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https://www.readbyqxmd.com/read/29443924/identification-of-key-pathways-and-genes-in-the-dynamic-progression-of-hcc-based-on-wgcna
#1
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
#2
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
#3
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
#4
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
#5
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
#6
Hongjin Wu, Sean Chen, Charles Wang, Juehua Yu, Ying Li, Xiao-Yan Zhang, Ling Yang, Hongfang Zhang, Qiang Hou, Mingfeng Jiang, F Charles Brunicardi, 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...
January 30, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29384847/identification-of-key-candidate-genes-and-pathways-in-hepatitis-b-virus-associated-acute-liver-failure-by-bioinformatical-analysis
#7
Huapeng Lin, Qian Zhang, Xiaocheng Li, Yushen Wu, Ye Liu, Yingchun Hu
Hepatitis B virus-associated acute liver failure (HBV-ALF) is a rare but life-threatening syndrome that carried a high morbidity and mortality. Our study aimed to explore the possible molecular mechanisms of HBV-ALF by means of bioinformatics analysis. In this study, genes expression microarray datasets of HBV-ALF from Gene Expression Omnibus were collected, and then we identified differentially expressed genes (DEGs) by the limma package in R. After functional enrichment analysis, we constructed the protein-protein interaction (PPI) network by the Search Tool for the Retrieval of Interacting Genes online database and weighted genes coexpression network by the WGCNA package in R...
February 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29381923/identification-of-regulatory-role-of-dna-methylation-in-colon-cancer-gene-expression-via-systematic-bioinformatics-analysis
#8
Yong Yang, Fu-Hao Chu, Wei-Ru Xu, Jia-Qi Sun, Xu Sun, Xue-Man Ma, Ming-Wei Yu, Guo-Wang Yang, Xiao-Min Wang
Colon cancer arises from the accumulations of genetic and epigenetic changes. Currently, profiles of DNA methylation and gene expression of colon cancer have not been elucidated clearly. This articles aims to characterize the profile of DNA methylation and gene expression of colon cancer systemically, and acquire candidate genes potentially regulated by altered methylation for this disease.Data were downloaded from The Cancer Genome Atlas database. Differentially methylated CpG sites (DMCs) and differentially methylated regions (DMRs) were calculated via COHCAP...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29377892/network-based-co-expression-analysis-for-exploring-the-potential-diagnostic-biomarkers-of-metastatic-melanoma
#9
Li-Xin Wang, Yang Li, Guan-Zhi Chen
Metastatic melanoma is an aggressive skin cancer and is one of the global malignancies with high mortality and morbidity. It is essential to identify and verify diagnostic biomarkers of early metastatic melanoma. Previous studies have systematically assessed protein biomarkers and mRNA-based expression characteristics. However, molecular markers for the early diagnosis of metastatic melanoma have not been identified. To explore potential regulatory targets, we have analyzed the gene microarray expression profiles of malignant melanoma samples by co-expression analysis based on the network approach...
2018: PloS One
https://www.readbyqxmd.com/read/29368590/identification-of-auxin-response-factor-gene-family-from-prunus-sibirica-and-its-expression-analysis-during-mesocarp-and-kernel-development
#10
Jun Niu, Quanxin Bi, Shuya Deng, Huiping Chen, Haiyan Yu, Libing Wang, Shanzhi Lin
BACKGROUND: Auxin response factors (ARFs) in auxin signaling pathway are an important component that can regulate the transcription of auxin-responsive genes involved in almost all aspects of plant growth and development. To our knowledge, the comprehensive and systematic characterization of ARF genes has never been reported in Prunus sibirica, a novel woody biodiesel feedstock in China. RESULTS: In this study, we identified 14 PsARF genes with a perfect open reading frame (ORF) in P...
January 24, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29351231/molecular-network-based-identification-of-competing-endogenous-rnas-in-thyroid-carcinoma
#11
Minjia Lu, Xingyu Xu, Baohang Xi, Qi Dai, Chenli Li, Li Su, Xiaonan Zhou, Min Tang, Yuhua Yao, Jialiang Yang
RNAs may act as competing endogenous RNAs (ceRNAs), a critical mechanism in determining gene expression regulations in many cancers. However, the roles of ceRNAs in thyroid carcinoma remains elusive. In this study, we have developed a novel pipeline called Molecular Network-based Identification of ceRNA (MNIceRNA) to identify ceRNAs in thyroid carcinoma. MNIceRNA first constructs micro RNA (miRNA)-messenger RNA (mRNA)long non-coding RNA (lncRNA) networks from miRcode database and weighted correlation network analysis (WGCNA), based on which to identify key drivers of differentially expressed RNAs between normal and tumor samples...
January 19, 2018: Genes
https://www.readbyqxmd.com/read/29335477/transcriptomic-signatures-of-cellular-and-humoral-immune-responses-in-older-adults-after-seasonal-influenza-vaccination-identified-by-data-driven-clustering
#12
Emily A Voigt, Diane E Grill, Michael T Zimmermann, Whitney L Simon, Inna G Ovsyannikova, Richard B Kennedy, Gregory A Poland
PBMC transcriptomes after influenza vaccination contain valuable information about factors affecting vaccine responses. However, distilling meaningful knowledge out of these complex datasets is often difficult and requires advanced data mining algorithms. We investigated the use of the data-driven Weighted Gene Correlation Network Analysis (WGCNA) gene clustering method to identify vaccine response-related genes in PBMC transcriptomic datasets collected from 138 healthy older adults (ages 50-74) before and after 2010-2011 seasonal trivalent influenza vaccination...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330528/application-of-weighted-gene-co-expression-network-analysis-for-data-from-paired-design
#13
Jianqiang Li, Doudou Zhou, Weiliang Qiu, Yuliang Shi, Ji-Jiang Yang, Shi Chen, Qing Wang, Hui Pan
Investigating how genes jointly affect complex human diseases is important, yet challenging. The network approach (e.g., weighted gene co-expression network analysis (WGCNA)) is a powerful tool. However, genomic data usually contain substantial batch effects, which could mask true genomic signals. Paired design is a powerful tool that can reduce batch effects. However, it is currently unclear how to appropriately apply WGCNA to genomic data from paired design. In this paper, we modified the current WGCNA pipeline to analyse high-throughput genomic data from paired design...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317304/lncrna-and-mrna-integration-network-reconstruction-reveals-novel-key-regulators-in-esophageal-squamous-cell-carcinoma
#14
Shervin Alaei, Balal Sadeghi, Ali Najafi, Ali Masoudi-Nejad
Many experimental and computational studies have identified key protein coding genes in initiation and progression of esophageal squamous cell carcinoma (ESCC). However, the number of researches that tried to reveal the role of long non-coding RNAs (lncRNAs) in ESCC has been limited. LncRNAs are one of the important regulators of cancers which are transcribed dominantly in the genome and in various conditions. The main goal of this study was to use a systems biology approach to predict novel lncRNAs as well as protein coding genes associated with ESCC and assess their prognostic values...
January 6, 2018: Genomics
https://www.readbyqxmd.com/read/29297292/repositioning-drugs-by-targeting-network-modules-a-parkinson-s-disease-case-study
#15
Zongliang Yue, Itika Arora, Eric Y Zhang, Vincent Laufer, S Louis Bridges, Jake Y Chen
BACKGROUND: Much effort has been devoted to the discovery of specific mechanisms between drugs and single targets to date. However, as biological systems maintain homeostasis at the level of functional networks robustly controlling the internal environment, such networks commonly contain multiple redundant mechanisms designed to counteract loss or perturbation of a single member of the network. As such, investigation of therapeutics that target dysregulated pathways or processes, rather than single targets, may identify agents that function at a level of the biological organization more relevant to the pathology of complex diseases such as Parkinson's Disease (PD)...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29281979/resistant-and-susceptible-chicken-lines-show-distinctive-responses-to-newcastle-disease-virus-infection-in-the-lung-transcriptome
#16
Melissa S Deist, Rodrigo A Gallardo, David A Bunn, Jack C M Dekkers, Huaijun Zhou, Susan J Lamont
BACKGROUND: Newcastle disease virus (NDV) is a threat to poultry production worldwide. A better understanding of mechanisms of resistance and susceptibility to this virus will improve measures for NDV prevention and control. Males and females from resistant Fayoumi and susceptible Leghorn lines were either challenged with a lentogenic strain of the virus or given a mock infection at 3 weeks of age. The lung transcriptomes generated by RNA-seq were studied using contrasts across the challenged and nonchallenged birds, the two lines, and three time points post-infection, and by using Weighted Gene Co-expression Network Analysis (WGNCA)...
December 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29280973/transcriptome-wide-identification-and-characterization-of-potato-circular-rnas-in-response-to-pectobacterium-carotovorum-subspecies-brasiliense-infection
#17
Ran Zhou, Yongxing Zhu, Jiao Zhao, Zhengwu Fang, Shuping Wang, Junliang Yin, Zhaohui Chu, Dongfang Ma
Little information about the roles of circular RNAs (circRNAs) during potato-Pectobacterium carotovorum subsp. brasiliense (Pcb) interaction is currently available. In this study, we conducted the systematic identification of circRNAs from time series samples of potato cultivars Valor (susceptible) and BP1 (disease tolerant) infected by Pcb. A total of 2098 circRNAs were detected and about half (931, 44.38%) were intergenic circRNAs. And differential expression analysis detected 429 significantly regulated circRNAs...
December 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29245939/identification-of-hub-genes-related-to-silicone-induced-immune-response-in-rats
#18
Xiaolu Huang, Yiwen Zhou, Wenhui Liu, Haizhou Li, Xiao Liang, Rui Jin, Hengyu Du, Jizhou He, Bangda Chai, Ran Duan, Qingfeng Li
Silicone implants are used widely in the field of plastic surgery and are used in a large population. However, their safety profile, especially the silicone-induced immune response, has been a major concern for plastic surgeons for decades. It has been hypothesized that there is a cause and effect relation between silicone and immunity, but this is controversial. The objective of the present study was to determine the hub genes and key pathways related to silicone implant-induced immune responses in a rat model...
November 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228631/identification-of-differentially-expressed-genes-lncrnas-and-mirnas-which-are-associated-with-tumor-malignant-phenotypes-in-hepatoblastoma-patients
#19
Sida Liu, Fujing Xie, Xiaohong Xiang, Sinan Liu, Shunbin Dong, Kai Qu, Ting Lin
Hepatoblastoma (HB) is one of the most common hepatic malignancies in the pediatric population. HB are composed of a variety of tumors, which derived from different origins and had varying clinical outcomes. However, the unclear underlying mechanisms of HB limited exploring novel biomarkers and effective therapeutic targets. We searched microarray datasets on Gene Expression Omnibus (GEO) database and selected GSE75271 and GSE75283 datasets for comprehensive analysis. Weighted gene correlation network analysis (WGCNA) was employed to identify genes which were associated with tumor malignant phenotypes, including HB subtypes, Cairo classification and tumor stage...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29226034/constructing-a-comprehensive-gene-co-expression-based-interactome-in-bos-taurus
#20
Yan Chen, Yining Liu, Min Du, Wengang Zhang, Ling Xu, Xue Gao, Lupei Zhang, Huijiang Gao, Lingyang Xu, Junya Li, Min Zhao
Integrating genomic information into cattle breeding is an important approach to exploring genotype-phenotype relationships for complex traits related to diary and meat production. To assist with genomic-based selection, a reference map of interactome is needed to fully understand and identify the functional relevant genes. To this end, we constructed a co-expression analysis of 92 tissues and this represents the systematic exploration of gene-gene relationship in Bos taurus. By using robust WGCNA (Weighted Gene Correlation Network Analysis), we described the gene co-expression network of 5,000 protein-coding genes with majority variations in expression across 92 tissues...
2017: PeerJ
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