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International Journal of Genomics

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https://www.readbyqxmd.com/read/29765977/systems-pharmacology-based-approach-of-connecting-disease-genes-in-genome-wide-association-studies-with-traditional-chinese-medicine
#1
Jihye Kim, Minjae Yoo, Jimin Shin, Hyunmin Kim, Jaewoo Kang, Aik Choon Tan
Traditional Chinese medicine (TCM) originated in ancient China has been practiced over thousands of years for treating various symptoms and diseases. However, the molecular mechanisms of TCM in treating these diseases remain unknown. In this study, we employ a systems pharmacology-based approach for connecting GWAS diseases with TCM for potential drug repurposing and repositioning. We studied 102 TCM components and their target genes by analyzing microarray gene expression experiments. We constructed disease-gene networks from 2558 GWAS studies...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29765976/differential-expression-profiling-of-long-noncoding-rna-and-mrna-during-osteoblast-differentiation-in-mouse
#2
Minjung Kim, Youngseok Yu, Ji-Hoi Moon, InSong Koh, Jae-Hyung Lee
Long noncoding RNAs (lncRNAs) are emerging as an important controller affecting metabolic tissue development, signaling, and function. However, little is known about the function and profile of lncRNAs in osteoblastic differentiation in mice. Here, we analyzed the RNA-sequencing (RNA-Seq) datasets obtained for 18 days in two-day intervals from neonatal mouse calvarial pre-osteoblast-like cells. Over the course of osteoblast differentiation, 4058 mRNAs and 3948 lncRNAs were differentially expressed, and they were grouped into 12 clusters according to the expression pattern by fuzzy c-means clustering...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29765975/relationship-of-snp-rs2645429-in-farnesyl-diphosphate-farnesyltransferase-1-gene-promoter-with-susceptibility-to-lung-cancer
#3
Mehdi Dehghani, Zahra Samani, Hassan Abidi, Leila Manzouri, Reza Mahmoudi, Saeed Hosseini Teshnizi, Mohsen Nikseresht
Background and Purpose: The mevalonate pathway is one of the major metabolic pathways that use acetyl-CoA to produce sterols and isoprenoids. These compounds can be effective in the growth and development of tumors. One of the enzymes involved in the mevalonate pathway is FDFT1. Different variants of this gene are involved in the risk of suffering various diseases. The present study examined the relationship between FDFT1 rs2645429 polymorphism and the risk of nonsmall cell lung cancer (NSCLC) in a population from southern Iran...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29750145/calibrating-transcriptional-activity-using-constitutive-synthetic-promoters-in-mutants-for-global-regulators-in-escherichia-coli
#4
Ananda Sanches-Medeiros, Lummy Maria Oliveira Monteiro, Rafael Silva-Rocha
The engineering of synthetic circuits in cells relies on the use of well-characterized biological parts that would perform predicted functions under the situation considered, and many efforts have been taken to set biological standards that could define the basic features of these parts. However, since most synthetic biology projects usually require a particular cellular chassis and set of growth conditions, defining standards in the field is not a simple task as gene expression measurements could be affected severely by genetic background and culture conditions...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29725597/data-mining-mycobacterium-tuberculosis-pathogenic-gene-transcription-factors-and-their-regulatory-network-nodes
#5
Guangxin Yuan, Yu Bai, Yuhang Zhang, Guangyu Xu
Tuberculosis (TB) is one of the deadliest infectious diseases worldwide. In Mycobacterium tuberculosis , changes in gene expression are highly variable and involve many genes, so traditional single-gene screening of M. tuberculosis targets has been unable to meet the needs of clinical diagnosis. In this study, using the National Center for Biotechnology Information (NCBI) GEO Datasets, whole blood gene expression profile data were obtained in patients with active pulmonary tuberculosis. Linear model-experience Bayesian statistics using the Limma package in R combined with t -tests were applied for nonspecific filtration of the expression profile data, and the differentially expressed human genes were determined...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29693000/clustering-pattern-and-functional-effect-of-snps-in-human-mirna-seed-regions
#6
Sha He, Haiyan Ou, Cunyou Zhao, Jian Zhang
miRNAs are a class of noncoding RNAs important in posttranscriptional repressors and involved in the regulation of almost every biological process by base paring with target genes through sequence in their seed regions. Genetic variations in the seed regions have vital effects on gene expression, phenotypic variation, and disease susceptibility in humans. The distribution pattern of genetic variation in miRNA seed regions might be related to miRNA function and is worth paying more attention to. We here employed computational analyses to explore the clustering pattern and functional effect of SNPs in human miRNA seed regions...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29686995/classification-of-complete-proteomes-of-different-organisms-and-protein-sets-based-on-their-protein-distributions-in-terms-of-some-key-attributes-of-proteins
#7
Hao-Bo Guo, Yue Ma, Gerald A Tuskan, Xiaohan Yang, Hong Guo
The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. Here, we propose an approach for classification of complete proteomes/protein sets based on protein distributions on some basic attributes. We demonstrate the usefulness of this approach by determining protein distributions in terms of two attributes: protein lengths and protein intrinsic disorder contents (ID). The protein distributions based on L and ID are surveyed for representative proteome organisms and protein sets from the three domains of life...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29675420/regulation-of-long-noncoding-rnas-responsive-to-phytoplasma-infection-in-paulownia-tomentosa
#8
Guoqiang Fan, Yabing Cao, Zhe Wang
Paulownia witches' broom caused by phytoplasma infection affects the production of Paulownia trees worldwide. Emerging evidence showed that long noncoding RNAs (lncRNA) play a protagonist role in regulating the expression of genes in plants. So far, the identification of lncRNAs has been limited to a few model plant species, and their roles in mediating responses to Paulownia tomentosa that free of phytoplasma infection are yet to be characterized. Here, whole-genome identification of lncRNAs, based on strand-specific RNA sequencing, from four Paulownia tomentosa samples, was performed and identified 3689 lncRNAs...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29607312/metabolic-pathway-genes-associated-with-susceptibility-genes-to-coronary-artery-disease
#9
Heng Lu, Yi Chen, Linlin Li
Coronary artery disease (CAD) is one of the leading threats to global health. Previous research has proven that metabolic pathway disorders, such as high blood lipids and diabetes, are one of the risk factors that mostly cause CAD. However, the crosstalk between metabolic pathways and CAD was mostly studied on physiology processes by analyzing a single gene function. A canonical correlation analysis was used to identify the metabolic pathways, which were integrated as a unit to coexpress with CAD susceptibility genes, and to resolve additional metabolic factors that are related to CAD...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29607311/shiftwork-mediated-disruptions-of-circadian-rhythms-and-sleep-homeostasis-cause-serious-health-problems
#10
REVIEW
Suliman Khan, Pengfei Duan, Lunguang Yao, Hongwei Hou
Shiftwork became common during the last few decades with the growing demands of human life. Despite the social inactivity and irregularity in habits, working in continuous irregular shifts causes serious health issues including sleep disorders, psychiatric disorders, cancer, and metabolic disorders. These health problems arise due to the disruption in circadian clock system, which is associated with alterations in genetic expressions. Alteration in clock controlling genes further affects genes linked with disorders including major depression disorder, bipolar disorder, phase delay and phase advance sleep syndromes, breast cancer, and colon cancer...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29607310/urinary-metabolomic-study-of-chlorogenic-acid-in-a-rat-model-of-chronic-sleep-deprivation-using-gas-chromatography-mass-spectrometry
#11
Wei-Ni Ma, Ming-Mei Zhou, Xiao-Jun Gou, Le Zhao, Fang Cen, Ying Xu, Hong-Yi Shen
The urinary metabolomic study based on gas chromatography-mass spectrometry (GC-MS) had been developed to investigate the possible antidepressant mechanism of chlorogenic acid (CGA) in a rat model of sleep deprivation (SD). According to pattern recognition analysis, there was a clear separation among big platform group (BP), sleep deprivation group (SD), and the CGA (model + CGA), and CGA group was much closer to the BP group by showing a tendency of recovering towards BP group. Thirty-six significantly changed metabolites related to antidepressant by CGA were identified and used to explore the potential mechanism...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29581960/identification-of-wheat-inflorescence-development-related-genes-using-a-comparative-transcriptomics-approach
#12
Lingjie Ma, Sheng-Wei Ma, Qingyan Deng, Yang Yuan, Zhaoyan Wei, Haiyan Jia, Zhengqiang Ma
Inflorescence represents the highly specialized plant tissue producing the grains. Although key genes regulating flower initiation and development are conserved, the mechanism regulating fertility is still not well explained. To identify genes and gene network underlying inflorescence morphology and fertility of bread wheat, expressed sequence tags (ESTs) from different tissues were analyzed using a comparative transcriptomics approach. Based on statistical comparison of EST frequencies of individual genes in EST pools representing different tissues and verification with RT-PCR and RNA-seq data, 170 genes of 59 gene sets predominantly expressed in the inflorescence were obtained...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29568738/noncoding-rnas-in-health-and-disease
#13
EDITORIAL
Davide Barbagallo, Gaetano Vittone, Massimo Romani, Michele Purrello
No abstract text is available yet for this article.
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29546047/ensemble-methods-with-voting-protocols-exhibit-superior-performance-for-predicting-cancer-clinical-endpoints-and-providing-more-complete-coverage-of-disease-related-genes
#14
Runyu Jing, Yu Liang, Yi Ran, Shengzhong Feng, Yanjie Wei, Li He
In genetic data modeling, the use of a limited number of samples for modeling and predicting, especially well below the attribute number, is difficult due to the enormous number of genes detected by a sequencing platform. In addition, many studies commonly use machine learning methods to evaluate genetic datasets to identify potential disease-related genes and drug targets, but to the best of our knowledge, the information associated with the selected gene set was not thoroughly elucidated in previous studies...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29511668/transcriptome-analysis-of-the-thymus-in-short-term-calorie-restricted-mice-using-rna-seq
#15
Zehra Omeroğlu Ulu, Salih Ulu, Soner Dogan, Bilge Guvenc Tuna, Nehir Ozdemir Ozgenturk
Calorie restriction (CR), which is a factor that expands lifespan and an important player in immune response, is an effective protective method against cancer development. Thymus, which plays a critical role in the development of the immune system, reacts to nutrition deficiency quickly. RNA-seq-based transcriptome sequencing was performed to thymus tissues of MMTV-TGF- α mice subjected to ad libitum (AL), chronic calorie restriction (CCR), and intermittent calorie restriction (ICR) diets in this study. Three cDNA libraries were sequenced using Illumina HiSeq™ 4000 to produce 100 base pair-end reads...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29487863/multitarget-effects-of-danqi-pill-on-global-gene-expression-changes-in-myocardial-ischemia
#16
Qiyan Wang, Hui Meng, Qian Zhang, Tianjiao Shi, Xuefeng Zhang, Mingyan Shao, Linghui Lu, Jing Wang, Wei Wang, Chun Li, Yong Wang
Danqi pill (DQP) is a widely prescribed traditional Chinese medicine (TCM) in the treatment of cardiovascular diseases. The objective of this study is to systematically characterize altered gene expression pattern induced by myocardial ischemia (MI) in a rat model and to investigate the effects of DQP on global gene expression. Global mRNA expression was measured. Differentially expressed genes among the sham group, model group, and DQP group were analyzed. The gene ontology enrichment analysis and pathway analysis of differentially expressed genes were carried out...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29464180/-lingguizhugan-decoction-protects-against-high-fat-diet-induced-nonalcoholic-fatty-liver-disease-by-alleviating-oxidative-stress-and-activating-cholesterol-secretion
#17
Lili Yang, Weili Lin, Colleen A Nugent, Shijun Hao, Haiyan Song, Tao Liu, Peiyong Zheng
Background: Nonalcoholic fatty liver disease (NAFLD) has become a leading cause of liver transplantation. Lingguizhugan decoction (LGZG), a classical Chinese herbal formula, has beneficial effects on NAFLD animal models. Our study examined the impact of LGZG on hepatic global transcriptome of high-fat-diet-induced NAFLD rats. Methods: Three groups of Wistar rats were included: normal, NAFLD model, and LGZG-treated NAFLD groups. Four weeks for the treatment, liver tissues were harvested for RNA sequencing...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29387713/microrna-and-putative-target-discoveries-in-chrysanthemum-polyploidy-breeding
#18
Fengjiao Zhang, Jingya Zhao, Sujuan Xu, Weimin Fang, Fadi Chen, Nianjun Teng
MicroRNAs (miRNAs), around 22 nucleotides (nt) in length, are a class of endogenous and noncoding RNA molecule that play an essential role in plant development, either by suppressing the transcription of target genes at a transcriptional level or inhibiting translation at a posttranscriptional level. To understand the roles of miRNAs and their target genes in chrysanthemum polyploidy breeding, three sRNA libraries of normal and abnormal embryos after hybridization were performed by RNA-Seq. As a result, a total of 170 miRNAs were identified and there are 41 special miRNAs in cross of paternal chromosome doubling, such as miR169b, miR440, and miR528-5p...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29379793/effect-of-gegen-qinlian-decoction-on-cardiac-gene-expression-in-diabetic-mice
#19
Jing Han, Zhenglin Wang, Wei Xing, Yueying Yuan, Yi Zhang, Tiantian Lv, Hongliang Wang, Yonggang Liu, Yan Wu
The aim of this research is to investigate the therapeutic effect of GGQL decoction on cardiac dysfunction and elucidate the pharmacological mechanisms. db/db mice were divided into DB group or GGQL group, and WT mice were used as control. All mice were accessed by echocardiography. And the total RNA of LV tissue samples was sequenced, then differential expression genes were analyzed. The RNA-seq results were validated by the results of RT-qPCR of 4 genes identified as differentially expressed. The content of pyruvate and ceramide in myocardial tissue was also measured...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29349062/circular-rnas-biogenesis-function-and-a-role-as-possible-cancer-biomarkers
#20
REVIEW
Luka Bolha, Metka Ravnik-Glavač, Damjan Glavač
Circular RNAs (circRNAs) are a class of noncoding RNAs (ncRNAs) that form covalently closed continuous loop structures, lacking the terminal 5' and 3' ends. CircRNAs are generated in the process of back-splicing and can originate from different genomic regions. Their unique circular structure makes circRNAs more stable than linear RNAs. In addition, they also display insensitivity to ribonuclease activity. Generally, circRNAs function as microRNA (miRNA) sponges and have a regulatory role in transcription and translation...
2017: International Journal of Genomics
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