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https://www.readbyqxmd.com/read/29670400/-anln-functions-as-a-key-candidate-gene-in-cervical-cancer-as-determined-by-integrated-bioinformatic-analysis
#1
Leilei Xia, Xiaoling Su, Jizi Shen, Qi Meng, Jiuqiong Yan, Caihong Zhang, Yu Chen, Han Wang, Mingjuan Xu
Background: Cervical cancer, one of the leading causes of female deaths, remains a top cause of mortality in gynecologic oncology and tends to affect younger individuals. However, the pathogenesis of cervical cancer is still far from clear. Given the high incidence and mortality of cervical cancer, uncovering the causes and pathogenesis as well as identifying novel biomarkers are of great significance and are desperately needed. Materials and methods: First, raw data were downloaded from the Gene Expression Omnibus database...
2018: Cancer Management and Research
https://www.readbyqxmd.com/read/29660070/full-length-transcriptome-sequencing-and-modular-organization-analysis-of-naringin-neoeriocitrin-related-gene-expression-pattern-in-drynaria-roosii
#2
Mei-Yu Sun, Jing-Yi Li, Dong Li, Feng-Jie Huang, Di Wang, Hui Li, Quan Xing, Hui-Bin Zhu, Lei Shi
Drynaria roosii (Nakaike) is a traditional Chinese medicinal fern, known as 'GuSuiBu'. The corresponding effective components of naringin/neoeriocitrin share highly similar chemical structure and medicinal function. Our HPLC-MS/MS results showed that the accumulation of naringin/neoeriocitrin depended on specific tissues or ages. However, little was known about the expression patterns of naringin/neoeriocitrin related genes involved in their regulatory pathways. For lack of the basic genetic information, we applied a combination of SMRT sequencing and SGS to generate the complete and full-length transcriptome of D...
April 12, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29620224/role-of-col6a3-in-colorectal-cancer
#3
Wei Liu, Li Li, Hua Ye, Huan Tao, Huaqin He
Public transcriptome databases provide a valuable resource for genome‑wide co‑expression network analysis and investigation of the molecular mechanisms that underlie pathogenesis. To discover genes that may affect patient survival, a large‑scale analysis of human colorectal cancer (CRC) datasets that were retrieved from the NCBI Gene Expression Omnibus was performed. A gene co‑expression network was constructed using weighted gene co‑expression network analysis (WGCNA). A total of 18 co‑expressed gene modules were identified, of which two genes corresponded to cell migration and the cell cycle, two genes were involved in immune responses, two genes corresponded to mitochondrial function, and one gene corresponded to RNA splicing...
March 23, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29616282/a-large-lung-gene-expression-study-identifying-il1b-as-a-novel-player-in-airway-inflammation-in-copd-airway-epithelial-cells
#4
Gao Yi, Min Liang, Ming Li, Xiangming Fang, Jifang Liu, Yuxiong Lai, Jitao Chen, Wenxia Yao, Xiao Feng, La Hu, Chunyi Lin, Xinke Zhou, Zhaoyu Liu
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a chronic and progressive lung disease characterized by a mixture of small airway disease and lung tissue parenchymal destruction. Abnormal inflammatory responses to cigarette smoking and other noxious particles are generally thought to be responsible for causing of COPD. Since airway inflammation is a key factor in COPD progress, it is crucial to unravel its underlying molecular mechanisms. Unbiased analysis of genome-wide gene expression profiles in lung small airway epithelial cells provides a powerful tool to investigate this...
April 3, 2018: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
https://www.readbyqxmd.com/read/29615930/arachidonic-acid-metabolism-pathway-is-not-only-dominant-in-metabolic-modulation-but-associated-with-phenotypic-variation-after-acute-hypoxia-exposure
#5
Chang Liu, Bao Liu, Lu Liu, Er-Long Zhang, Bind-da Sun, Gang Xu, Jian Chen, Yu-Qi Gao
Background: The modulation of arachidonic acid (AA) metabolism pathway is identified in metabolic alterations after hypoxia exposure, but its biological function is controversial. We aimed at integrating plasma metabolomic and transcriptomic approaches to systematically explore the roles of the AA metabolism pathway in response to acute hypoxia using an acute mountain sickness (AMS) model. Methods: Blood samples were obtained from 53 enrolled subjects before and after exposure to high altitude. Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry and RNA sequencing were separately performed for metabolomic and transcriptomic profiling, respectively...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29599431/two-dimensional-analysis-provides-molecular-insight-into-flower-scent-of-lilium-siberia
#6
Shaochuan Shi, Guangyou Duan, Dandan Li, Jie Wu, Xintong Liu, Bo Hong, Mingfang Yi, Zhao Zhang
Lily is a popular flower around the world not only because of its elegant appearance, but also due to its appealing scent. Little is known about the regulation of the volatile compound biosynthesis in lily flower scent. Here, we conducted an approach combining two-dimensional analysis and weighted gene co-expression network analysis (WGCNA) to explore candidate genes regulating flower scent production. In the approach, changes of flower volatile emissions and corresponding gene expression profiles at four flower developmental stages and four circadian times were both captured by GC-MS and RNA-seq methods...
March 29, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29571247/comprehensive-analysis-and-experimental-verification-of-linc01314-as-a-tumor-suppressor-in-hepatoblastoma
#7
Benji Lv, Lianhai Zhang, Runchen Miao, Xiaohong Xiang, Shunbin Dong, Ting Lin, Ke Li, Qu Kai
Hepatoblastoma (HB), as a common pediatric liver malignancy, is composed of a variety of subgroups with different clinical outcomes. Long-noncoding RNA (lncRNA) has crucial roles in cancer biology. However, the association between lncRNA and HB has not been fully investigated. In this study, we screened lncRNA expression profiles that were annotated from the GSE75271 dataset. A total of 225 differentially expressed lncRNAs (DELs) were identified based on comparison between three prognostic subgroups, and seven of them (XR_241302, XR_923061, NR_038322, XR_951687, XR_934593, NR_120317 and XR_93406) that exhibited highly predictive accuracies were selected for functional analysis...
February 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29565640/sigmoid-colon-mucosal-gene-expression-supports-alterations-of-neuronal-signaling-in-irritable-bowel-syndrome-with-constipation
#8
Elizabeth J Videlock, Swapna Mahurkar-Joshi, Jill M Hoffman, Dimitrios Iliopoulos, Charalabos Pothoulakis, Emeran A Mayer, Lin Chang
OBJECTIVE: Peripheral factors likely play a role in at least a subset of irritable bowel syndrome (IBS) patients. Few studies have investigated mucosal gene expression using an unbiased approach. Here, we performed mucosal gene profiling in a sex-balanced sample to identify relevant signaling pathways and gene networks and compare to publicly available profiling data from additional cohorts. DESIGN: 20 Rome III+ IBS patients (10 IBS with constipation (IBS-C), 10 IBS with diarrhea (IBS-D) 5 men/women each) and 10 age/sex-matched healthy controls (HCs) underwent sigmoidoscopy with biopsy for gene microarray analysis, including differential expression, weighted gene co-expression network analysis (WGCNA), gene set enrichment analysis and comparison with publicly available data...
March 22, 2018: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/29534679/integrated-genomic-analysis-identifies-clinically-relevant-subtypes-of-renal-clear-cell-carcinoma
#9
Peng Wu, Jia-Li Liu, Shi-Mei Pei, Chang-Peng Wu, Kai Yang, Shu-Peng Wang, Song Wu
BACKGROUND: Renal cell carcinoma (RCC) account for over 80% of renal malignancies. The most common type of RCC can be classified into three subtypes including clear cell, papillary and chromophobe. ccRCC (the Clear Cell Renal Cell Carcinoma) is the most frequent form and shows variations in genetics and behavior. To improve accuracy and personalized care and increase the cure rate of cancer, molecular typing for individuals is necessary. METHODS: We adopted the genome, transcriptome and methylation HMK450 data of ccRCC in The Cancer Genome Atlas Network in this research...
March 13, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29518040/construction-and-analysis-of-gene-co-expression-networks-in-escherichia-coli
#10
Wei Liu, Li Li, Xuhe Long, Weixin You, Yuexian Zhong, Menglin Wang, Huan Tao, Shoukai Lin, Huaqin He
Network-based systems biology has become an important method for analyzing high-throughput gene expression data and gene function mining. Escherichia coli ( E. coli ) has long been a popular model organism for basic biological research. In this paper, weighted gene co-expression network analysis (WGCNA) algorithm was applied to construct gene co-expression networks in E. coli . Thirty-one gene co-expression modules were detected from 1391 microarrays of E. coli data. Further characterization of these modules with the database for annotation, visualization, and integrated discovery (DAVID) tool showed that these modules are associated with several kinds of biological processes, such as carbohydrate catabolism, fatty acid metabolism, amino acid metabolism, transportation, translation, and ncRNA metabolism...
March 8, 2018: Cells
https://www.readbyqxmd.com/read/29516375/gonad-transcriptome-analysis-of-the-pacific-oyster-crassostrea-gigas-identifies-potential-genes-regulating-the-sex-determination-and-differentiation-process
#11
Chenyang Yue, Qi Li, Hong Yu
The Pacific oyster Crassostrea gigas is a commercially important bivalve in aquaculture worldwide. C. gigas has a fascinating sexual reproduction system consisting of dioecism, sex change, and occasional hermaphroditism, while knowledge of the molecular mechanisms of sex determination and differentiation is still limited. In this study, the transcriptomes of male and female gonads at different gametogenesis stages were characterized by RNA-seq. Hierarchical clustering based on genes differentially expressed revealed that 1269 genes were expressed specifically in female gonads and 817 genes were expressed increasingly over the course of spermatogenesis...
March 8, 2018: Marine Biotechnology
https://www.readbyqxmd.com/read/29483831/ten-hub-genes-associated-with-progression-and-prognosis-of-pancreatic-carcinoma-identified-by-co-expression-analysis
#12
Zhou Zhou, Yian Cheng, Yinan Jiang, Shi Liu, Meng Zhang, Jing Liu, Qiu Zhao
Since the five-year survival rate is less than 5%, pancreatic ductal adenocarcinoma (PDAC) remains the 4th cause of cancer-related death. Although PDAC has been repeatedly researched in recent years, it is still predicted to be the second leading cause of cancer death by year 2030. In our study, the differentially expressed genes in dataset GSE62452 were used to construct a co-expression network by WGCNA. The yellow module related to grade of PDAC was screened. Combined with co-expression network and PPI network, 36 candidates were screened...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29474866/targeted-proteomic-analysis-of-cognitive-dysfunction-in-remitted-major-depressive-disorder-opportunities-of-multi-omics-approaches-towards-predictive-preventive-and-personalized-psychiatry
#13
K Oliver Schubert, David Stacey, Georgia Arentz, Scott R Clark, Tracy Air, Peter Hoffmann, Bernhard T Baune
In order to accelerate the understanding of pathophysiological mechanisms and clinical biomarker discovery and in psychiatry, approaches that integrate multiple -omics platforms are needed. We introduce a workflow that investigates a narrowly defined psychiatric phenotype, makes use of the potent and cost-effective discovery technology of gene expression microarrays, applies Weighted Gene Co-Expression Network Analysis (WGCNA) to better capture complex and polygenic traits, and finally explores gene expression findings on the proteomic level using targeted mass-spectrometry (MS) technologies...
February 20, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29474693/the-use-of-rna-sequencing-and-correlation-network-analysis-to-study-potential-regulators-of-leaf-color-transformation
#14
Tuo Yang, Keting Li, Suxiao Hao, Jie Zhang, Tingting Song, Ji Tian, Yuncong Yao
Anthocyanins are plant pigments that contribute to the color of leaves, flowers and fruits, and that beneficial to human health in the form of dietary antioxidants. The study of a transformable crabapple cultivar, 'India magic', which has red buds and green mature leaves, using mRNA profiling of four leaf developmental stages, allowed us to characterize molecular mechanisms regulating red color formation in early leaf development and the subsequent rapid down-regulation of anthocyanin biosynthesis. This analysis of differential gene expression during leaf development, revealed that ethylene signaling responsive genes are upregulated during leaf pigmentation...
February 20, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29443924/identification-of-key-pathways-and-genes-in-the-dynamic-progression-of-hcc-based-on-wgcna
#15
Li Yin, Zhihui Cai, Baoan Zhu, Cunshuan Xu
Hepatocellular carcinoma (HCC) is a devastating disease worldwide. Though many efforts have been made to elucidate the process of HCC, its molecular mechanisms of development remain elusive due to its complexity. To explore the stepwise carcinogenic process from pre-neoplastic lesions to the end stage of HCC, we employed weighted gene co-expression network analysis (WGCNA) which has been proved to be an effective method in many diseases to detect co-expressed modules and hub genes using eight pathological stages including normal, cirrhosis without HCC, cirrhosis, low-grade dysplastic, high-grade dysplastic, very early and early, advanced HCC and very advanced HCC...
February 14, 2018: Genes
https://www.readbyqxmd.com/read/29435142/co-expression-analysis-revealed-ptch1-3-utr-promoted-cell-migration-and-invasion-by-activating-mir-101-3p-slc39a6-axis-in-non-small-cell-lung-cancer-implicating-the-novel-function-of-ptch1
#16
Xuechao Wan, Zhe Kong, Kaili Chu, Chuanyou Yi, Jian Hu, Rui Qin, Chen Zhao, Fangqiu Fu, Hai Wu, Yao Li, Yan Huang
Metastasis is the most common cause of mortality for non-small cell lung cancer (NSCLC). PTCH1, a receptor of Hedgehog (Hh) pathway, is reported to suppress cell proliferation. Interestingly, our previous study showed PTCH1 silencing promoted cell proliferation but inhibited cell migration and invasion of NSCLC cells. However, the precise mechanisms of PTCH1 regulating NSCLC metastasis remain unclear. PTCH1 has multiple splicing variants, which all share the same 3'UTR sequence, meanwhile, emerging studies have shown competing endogenous RNAs (ceRNAs) play important roles in regulating cancer progression...
January 12, 2018: Oncotarget
https://www.readbyqxmd.com/read/29416676/long-non-coding-rna-gas5-and-zfas1-are-prognostic-markers-involved-in-translation-targeted-by-mir-940-in-prostate-cancer
#17
Xin Chen, Chao Yang, Shengli Xie, Edwin Cheung
Identification of prognostic biomarkers helps facilitate the prediction of patient outcomes as well as guide treatments. Accumulating evidence now suggests that long non-coding RNAs (lncRNAs) play key roles in tumor progression with diagnostic and prognostic values. However, little is known about the biological functions of lncRNAs and how they contribute to the pathogenesis of cancer. Herein, we performed weighted correlation network analysis (WGCNA) on 380 RNA-seq samples from prostate cancer patients to create networks comprising of microRNAs, lncRNAs, and protein-coding genes...
January 2, 2018: Oncotarget
https://www.readbyqxmd.com/read/29416627/transcriptome-evolution-from-breast-epithelial-cells-to-basal-like-tumors
#18
Gabriel Santpere, Ana Alcaráz-Sanabria, Verónica Corrales-Sánchez, Atanasio Pandiella, Balázs Győrffy, Alberto Ocaña
In breast cancer, it is unclear the functional modifications at a transcriptomic level that are associated with the evolution from epithelial cells and ductal carcinoma in situ (DCIS) to basal-like tumors. By applying weighted gene co-expression network analysis (WGCNA), we identified 17 gene co-expression modules in normal, DCIS and basal-like tumor samples. We then correlated the expression pattern of these gene modules with disease progression from normal to basal-like tumours and found eight modules exhibiting a high and statistically significant correlation...
January 2, 2018: Oncotarget
https://www.readbyqxmd.com/read/29415651/integrative-analysis-of-micrornas-and-mrnas-revealed-regulation-of-composition-and-metabolism-in-nelore-cattle
#19
Gabriella B Oliveira, Luciana C A Regitano, Aline S M Cesar, James M Reecy, Karina Y Degaki, Mirele D Poleti, Andrezza M Felício, James E Koltes, Luiz L Coutinho
BACKGROUND: The amount of intramuscular fat can influence the sensory characteristics and nutritional value of beef, thus the selection of animals with adequate fat deposition is important to the consumer. There is growing knowledge about the genes and pathways that control the biological processes involved in fat deposition in muscle. MicroRNAs (miRNAs) belong to a well-conserved class of non-coding small RNAs that modulate gene expression across a range of biological functions in animal development and physiology...
February 7, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29410067/single-cell-transcriptome-analyses-reveal-molecular-signals-to-intrinsic-and-acquired-paclitaxel-resistance-in-esophageal-squamous-cancer-cells
#20
Hongjin Wu, Sean Chen, Juehua Yu, Ying Li, Xiao-Yan Zhang, Ling Yang, Hongfang Zhang, Qiang Hou, Mingfeng Jiang, F Charles Brunicardi, Charles Wang, Shixiu Wu
Paclitaxel is widely used in the combination chemotherapy for many cancers including esophageal squamous cell carcinoma (ESCC). However, the paclitaxel resistance occurs frequently in treating ESCC and the mechanism is not fully understood yet. The heterogeneity of gene expression within the drug-resistant cancer cells may be one of the major factors contributing to its resistance. In the present study, we successfully induced paclitaxel resistance in ESCC cell line KYSE-30 through low dose and long-term treatment of paclitaxel...
April 28, 2018: Cancer Letters
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