keyword
MENU ▼
Read by QxMD icon Read
search

functional annotation

keyword
https://www.readbyqxmd.com/read/28346370/de-novo-assembly-annotation-and-characterization-of-root-transcriptomes-of-three-caladium-cultivars-with-a-focus-on-necrotrophic-pathogen-resistance-defense-related-genes
#1
Zhe Cao, Zhanao Deng
Roots are vital to plant survival and crop yield, yet few efforts have been made to characterize the expressed genes in the roots of non-model plants (root transcriptomes). This study was conducted to sequence, assemble, annotate, and characterize the root transcriptomes of three caladium cultivars (Caladium × hortulanum) using RNA-Seq. The caladium cultivars used in this study have different levels of resistance to Pythiummyriotylum, the most damaging necrotrophic pathogen to caladium roots. Forty-six to 61 million clean reads were obtained for each caladium root transcriptome...
March 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28346365/an-amylase-like-protein-amyd-is-the-major-negative-regulator-for-%C3%AE-glucan-synthesis-in-aspergillus-nidulans-during-the-asexual-life-cycle
#2
Xiaoxiao He, Shengnan Li, Susan Kaminskyj
α-Glucan affects fungal cell-cell interactions and is important for the virulence of pathogenic fungi. Interfering with production of α-glucan could help to prevent fungal infection. In our previous study, we reported that an amylase-like protein, AmyD, could repress α-glucan accumulation in Aspergillus nidulans. However, the underlying molecular mechanism was not clear. Here, we examined the localization of AmyD and found it was a membrane-associated protein. We studied AmyD function in α-glucan degradation, as well as with other predicted amylase-like proteins and three annotated α-glucanases...
March 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28345861/identification-of-gene-transcription-start-sites-and-enhancers-responding-to-pulmonary-carbon-nanotube-exposure-in-vivo
#3
Jette Bornholdt, Anne Thoustrup Saber, Berit Lilje, Mette Boyd, Mette Jørgensen, Yun Chen, Morana Vitezic, Nicklas Raun Jacobsen, Sarah Søs Poulsen, Trine Berthing, Simon Bressendorff, Kristoffer Vitting-Seerup, Robin Andersson, Karin Sørig Hougaard, Carole L Yauk, Sabina Halappanavar, Håkan Wallin, Ulla Vogel, Albin Sandelin
Increased use of nanomaterials in industry, medicine and consumer products has raised concerns over their toxicity. To ensure safe use of nanomaterials, understanding their biological effects at the molecular level is crucial. In particular, the regulatory mechanisms responsible for the cascade of genes activated by nanomaterial exposure are not well characterized. To this end, we profiled the genome-wide usage of gene transcription start sites and linked active enhancer regions in lungs of C57BL/6 mice 24h after intratracheal instillation of a single dose of the multiwalled carbon nanotube Mitsui-7...
March 27, 2017: ACS Nano
https://www.readbyqxmd.com/read/28343001/comprehensive-functional-analysis-of-large-lists-of-genes-and-proteins
#4
Bernhard Mlecnik, Jérôme Galon, Gabriela Bindea
The interpretation of high dimensional datasets resulting from genomic and proteomic experiments in a timely and efficient manner is challenging. ClueGO software is a Cytoscape App that extracts representative functional biological information for large lists of genes or proteins. The functional enrichment analysis is based on the latest publicly available data from multiple annotation and ontology resources that can be automatically accessed through ClueGO. Predefined settings for the selection of the terms are provided to facilitate the analysis...
March 22, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28342236/resolving-protein-structure-function-binding-site-relationships-from-a-binding-site-similarity-network-perspective
#5
Richa Mudgal, Narayanaswamy Srinivasan, Nagasuma Chandra
Functional annotation is seldom straightforward with complexities arising due to functional divergence in protein families or functional convergence between non-homologous protein families, leading to mis-annotations. An enzyme may contain multiple domains and not all domains may be involved in a given function, adding to the complexity in function annotation. To address this, we use binding site information from bound cognate ligands and catalytic residues, since it can help in resolving fold-function relationships at a finer level and with higher confidence...
March 25, 2017: Proteins
https://www.readbyqxmd.com/read/28342107/interactive-segmentation-in-mri-for-orthopedic-surgery-planning-bone-tissue
#6
Firat Ozdemir, Neerav Karani, Philipp Fürnstahl, Orcun Goksel
PURPOSE: Planning orthopedic surgeries is commonly performed in computed tomography (CT) images due to the higher contrast of bony structure. However, soft tissues such as muscles and ligaments that may determine the functional outcome of a procedure are not easy to identify in CT, for which fast and accurate segmentation in MRI would be desirable. To be usable in daily practice, such method should provide convenient means of interaction for modifications and corrections, e.g., during perusal by the surgeon or the planning physician for quality control...
March 24, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28339073/identification-of-proteins-in-the-aqueous-humor-associated-with-cataract-development-using-itraq-methodology
#7
Minhong Xiang, Xingru Zhang, Qingsong Li, Hanmin Wang, Zhenyong Zhang, Zhumei Han, Meiqing Ke, Xingxing Chen
Proteins in the aqueous humor (AH) are important in the induction of cataract development. The identification of cataract-associated proteins assists in identifying patients and predisposed to the condition and improve treatment efficacy. Proteomics analysis has previously been used for identifying protein markers associated with eye diseases; however, few studies have examined the proteomic alterations in cataract development due to high myopia, glaucoma and diabetes. The present study, using the isobaric tagging for relative and absolute protein quantification methodology, aimed to examine cataract-associated proteins in the AH from patients with high myopia, glaucoma or diabetes, and controls...
March 21, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28339008/detection-of-lower-levels-of-snap25-using-multiple-microarray-systems-and-its-functional-significance-in-medulloblastoma
#8
Chi-Jung Huang, Chia-Long Lee, Chih-Yi Liu, Shih-Hung Huang, Jia-Woei Hou, Yi-Hou Chen, Chih-Cheng Chien, Chih-Ming Ho, Wen-Cheng Lo, Kun-Long Hung
Medulloblastoma (MB) is the most common pediatric malignant brain tumor and patients with high-risk or recurrent MB respond poorly to current therapies, and have a higher related mortality. For this reason, potential molecules related to MB need be identified in order to develop targets for the development of novel therapeutics. In the present study, we compared MB microarray data obtained using different microarray systems and significant targets were selected by gene annotation and enrichment analysis. Genes for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) annotated with the function 'vesicle' were identified and one of these proteins, synaptosomal-associated protein 25 (SNAP25), was found to have significantly lower expression levels in MB...
March 20, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28338930/expath-tool-a-system-for-comprehensively-analyzing-regulatory-pathways-and-coexpression-networks-from-high-throughput-transcriptome-data
#9
Han-Qin Zheng, Nai-Yun Wu, Chi-Nga Chow, Kuan-Chieh Tseng, Chia-Hung Chien, Yu-Cheng Hung, Guan-Zhen Li, Wen-Chi Chang
Next generation sequencing (NGS) has become the mainstream approach for monitoring gene expression levels in parallel with various experimental treatments. Unfortunately, there is no systematical webserver to comprehensively perform further analysis based on the huge amount of preliminary data that is obtained after finishing the process of gene annotation. Therefore, a user-friendly and effective system is required to mine important genes and regulatory pathways under specific conditions from high-throughput transcriptome data...
March 13, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28337675/an-ontology-based-search-engine-for-digital-reconstructions-of-neuronal-morphology
#10
Sridevi Polavaram, Giorgio A Ascoli
Neuronal morphology is extremely diverse across and within animal species, developmental stages, brain regions, and cell types. This diversity is functionally important because neuronal structure strongly affects synaptic integration, spiking dynamics, and network connectivity. Digital reconstructions of axonal and dendritic arbors are thus essential to quantify and model information processing in the nervous system. NeuroMorpho.Org is an established repository containing tens of thousands of digitally reconstructed neurons shared by several hundred laboratories worldwide...
March 23, 2017: Brain Informatics
https://www.readbyqxmd.com/read/28336965/exploring-approaches-for-detecting-protein-functional-similarity-within-an-orthology-based-framework
#11
Christian X Weichenberger, Antonia Palermo, Peter P Pramstaller, Francisco S Domingues
Protein functional similarity based on gene ontology (GO) annotations serves as a powerful tool when comparing proteins on a functional level in applications such as protein-protein interaction prediction, gene prioritization, and disease gene discovery. Functional similarity (FS) is usually quantified by combining the GO hierarchy with an annotation corpus that links genes and gene products to GO terms. One large group of algorithms involves calculation of GO term semantic similarity (SS) between all the terms annotating the two proteins, followed by a second step, described as "mixing strategy", which involves combining the SS values to yield the final FS value...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28336542/seten-a-tool-for-systematic-identification-and-comparison-of-processes-phenotypes-and-diseases-associated-with-rna-binding-proteins-from-condition-specific-clip-seq-profiles
#12
Gungor Budak, Rajneesh Srivastava, Sarath Chandra Janga
RNA-binding proteins (RBPs) control the regulation of gene expression in eukaryotic genomes at post-transcriptional level by binding to their cognate RNAs. Although several variants of CLIP (crosslinking and immunoprecipitation) protocols are currently available to study the global protein-RNA interaction landscape at single nucleotide resolution in a cell, currently there are very few tools which can facilitate understanding and dissecting the functional associations of RBPs from the resulting binding maps...
March 23, 2017: RNA
https://www.readbyqxmd.com/read/28335741/high-throughput-sequencing-of-pituitary-and-hypothalamic-microrna-transcriptome-associated-with-high-rate-of-egg-production
#13
Nan Wu, Qing Zhu, Binlong Chen, Jian Gao, Zhongxian Xu, Diyan Li
BACKGROUND: MicroRNAs exist widely in viruses, plants and animals. As endogenous small non-coding RNAs, miRNAs regulate a variety of biological processes. Tissue miRNA expression studies have discovered numerous functions for miRNAs in various tissues of chicken, but the regulation of miRNAs in chicken pituitary and hypothalamic development related to high and low egg-laying performance has remained unclear. RESULTS: In this study, using high-throughput sequencing technology, we sequenced two tissues (pituitary and hypothalamus) in 3 high- and 3 low-rate egg production Luhua chickens at the age of 300 days...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335718/rnav-2-0-a-visualization-tool-for-bacterial-srna-mediated-regulatory-networks-mining
#14
Romain Bourqui, Isabelle Dutour, Jonathan Dubois, William Benchimol, Patricia Thébault
BACKGROUND: Bacterial sRNA-mediated regulatory networks has been introduced as a powerful way to analyze the fast rewiring capabilities of a bacteria in response to changing environmental conditions. The identification of mRNA targets of bacterial sRNAs is essential to investigate their functional activities. However, this step remains challenging with the lack of knowledge of the topological and biological constraints behind the formation of sRNA-mRNA duplexes. Even with the most sophisticated bioinformatics target prediction tools, the large proportion of false predictions may be prohibitive for further analyses...
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28335496/quantitative-analysis-of-the-kshv-transcriptome-following-primary-infection-of-blood-and-lymphatic-endothelial-cells
#15
A Gregory Bruce, Serge Barcy, Terri DiMaio, Emilia Gan, H Jacques Garrigues, Michael Lagunoff, Timothy M Rose
The transcriptome of the Kaposi's sarcoma-associated herpesvirus (KSHV/HHV8) after primary latent infection of human blood (BEC), lymphatic (LEC) and immortalized (TIME) endothelial cells was analyzed using RNAseq, and compared to long-term latency in BCBL-1 lymphoma cells. Naturally expressed transcripts were obtained without artificial induction, and a comprehensive annotation of the KSHV genome was determined. A set of unique coding sequence (UCDS) features and a process to resolve overlapping transcripts were developed to accurately quantitate transcript levels from specific promoters...
March 19, 2017: Pathogens
https://www.readbyqxmd.com/read/28335474/coccolithoviruses-a-review-of-cross-kingdom-genomic-thievery-and-metabolic-thuggery
#16
Jozef I Nissimov, António Pagarete, Fangrui Ma, Sean Cody, David D Dunigan, Susan A Kimmance, Michael J Allen
Coccolithoviruses (Phycodnaviridae) infect and lyse the most ubiquitous and successful coccolithophorid in modern oceans, Emiliania huxleyi. So far, the genomes of 13 of these giant lytic viruses (i.e., Emiliania huxleyi viruses-EhVs) have been sequenced, assembled, and annotated. Here, we performed an in-depth comparison of their genomes to try and contextualize the ecological and evolutionary traits of these viruses. The genomes of these EhVs have from 444 to 548 coding sequences (CDSs). Presence/absence analysis of CDSs identified putative genes with particular ecological significance, namely sialidase, phosphate permease, and sphingolipid biosynthesis...
March 18, 2017: Viruses
https://www.readbyqxmd.com/read/28334930/rcas-an-rna-centric-annotation-system-for-transcriptome-wide-regions-of-interest
#17
Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Nikolaus Rajewsky, Uwe Ohler, Altuna Akalin
In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334231/protvista-visualization-of-protein-sequence-annotations
#18
Xavier Watkins, Leyla J Garcia, Sangya Pundir, Maria J Martin, The UniProt Consortium
Summary: ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations...
March 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334004/the-mouse-genome-displays-highly-dynamic-populations-of-krab-zinc-finger-protein-genes-and-related-genetic-units
#19
Annamaria Kauzlaric, Gabriela Ecco, Marco Cassano, Julien Duc, Michael Imbeault, Didier Trono
KRAB-containing poly-zinc finger proteins (KZFPs) constitute the largest family of transcription factors encoded by mammalian genomes, and growing evidence indicates that they fulfill functions critical to both embryonic development and maintenance of adult homeostasis. KZFP genes underwent broad and independent waves of expansion in many higher vertebrates lineages, yet comprehensive studies of members harbored by a given species are scarce. Here we present a thorough analysis of KZFP genes and related units in the murine genome...
2017: PloS One
https://www.readbyqxmd.com/read/28333993/integrated-transcriptomic-and-proteomic-analysis-of-the-molecular-cargo-of-extracellular-vesicles-derived-from-porcine-adipose-tissue-derived-mesenchymal-stem-cells
#20
Alfonso Eirin, Xiang-Yang Zhu, Amrutesh S Puranik, John R Woollard, Hui Tang, Surendra Dasari, Amir Lerman, Andre J van Wijnen, Lilach O Lerman
BACKGROUND: Mesenchymal stromal/stem cell (MSC) transplantation is a promising therapy for tissue regeneration. Extracellular vesicles (EVs) released by MSCs act as their paracrine effectors by delivering proteins and genetic material to recipient cells. To assess how their cargo mediates biological processes that drive their therapeutic effects, we integrated miRNA, mRNA, and protein expression data of EVs from porcine adipose tissue-derived MSCs. METHODS: Simultaneous expression profiles of miRNAs, mRNAs, and proteins were obtained by high-throughput sequencing and LC-MS/MS proteomic analysis in porcine MSCs and their daughter EVs (n = 3 each)...
2017: PloS One
keyword
keyword
117644
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"