analysis, ITGAM and ACTN2 had the highest decrees of connectivity in the upregulated and downregulated DEGs, respectively. These findings suggested that deregulation of the immune system and smooth muscle cell cytoskeleton accelerates the progression of carotid atherosclerotic plaques. The DEGs identified may offer potential in the prevention and treatment of atherosclerosis in the carotid artery.

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“… [ 333–336 ] Gene expression profiling of colorectal cancer, in comparison to normal colonic tissue, showed downregulation in cancer of genes associated with PD, AD, HD and oxidative phosphorylation. [ 337 ] Meta-analysis of transcriptomic data for AD, PD and schizophrenia, in relation to lung, prostate and colorectal cancer, showed opposite gene-expression changes between these two sets of diseases. [ 338 ] SIR, standard incidence rate; RR, relative risk; OR, odds ratio; HR, hazard ratio; ES, effect size; CI, confidence interval.…”

Section: Cancer Versus Neurodegenerative Diseasesmentioning

confidence: 99%

Diametrical diseases reflect evolutionary-genetic tradeoffs

Crespi¹,

2015

EMPH

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Tradeoffs centrally mediate the expression of human adaptations. We propose that tradeoffs also influence the prevalence and forms of human maladaptation manifest in disease. By this logic, increased risk for one set of diseases commonly engenders decreased risk for another, diametric, set of diseases. We describe evidence for such diametric sets of diseases from epidemiological, genetic and molecular studies in four clinical domains: (i) psychiatry (autism vs psychotic-affective conditions), (ii) rheumatology (osteoarthritis vs osteoporosis), (iii) oncology and neurology (cancer vs neurodegenerative disorders) and (iv) immunology (autoimmunity vs infectious disease). Diametric disorders are important to recognize because genotypes or environmental factors that increase risk for one set of disorders protect from opposite disorders, thereby providing novel and direct insights into disease causes, prevention and therapy. Ascertaining the mechanisms that underlie disease-related tradeoffs should also indicate means of circumventing or alleviating them, and thus reducing the incidence and impacts of human disease in a more general way.

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Gene expression profile analysis of colorectal cancer to investigate potential mechanisms using bioinformatics

Cited by 14 publications

References 33 publications

Identification of miRNA-mRNA Network Associated with Acute Myeloid Leukemia Survival

Identification of miRNA-mRNA Network Associated with Acute Myeloid Leukemia Survival

Gene expression profile analysis of the progression of carotid atherosclerotic plaques

Diametrical diseases reflect evolutionary-genetic tradeoffs

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