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Gene ontology, clustering

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https://www.readbyqxmd.com/read/28069422/identification-of-ecdysteroid-receptor-mediated-signaling-pathways-in-the-hepatopancreas-of-the-red-swamp-crayfish-procambarus-clarkii
#1
Baojian Zhu, Lin Tang, Yingying Yu, Huimin Yu, Lei Wang, Cen Qian, Guoqing Wei, Chaoliang Liu
The hepatopancreas of crustaceans plays an important role in lipid and carbohydrate metabolism, digestion of food, and biogenesis. In this study, the hepatopancreas transcriptome from the red crayfish Procambarus clarkii was characterized for the first time using high-throughput sequencing, producing approximately 41.4 million reads were obtained. After de novo assembly, 57,363 unigenes with an average length of 725 bp were identified, Gene Ontology analysis categorized 22,580 as being involved in biological processes, among which metabolic process and cellular process groups were the most highly enriched...
January 6, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28056803/de-novo-transcriptome-and-expression-profile-analyses-of-the-asian-corn-borer-ostrinia-furnacalis-reveals-relevant-flubendiamide-response-genes
#2
Li Cui, Changhui Rui, Daibin Yang, Zhenying Wang, Huizhu Yuan
BACKGROUND: The Asian corn borer (ACB), Ostrinia furnacalis (Guenée), has become the most damaging insect pest of corn in Asia. However, the lack of genome or transcriptome information heavily hinders our further understanding of ACB in every aspect at a molecular level and on a genome-wide scale. Here, we used the Ion Torrent Personal Genome Machine (PGM) Sequencer to explore the ACB transcriptome and to identify relevant genes in response to flubendiamide, showing high selective activity against ACB...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28054239/the-protein-content-of-extracellular-vesicles-derived-from-expanded-human-umbilical-cord-blood-derived-cd133-and-human-bone-marrow-derived-mesenchymal-stem-cells-partially-explains-why-both-sources-are-advantageous-for-regenerative-medicine
#3
Addeli B B Angulski, Luiz G Capriglione, Michel Batista, Bruna H Marcon, Alexandra C Senegaglia, Marco A Stimamiglio, Alejandro Correa
Adult stem cells have beneficial effects when exposed to damaged tissue due, at least in part, to their paracrine activity, which includes soluble factors and extracellular vesicles (EVs). Given the multiplicity of signals carried by these vesicles through the horizontal transfer of functional molecules, human mesenchymal stem cell (hMSCs) and CD133(+) cell-derived EVs have been tested in various disease models and shown to recover damaged tissues. In this study, we profiled the protein content of EVs derived from expanded human CD133(+) cells and bone marrow-derived hMSCs with the intention of better understanding the functions performed by these vesicles/cells and delineating the most appropriate use of each EV in future therapeutic procedures...
January 4, 2017: Stem Cell Reviews
https://www.readbyqxmd.com/read/28039103/itraq-based-proteome-analysis-of-fluoroquinolone-resistant-staphylococcus-aureus
#4
Van Chi Thai, Teck Kwang Lim, Kim Phuong Uyen Le, Qingsong Lin, Thi Thu Hoai Nguyen
OBJECTIVES: The aim of this study was to compare global protein expression changes during fluoroquinolone (FQ) exposure of Staphylococcus aureus. METHODS: Total protein extracts of wild-type S. aureus ATCC 29213 and six multidrug-resistant (MDR) strains derived from the wild-type under different FQ exposures were analysed using the 8-plex isobaric tag for relative and absolute quantitation (iTRAQ) method combined with LC-MS/MS analysis. Differentially expressed proteins were searched for their Gene Ontology (GO) annotation (UniProt database) and protein-protein interaction network (STRING v...
December 27, 2016: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28029629/discovering-perturbation-of-modular-structure-in-hiv-progression-by-integrating-multiple-data-sources-through-non-negative-matrix-factorization
#5
Sumanta Ray, Ujjwal Maulik
Detecting perturbation in modular structure during HIV-1 disease progression is an important step to understand stage specific infection pattern of HIV-1 virus in human cell. In this article, we proposed a novel methodology on integration of multiple biological information to identify such disruption in human gene module during different stages of HIV-1 infection. We integrate three different biological information: gene expression information, protein-protein interaction information and gene ontology information in single gene meta-module, through non negative matrix factorization (NMF)...
December 20, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28029628/evolutionary-graph-clustering-for-protein-complex-identification
#6
Tiantian He, Keith C C Chan
This paper presents a graph clustering algorithm, called EGCPI, to discover protein complexes in protein-protein interaction (PPI) networks. In performing its task, EGCPI takes into consideration both network topologies and attributes of interacting proteins, both of which have been shown to be important for protein complex discovery. EGCPI formulates the problem as an optimization problem and tackles it with evolutionary clustering. Given a PPI network, EGCPI first annotates each protein with corresponding attributes that are provided in Gene Ontology database...
December 20, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28018170/mrna-transcriptomics-of-galectins-unveils-heterogeneous-organization-in-mouse-and-human-brain
#7
Sebastian John, Rashmi Mishra
Background: Galectins, a family of non-classically secreted, β-galactoside binding proteins is involved in several brain disorders; however, no systematic knowledge on the normal neuroanatomical distribution and functions of galectins exits. Hence, the major purpose of this study was to understand spatial distribution and predict functions of galectins in brain and also compare the degree of conservation vs. divergence between mouse and human species. The latter objective was required to determine the relevance and appropriateness of studying galectins in mouse brain which may ultimately enable us to extrapolate the findings to human brain physiology and pathologies...
2016: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28013168/integrated-analysis-identifies-molecular-signatures-and-specific-prognostic-factors-for-different-gastric-cancer-subtypes
#8
Li Min, Yu Zhao, Shengtao Zhu, Xintao Qiu, Rui Cheng, Jie Xing, Linlin Shao, Shuilong Guo, Shutian Zhang
BACKGROUND: Gastric cancer (GC) is the fifth leading cause of cancer-related deaths worldwide. As an effective and easily performed method, microscopy-based Lauren classification has been widely accepted by gastrointestinal surgeons and pathologists for GC subtyping, but molecular characteristics of different Lauren subtypes were poorly revealed. METHODS: GSE62254 was used as a derivation cohort, and GSE15459 was used as a validation cohort. The difference between diffuse and intestinal GC on the gene expression level was measured...
December 22, 2016: Translational Oncology
https://www.readbyqxmd.com/read/28005906/a-stromal-immune-module-correlated-with-the-response-to-neoadjuvant-chemotherapy-prognosis-and-lymphocyte-infiltration-in-her2-positive-breast-carcinoma-is-inversely-correlated-with-hormonal-pathways
#9
Anne-Sophie Hamy, Hélène Bonsang-Kitzis, Marick Lae, Matahi Moarii, Benjamin Sadacca, Alice Pinheiro, Marion Galliot, Judith Abecassis, Cecile Laurent, Fabien Reyal
INTRODUCTION: HER2-positive breast cancer (BC) is a heterogeneous group of aggressive breast cancers, the prognosis of which has greatly improved since the introduction of treatments targeting HER2. However, these tumors may display intrinsic or acquired resistance to treatment, and classifiers of HER2-positive tumors are required to improve the prediction of prognosis and to develop novel therapeutic interventions. METHODS: We analyzed 2893 primary human breast cancer samples from 21 publicly available datasets and developed a six-metagene signature on a training set of 448 HER2-positive BC...
2016: PloS One
https://www.readbyqxmd.com/read/28000438/gogadget-an-r-package-for-interpretation-and-visualization-of-go-enrichment-results
#10
Benjamin Nota
Gene expression profiling followed by gene ontology (GO) term enrichment analysis can generate long lists of significant GO terms. To interpret these results and get biological insight in the data, filtering and rearranging these long lists of GO terms might be desirable. The R package gogadget provides functions to modify GO analysis results, with a simple filter strategy. Furthermore, it groups redundant GO terms with hierarchical clustering and presents the results in a colorful heatmap. The filtered GO term enrichment results can also be exported by the package for subsequent analysis in Cytoscape Enrichment Map...
December 21, 2016: Molecular Informatics
https://www.readbyqxmd.com/read/27997584/prediction-of-possible-biomarkers-and-novel-pathways-conferring-risk-to-post-traumatic-stress-disorder
#11
Kumaraswamy Naidu Chitrala, Prakash Nagarkatti, Mitzi Nagarkatti
Post-traumatic stress disorder is one of the common mental ailments that is triggered by exposure to traumatic events. Till date, the molecular factors conferring risk to the development of PTSD is not well understood. In this study, we have conducted a meta-analysis followed by hierarchical clustering and functional enrichment, to uncover the potential molecular networks and critical genes which play an important role in PTSD. Two datasets of expression profiles from Peripheral Blood Mononuclear Cells from 62 control samples and 63 PTSD samples were included in our study...
2016: PloS One
https://www.readbyqxmd.com/read/27990252/cluster-analysis-of-plasmodium-rna-seq-time-course-data-identifies-stage-specific-co-regulated-biological-processes-and-regulatory-elements
#12
Efejiro Ashano, Itunuoluwa Isewon, Jelili Oyelade, Ezekiel Adebiyi
In this study, we interpreted RNA-seq time-course data of three developmental stages of Plasmodium species by clustering genes based on similarities in their expression profile without prior knowledge of the gene function. Functional enrichment of clusters of upregulated genes at specific time-points reveals potential targetable biological processes with information on their timings. We identified common consensus sequences that these clusters shared as potential points of coordinated transcriptional control...
2016: F1000Research
https://www.readbyqxmd.com/read/27989555/combining-sequence-and-gene-ontology-for-protein-module-detection-in-the-weighted-network
#13
Yang Yu, Jie Liu, Nuan Feng, Bo Song, Zeyu Zheng
Studies of protein modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in locating protein modules. In this paper, a new approach combining Gene Ontology and amino acid background frequency is introduced to detect the protein modules in the weighted PPI networks. The proposed approach mainly consists of three parts: the feature extraction, the weighted graph construction and the protein complex detection...
October 29, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27984079/combining-sequence-and-gene-ontology-for-protein-module-detection-in-the-weighted-network
#14
Yang Yu, Jie Liu, Nuan Feng, Bo Song, Zeyu Zheng
Studies of protein modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in locating protein modules. In this paper, a new approach combining Gene Ontology and amino acid background frequency is introduced to detect the protein modules in the weighted PPI networks. The proposed approach mainly consists of three parts: the feature extraction, the weighted graph construction and the protein complex detection...
January 7, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27979689/effect-of-intraoral-mechanical-stress-application-on-the-expression-of-a-force-responsive-prognostic-marker-associated-with-system-disease-progression
#15
Yimei Zhang, Xiaoxing Kou, Nan Jiang, Yan Liu, Franklin R Tay, Yanheng Zhou
OBJECTIVES: Malocclusion may be corrected nonsurgically by mechanical tooth movement. The plasma protein profiles of human subjects receiving the first phase of orthodontic treatment were examined to test the hypothesis that application of mechanical stresses to teeth induces systemic proteomic alterations. METHODS: Tandem mass tag-based liquid chromatography-mass spectrometry (LC-MS/MS) was used to examine systemic proteomic alterations in subjects undergoing controlled stress application (N=10) and in volunteers not receiving treatment (N=7) at 3 time intervals within 24h...
December 12, 2016: Journal of Dentistry
https://www.readbyqxmd.com/read/27957850/comparative-toxicogenomic-responses-to-the-flame-retardant-mitp-in-developing-zebrafish
#16
Derik E Haggard, Siba R Das, Robert L Tanguay
Monosubstituted isopropylated triaryl phosphate (mITP) is a major component of Firemaster 550, an additive flame retardant mixture commonly used in polyurethane foams. Developmental toxicity studies in zebrafish established mITP as the most toxic component of FM 550, which causes pericardial edema and heart looping failure. Mechanistic studies showed that mITP is an aryl hydrocarbon receptor (AhR) ligand; however, the cardiotoxic effects of mITP were independent of the AhR. We performed comparative whole genome transcriptomics in wild-type and ahr2(hu3335) zebrafish, which lack functional ahr2, to identify transcriptional signatures causally involved in the mechanism of mITP-induced cardiotoxicity...
December 13, 2016: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/27941916/lncrnas-expression-profiling-in-normal-ovary-benign-ovarian-cyst-and-malignant-epithelial-ovarian-cancer
#17
Huan Wang, Ziyi Fu, Chencheng Dai, Jian Cao, Xiaoguang Liu, Juan Xu, Mingming Lv, Yun Gu, Jingmin Zhang, Xiangdong Hua, Genmei Jia, Sujuan Xu, Xuemei Jia, Pengfei Xu
Long noncoding RNA (lncRNA) has been recognized as a regulator of gene expression, and the dysregulation of lncRNAs is involved in the progression of many types of cancer, including epithelial ovarian cancer (EOC). To explore the potential roles of lncRNAs in EOC, we performed lncRNA and mRNA microarray profiling in malignant EOC, benign ovarian cyst and healthy control tissues. In this study, 663 transcripts of lncRNAs were found to be differentially expressed in malignant EOC compared with benign and normal control tissues...
December 12, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27934965/role-and-mechanism-of-the-ampk-pathway-in-waterborne-zn-exposure-influencing-the-hepatic-energy-metabolism-of-synechogobius-hasta
#18
Kun Wu, Chao Huang, Xi Shi, Feng Chen, Yi-Huan Xu, Ya-Xiong Pan, Zhi Luo, Xu Liu
Previous studies have investigated the physiological responses in the liver of Synechogobius hasta exposed to waterborne zinc (Zn). However, at present, very little is known about the underlying molecular mechanisms of these responses. In this study, RNA sequencing (RNA-seq) was performed to analyse the differences in the hepatic transcriptomes between control and Zn-exposed S. hasta. A total of 36,339 unigenes and 1,615 bp of unigene N50 were detected. These genes were further annotated to the Nonredundant protein (NR), Nonredundant nucleotide (Nt), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG) and Gene Ontology (GO) databases...
December 9, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27931240/skeletal-muscle-characteristics-are-preserved-in-htert-cdk4-human-myogenic-cell-lines
#19
Matthew Thorley, Stéphanie Duguez, Emilia Maria Cristina Mazza, Sara Valsoni, Anne Bigot, Kamel Mamchaoui, Brennan Harmon, Thomas Voit, Vincent Mouly, William Duddy
BACKGROUND: hTERT/cdk4 immortalized myogenic human cell lines represent an important tool for skeletal muscle research, being used as therapeutically pertinent models of various neuromuscular disorders and in numerous fundamental studies of muscle cell function. However, the cell cycle is linked to other cellular processes such as integrin regulation, the PI3K/Akt pathway, and microtubule stability, raising the question as to whether genetic modification related to the cell cycle results in secondary effects that could undermine the validity of these cell models...
December 8, 2016: Skeletal Muscle
https://www.readbyqxmd.com/read/27918468/transcriptome-analysis-of-the-tadpole-shrimp-triops-longicaudatus-by-illumina-paired-end-sequencing-assembly-annotation-and-marker-discovery
#20
Jiyeon Seong, Se Won Kang, Bharat Bhusan Patnaik, So Young Park, Hee Ju Hwang, Jong Min Chung, Dae Kwon Song, Mi Young Noh, Seung-Hwan Park, Gwang Joo Jeon, Hong Sik Kong, Soonok Kim, Ui Wook Hwang, Hong Seog Park, Yeon Soo Han, Yong Seok Lee
The tadpole shrimp (Triops longicaudatus) is an aquatic crustacean that helps control pest populations. It inhabits freshwater ponds and pools and has been described as a living fossil. T. longicaudatus was officially declared an endangered species South Korea in 2005; however, through subsequent protection and conservation management, it was removed from the endangered species list in 2012. The limited number of available genetic resources on T. longicaudatus makes it difficult to obtain valuable genetic information for marker-aided selection programs...
December 2, 2016: Genes
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