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Gene ontology, clustering

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https://www.readbyqxmd.com/read/28728275/-changes-and-differences-of-dna-methylation-in-human-macrophages-infected-with-virulent-and-avirulent-mycobacterium-tuberculosis
#1
L N Lyu, H Y Jia, Z H Li, Z Q Liu, Z D Zhang
Objective: To profile DNA methylation and compare differentially methylated region (DMR) of macrophages infected with virulent and avirulent strains of Mycobacterium tuberculosis (MTB). Methods: PMA(50 ng/ml) treated THP-1 macrophages were left uninfected or infected with the virulent H37Rv(THP-1/Rv) or avirulent H37Ra(THP-1/Ra). The genomic DNA was then extracted and DNA methylation was profiled via Reduced Representation Bisulfite Sequencing (RRBS). The DNA methylation pattern and DMRs between the tested samples were indentified...
July 12, 2017: Chinese Journal of Tuberculosis and Respiratory Diseases
https://www.readbyqxmd.com/read/28718798/co-expression-network-and-pathway-analyses-reveal-important-modules-of-mirnas-regulating-milk-yield-and-component-traits
#2
Duy N Do, Pier-Luc Dudemaine, Ran Li, Eveline M Ibeagha-Awemu
Co-expression network analyses provide insights into the molecular interactions underlying complex traits and diseases. In this study, co-expression network analysis was performed to detect expression patterns (modules or clusters) of microRNAs (miRNAs) during lactation, and to identify miRNA regulatory mechanisms for milk yield and component traits (fat, protein, somatic cell count (SCC), lactose, and milk urea nitrogen (MUN)) via miRNA target gene enrichment analysis. miRNA expression (713 miRNAs), and milk yield and components (Fat%, Protein%, lactose, SCC, MUN) data of nine cows at each of six different time points (day 30 (D30), D70, D130, D170, D230 and D290) of an entire lactation curve were used...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28717649/circular-rna-profiling-and-bioinformatic-modeling-identify-its-regulatory-role-in-hepatic-steatosis
#3
Xing-Ya Guo, Chong-Xin He, Yu-Qin Wang, Chao Sun, Guang-Ming Li, Qing Su, Qin Pan, Jian-Gao Fan
Circular RNAs (circRNAs) exhibit a wide range of physiological and pathological activities. To uncover their role in hepatic steatosis, we investigated the expression profile of circRNAs in HepG2-based hepatic steatosis induced by high-fat stimulation. Differentially expressed circRNAs were subjected to validation using QPCR and functional analyses using principal component analysis, hierarchical clustering, target prediction, gene ontology (GO), and pathway annotation, respectively. Bioinformatic integration established the circRNA-miRNA-mRNA regulatory network so as to identify the mechanisms underlying circRNAs' metabolic effect...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28716896/poor-prognosis-indicated-by-venous-circulating-tumor-cell-clusters-in-early-stage-lung-cancers
#4
Vasudha Murlidhar, Rishindra M Reddy, Shamileh Fouladdel, Lili Zhao, Martin K Ishikawa, Svetlana Grabauskiene, Zhuo Zhang, Jules Lin, Andrew C Chang, Philip W Carrott, William R Lynch, Mark B Orringer, Chandan Kumar-Sinha, Nallasivam Palanisamy, David G Beer, Max S Wicha, Nithya Ramnath, Ebrahim Azizi, Sunitha Nagrath
Early detection of metastasis can be aided by circulating tumor cells (CTCs), which also show potential to predict early relapse. Due to the limited CTC numbers in peripheral blood in early stages, we investigated CTCs in pulmonary vein blood accessed during surgical resection of tumors. Pulmonary vein (PV) and peripheral vein (Pe) blood specimens from patients with lung cancer were drawn during the perioperative period and assessed for CTC burden using a microfluidic device. From 108 blood samples analyzed from 36 patients, PV had significantly higher number of CTCs compared to pre-operative Pe (p<0...
July 17, 2017: Cancer Research
https://www.readbyqxmd.com/read/28716001/variant-ranker-a-web-tool-to-rank-genomic-data-according-to-functional-significance
#5
John Alexander, Dimitris Mantzaris, Marianthi Georgitsi, Petros Drineas, Peristera Paschou
BACKGROUND: The increasing volume and complexity of high-throughput genomic data make analysis and prioritization of variants difficult for researchers with limited bioinformatics skills. Variant Ranker allows researchers to rank identified variants and determine the most confident variants for experimental validation. RESULTS: We describe Variant Ranker, a user-friendly simple web-based tool for ranking, filtering and annotation of coding and non-coding variants...
July 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28713995/bioinformatic-analysis-of-computational-identified-differentially-expressed-genes-in-tumor-stoma-of-pregnancy%C3%A2-associated-breast-cancer
#6
Qian Zhou, Erhu Sun, Lijun Ling, Xiaofeng Liu, Min Zhang, Hong Yin, Cheng Lu
The present study aimed to screen the differentially expressed genes (DEGs) in tumor‑associated stroma of pregnancy‑associated breast cancer (PABC). By analyzing Affymetrix microarray data (GSE31192) from the Gene Expression Omnibus database, DEGs between tumor asso-ciated stromal cells and normal stromal cells in PABC were identified. Gene Ontology (GO) function and pathway enrichment analyses for the DEGs were then performed, followed by construction of a protein‑protein interaction (PPI) network. A total of 94 upregulated and 386 downregulated DEGs were identified between tumor associated stromal cells and normal stromal cells in patients with PABC...
July 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28713962/bioinformatics-analysis-of-key-genes-and-signaling-pathways-associated-with-myocardial-infarction-following-telomerase-activation
#7
Yi Yang, Guang Yang, Hongwei Du, Nana Dong, Bo Yu
The present study aimed to identify key genes and signaling pathways associated with myocardial infarction (MI) following telomerase activation, and investigate the possible underlying molecular mechanisms involved in this process. Array data of GSE62973 was downloaded, including 11 samples from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were analyzed in infarct vs. control, infarct + telomerase vs. control, and infarct + telomerase vs. infarct with the Linear Models for Microarray and RNA‑Seq Data package...
July 6, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28704455/a-density-based-approach-for-detecting-complexes-in-weighted-ppi-networks-by-semantic-similarity
#8
HongFang Zhou, Jie Liu, JunHuai Li, WenCong Duan
Protein complex detection in PPI networks plays an important role in analyzing biological processes. A new algorithm-DBGPWN-is proposed for predicting complexes in PPI networks. Firstly, a method based on gene ontology is used to measure semantic similarities between interacted proteins, and the similarity values are used as their weights. Then, a density-based graph partitioning algorithm is developed to find clusters in the weighted PPI networks, and the identified ones are considered to be dense and similar...
2017: PloS One
https://www.readbyqxmd.com/read/28703336/a-genome-wide-association-study-reveals-candidate-genes-for-the-supernumerary-nipple-phenotype-in-sheep-ovis-aries
#9
W-F Peng, S-S Xu, X Ren, F-H Lv, X-L Xie, Y-X Zhao, M Zhang, Z-Q Shen, Y-L Ren, L Gao, M Shen, J Kantanen, M-H Li
Genome-wide association studies (GWASs) have been widely applied in livestock to identify genes associated with traits of economic interest. Here, we conducted the first GWAS of the supernumerary nipple phenotype in Wadi sheep, a native Chinese sheep breed, based on Ovine Infinium HD SNP BeadChip genotypes in a total of 144 ewes (75 cases with four teats, including two normal and two supernumerary teats, and 69 control cases with two teats). We detected 63 significant SNPs at the chromosome-wise threshold. Additionally, one candidate region (chr1: 170...
July 12, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28700355/identification-of-cd14-as-a-potential-biomarker-of-hepatocellular-carcinoma-using-itraq-quantitative-proteomics
#10
Jiao Guo, Rui Jing, Jian-Hong Zhong, Xin Dong, Yun-Xi Li, Yin-Kun Liu, Tian-Ren Huang, Chun-Yan Zhang
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors without effective diagnostic biomarkers. This study intended to dynamically analyze serum proteomics in different pathological stages of liver diseases, and discover potential diagnostic biomarkers for early HCC. Patients with hepatitis B virus (HBV) infection, liver cirrhosis (LC), or HCC together with healthy controls (HC) were enrolled. Proteins differentially expressed between groups were screened using isobaric tagging for relative and absolute quantitation (iTRAQ), and promising HCC biomarker candidates were subjected to bioinformatics analysis, including K-means clustering, gene ontology (GO) and string network analysis...
June 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28698996/genome-sequencing-of-strain-cellulosimicrobium-sp-th-20-with-ginseng-biotransformation-ability
#11
REVIEW
Fei Zheng, Wei Zhang, Xiaodan Chu, Yulin Dai, Jing Li, Huanxi Zhao, Liankui Wen, Hao Yue, Shanshan Yu
Biotransformation for increasing the pharmaceutical effect of ginsenosides is getting more and more attractions. Strain Cellulosimicrobium sp. TH-20 isolated from ginseng soil samples was identified to produce enzymes contributing to its excellent biotransformation activity against ginsenosides, the main active components of ginseng. Based on phylogenetic tree and homology analysis, the strain can be designated as Cellulosimicrobium sp. Genome sequencing was performed using the Illumina Miseq to explore the functional genes involved in ginsenoside transformation...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28673327/special-role-of-jun-in-papillary-thyroid-carcinoma-based-on-bioinformatics-analysis
#12
Wenzheng Chen, Qingfeng Liu, Yunxia Lv, Debin Xu, Wanzhi Chen, Jichun Yu
BACKGROUND: Papillary thyroid carcinoma (PTC) is the most common malignancy in thyroid tissue, and the number of patients with PTC has been increasing in recent years. Discovering the mechanism of PTC genesis and progression and finding new potential diagnostic biomarkers/therapeutic target genes of PTC are of great significance. METHODS: In this work, the datasets GSE3467 and GSE3678 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified with the limma package in R...
July 3, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28671602/mechanism-investigation-of-rifampicin-induced-liver-injury-using-comparative-toxicoproteomics-in-mice
#13
Ju-Hyun Kim, Woong Shik Nam, Sun Joo Kim, Oh Kwang Kwon, Eun Ji Seung, Jung Jae Jo, Riya Shresha, Tae Hee Lee, Tae Won Jeon, Sung Hwan Ki, Hye Suk Lee, Sangkyu Lee
Tuberculosis is one of the top causes of death among curable infectious diseases; it is an airborne infectious disease that killed 1.1 million people worldwide in 2010. Anti-tuberculosis drug-induced liver injury is the primary cause of drug-induced liver injury (DILI). Rifampicin is one of the most common anti-tuberculosis therapies and has well-known hepatotoxicity. To understand the mechanism of rifampicin-induced liver injury, we performed a global proteomic analysis of liver proteins by LC-MS/MS in a mouse model after the oral administration of 177 and 442...
July 2, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28671202/transcriptome-dynamics-of-human-pluripotent-stem-cell-derived-contracting-cardiomyocytes-using-an-embryoid-body-model-with-fetal-bovine-serum
#14
Kwang Bo Jung, Ye Seul Son, Hana Lee, Cho-Rok Jung, Janghwan Kim, Mi-Young Son
Cardiomyocyte (CM) differentiation techniques for generating adult-like mature CMs remain imperfect, and the plausible underlying mechanisms remain unclear; however, there are a number of current protocols available. Here, to explore the mechanisms controlling cardiac differentiation, we analyzed the genome-wide transcription dynamics occurring during the differentiation of human pluripotent stem cells (hPSCs) into CMs using embryoid body (EB) formation. We optimized and updated the protocol to efficiently generate contracting CMs from hPSCs by adding fetal bovine serum (FBS) as a medium supplement, which could have a significant impact on the efficiency of cardiac differentiation...
July 3, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28670134/identification-of-key-genes-and-molecular-mechanisms-associated-with-dedifferentiated-liposarcoma-based-on-bioinformatic-methods
#15
Hongliang Yu, Dong Pei, Longyun Chen, Xiaoxiang Zhou, Haiwen Zhu
BACKGROUND: Dedifferentiated liposarcoma (DDLPS) is one of the most deadly types of soft tissue sarcoma. To date, there have been few studies dedicated to elucidating the molecular mechanisms behind the disease; therefore, the molecular mechanisms behind this malignancy remain largely unknown. MATERIALS AND METHODS: Microarray profiles of 46 DDLPS samples and nine normal fat controls were extracted from Gene Expression Omnibus (GEO). Quality control for these microarray profiles was performed before analysis...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28665070/identification-of-downstream-genes-of-the-mtor-pathway-that-predict-recurrence-and-progression-in-non-muscle-invasive-high-grade-urothelial-carcinoma-of-the-bladder
#16
Subin Jin, In Ho Chang, Jin Wook Kim, Young Mi Whang, Ha Jeong Kim, Soon Auck Hong, Tae Jin Lee
Microarray analysis was used to investigate the lack of identified mammalian target of rapamycin (mTOR) pathway downstream genes to overcome cross-talk at non-muscle invasive high-grade (HG)-urothelial carcinoma (UC) of the bladder, gene expression patterns, gene ontology, and gene clustering by triple (p70S6K, S6K, and eIF4E) small interfering RNAs (siRNAs) or rapamycin in 5637 and T24 cell lines. We selected mTOR pathway downstream genes that were suppressed by siRNAs more than 2-fold, or were up-regulated or down-regulated by rapamycin more than 2-fold...
August 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/28662071/the-developmental-transcriptome-of-the-bamboo-snout-beetle-cyrtotrachelus-buqueti-and-insights-into-candidate-pheromone-binding-proteins
#17
Hua Yang, Ting Su, Wei Yang, Chunping Yang, Lin Lu, Zhangming Chen
Cyrtotrachelus buqueti is an extremely harmful bamboo borer, and the larvae of this pest attack clumping bamboo shoots. Pheromone-binding proteins (PBPs) play an important role in identifying insect sex pheromones, but the C. buqueti genome is not readily available for PBP analysis. Developmental transcriptomes of eggs, larvae from the first instar to the prepupal stage, pupae, and adults (females and males) from emergence to mating were built by RNA sequencing (RNA-Seq) in the present study to establish a sequence background of C...
2017: PloS One
https://www.readbyqxmd.com/read/28661723/differences-of-rna-expression-in-the-tendon-according-to-anatomic-outcomes-in-rotator-cuff-repair
#18
Jin-Ok Ahn, Jin-Young Chung, Do Hoon Kim, Wooseok Im, Sae Hoon Kim
BACKGROUND: Despite increased understanding of the pathophysiology of rotator cuff tears and the evolution of rotator cuff repair, healing failure remains a substantial problem. The critical roles played by biological factors have been emphasized, but little is known of the implications of gene expression profile differences at the time of repair. PURPOSE: To document the relationship between the perioperative gene expression of healed and unhealed rotator cuffs by RNA microarray analysis...
June 1, 2017: American Journal of Sports Medicine
https://www.readbyqxmd.com/read/28660252/abnormal-expression-of-homeobox-genes-and-transthyretin-in-c9orf72-expansion-carriers
#19
NiCole A Finch, Xue Wang, Matthew C Baker, Michael G Heckman, Tania F Gendron, Kevin F Bieniek, Joanne Wuu, Mariely DeJesus-Hernandez, Patricia H Brown, Jeannie Chew, Karen R Jansen-West, Lillian M Daughrity, Alexandra M Nicholson, Melissa E Murray, Keith A Josephs, Joseph E Parisi, David S Knopman, Ronald C Petersen, Leonard Petrucelli, Bradley F Boeve, Neill R Graff-Radford, Yan W Asmann, Dennis W Dickson, Michael Benatar, Robert Bowser, Kevin B Boylan, Rosa Rademakers, Marka van Blitterswijk
OBJECTIVE: We performed a genome-wide brain expression study to reveal the underpinnings of diseases linked to a repeat expansion in chromosome 9 open reading frame 72 (C9ORF72). METHODS: The genome-wide expression profile was investigated in brain tissue obtained from C9ORF72 expansion carriers (n = 32), patients without this expansion (n = 30), and controls (n = 20). Using quantitative real-time PCR, findings were confirmed in our entire pathologic cohort of expansion carriers (n = 56) as well as nonexpansion carriers (n = 31) and controls (n = 20)...
August 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28653889/bioinformatics-methods-for-identifying-differentially-expressed-genes-and-signaling-pathways-in-nano-silica-stimulated-macrophages
#20
Lin Zhang, Changfu Hao, Juan Li, Yaqian Qu, Lei Bao, Yiping Li, Zhongzheng Yue, Miao Zhang, Xinghao Yu, Huiting Chen, Jianhui Zhang, Di Wang, Wu Yao
The incidence of disease relating to nanoparticle exposure has been rising rapidly in recent years, for which there is no effective treatment. Macrophage is suggested to play a crucial role in the development of pulmonary disease. To investigate the changes in macrophage after being stimulated by nanometer silica dust and to explore potential biomarkers and signaling pathways, the gene chip GSE13005 was downloaded from Gene Expression Omnibus database, which contained 21 samples: 3 samples per group and 7 groups in total...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
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