keyword
MENU ▼
Read by QxMD icon Read
search

Gene noise

keyword
https://www.readbyqxmd.com/read/28441042/aberrantly-expressed-long-noncoding-rnas-in-recurrent-implantation-failure-a-microarray-related-study
#1
Li-Juan Fan, Hong-Jing Han, Jing Guan, Xiao-Wei Zhang, Qing-Hua Cui, Huan Shen, Cheng Shi
Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs longer than 200 nucleotides. They were long regarded as transcription noise for their low expression and non-protein coding features. Recent published reports indicate that lncRNAs are involved in virtually every aspect of human biology. We aimed to profile the endometrial lncRNA expression pattern in women with recurrent implantation failure (RIF) and predict the function of the genes of the dysregulated lncRNA transcripts. Endometrial samples (24) were collected during window of implantation (14 RIF women and 10 women who conceived after embryo transfer)...
April 25, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28438642/diagnostic-microarray-for-14-water-and-foodborne-pathogens-using-a-flatbed-scanner
#2
Vidya Srinivasan, Robert D Stedtfeld, Dieter M Tourlousse, Samuel W Baushke, Yu Xin, Sarah M Miller, Trinh Pham, Jean-Marie Rouillard, Erdogan Gulari, James M Tiedje, Syed A Hashsham
Parallel detection approaches are of interest to many researchers interested in identifying multiple water and foodborne pathogens simultaneously. Availability and cost-effectiveness are two key factors determining the usefulness of such approaches for laboratories with limited resources. In this study, we developed and validated a high-density microarray for simultaneous screening of 14 bacterial pathogens using an approach that employs gold labeling with silver enhancement (GLS) protocol. In total, 8887 probes (50-mer) were designed using an in-house database of virulence and marker genes (VMGs), and synthesized in quadruplicate on glass slides using an in-situ synthesis technology...
April 21, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28437444/transcriptional-bursting-in-drosophila-development-stochastic-dynamics-of-eve-stripe-2-expression
#3
David M Holloway, Alexander V Spirov
Anterior-posterior (AP) body segmentation of the fruit fly (Drosophila) is first seen in the 7-stripe spatial expression patterns of the pair-rule genes, which regulate downstream genes determining specific segment identities. Regulation of pair-rule expression has been extensively studied for the even-skipped (eve) gene. Recent live imaging, of a reporter for the 2nd eve stripe, has demonstrated the stochastic nature of this process, with 'bursts' in the number of RNA transcripts being made over time. We developed a stochastic model of the spatial and temporal expression of eve stripe 2 (binding by transcriptional activators (Bicoid and Hunchback proteins) and repressors (Giant and Krüppel proteins), transcriptional initiation and termination; with all rate parameters constrained by features of the experimental data) in order to analyze the noisy experimental time series and test hypotheses for how eve transcription is regulated...
2017: PloS One
https://www.readbyqxmd.com/read/28432993/chemical-biological-and-dna-markers-for-tracing-slaughterhouse-effluent
#4
P J Harvey, M P Taylor, H K Handley, S Foster, M R Gillings, A J Asher
Agricultural practices, if not managed correctly, can have a negative impact on receiving environments via waste disposal and discharge. In this study, a chicken slaughter facility on the rural outskirts of Sydney, Australia, has been identified as a possible source of persistent effluent discharge into a peri-urban catchment. Questions surrounding the facility's environmental management practices go back more than four decades. Despite there having never been a definitive determination of the facility's impact on local stream water quality, the New South Wales Environment Protection Authority (NSW EPA) has implemented numerous pollution reduction requirements to manage noise and water pollution at the slaughter facility...
April 19, 2017: Environmental Research
https://www.readbyqxmd.com/read/28427910/stochasticity-of-gene-expression-as-a-motor-of-epigenetics-in-bacteria-from-individual-to-collective-behavior
#5
REVIEW
Stéphanie Bury-Moné, Bianca Sclavi
Measuring gene expression at the single cell and single molecule level has recently made possible the quantitative measurement of stochasticity of gene expression. This enables identification of the probable sources and roles of noise. Stochastic gene expression can result in bacterial population heterogeneity, offering specific advantages for fitness and survival in various environments. This trait is therefore selected during the evolution of the species, and is consequently regulated by specific genetic network architecture...
April 18, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28427183/random-walk-based-method-to-identify-prognostic-genes-in-colorectal-cancer
#6
Xue Yang, Chen Zhao, Ning An
Currently, colorectal cancer remains one of the major causes of cancer mortality worldwide, despite significant advances in understanding its molecular mechanism. It has been putatively accepted that CRC, in most case, is a highly complicated process through adenoma-carcinoma sequence. Therefore, thorough researches regarding the molecular abnormalities, especially in precancerous stage, might be helpful in discovering potential biomarkers and promising therapeutic targets. Moreover, differentially expressed genes consistently dysregulated throughout the whole carcinogenic process might substantially reduce potential noise created by large-scale tumor heterogeneity...
March 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28426659/three-distinct-mechanisms-of-long-distance-modulation-of-gene-expression-in-yeast
#7
Manyu Du, Qian Zhang, Lu Bai
Recent Hi-C measurements have revealed numerous intra- and inter-chromosomal interactions in various eukaryotic cells. To what extent these interactions regulate gene expression is not clear. This question is particularly intriguing in budding yeast because it has extensive long-distance chromosomal interactions but few cases of gene regulation over-a-distance. Here, we developed a medium-throughput assay to screen for functional long-distance interactions that affect the average expression level of a reporter gene as well as its cell-to-cell variability (noise)...
April 20, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28414750/effect-of-transcription-factor-resource-sharing-on-gene-expression-noise
#8
Dipjyoti Das, Supravat Dey, Robert C Brewster, Sandeep Choubey
Gene expression is intrinsically a stochastic (noisy) process with important implications for cellular functions. Deciphering the underlying mechanisms of gene expression noise remains one of the key challenges of regulatory biology. Theoretical models of transcription often incorporate the kinetics of how transcription factors (TFs) interact with a single promoter to impact gene expression noise. However, inside single cells multiple identical gene copies as well as additional binding sites can compete for a limiting pool of TFs...
April 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28398576/defining-functional-genic-regions-in-the-human-genome-through-integration-of-biochemical-evolutionary-and-genetic-evidence
#9
Zing Tsung-Yeh Tsai, John P Lloyd, Shin-Han Shiu
The human genome is dominated by large tracts of DNA with extensive biochemical activity but no known function. In particular, it is well established that transcriptional activities are not restricted to known genes. However, whether this intergenic transcription represents activity with functional significance or noise is under debate, highlighting the need for an effective method of defining functional genomic regions. Moreover, these discoveries raise the question whether genomic regions can be defined as functional based solely on the presence of biochemical activities, without considering evolutionary (conservation) and genetic (effects of mutations) evidence...
April 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28397688/engineering-of-a-synthetic-quadrastable-gene-network-to-approach-waddington-landscape-and-cell-fate-determination
#10
Fuqing Wu, Ri-Qi Su, Ying-Cheng Lai, Xiao Wang
The process of cell fate determination has been depicted intuitively as cells travelling and resting on a rugged landscape, which has been probed by various theoretical studies. However, few studies have experimentally demonstrated how underlying gene regulatory networks shape the landscape and hence orchestrate cellular decision-making in the presence of both signal and noise. Here we tested different topologies and verified a synthetic gene circuit with mutual inhibition and auto-activations to be quadrastable, which enables direct study of quadruple cell fate determination on an engineered landscape...
April 11, 2017: ELife
https://www.readbyqxmd.com/read/28396505/genetic-characterisation-of-dog-personality-traits
#11
Joanna Ilska, Marie J Haskell, Sarah C Blott, Enrique Sánchez-Molano, Zita Polgar, Sarah E Lofgren, Dylan N Clements, Pam Wiener
The genetic architecture of behavioural traits in dogs is of great interest to owners, breeders and professionals involved in animal welfare, as well as to scientists studying the genetics of animal (including human) behaviour. The genetic component of dog behaviour is supported by between-breed differences and some evidence of within-breed variation. However, it is a challenge to gather sufficiently large datasets to dissect the genetic basis of complex traits such as behaviour, which are both time-consuming and logistically difficult to measure, and known to be influenced by non-genetic factors...
April 10, 2017: Genetics
https://www.readbyqxmd.com/read/28392986/prioritisation-of-structural-variant-calls-in-cancer-genomes
#12
Miika J Ahdesmäki, Brad A Chapman, Pablo Cingolani, Oliver Hofmann, Aleksandr Sidoruk, Zhongwu Lai, Gennadii Zakharov, Mikhail Rodichenko, Mikhail Alperovich, David Jenkins, T Hedley Carr, Daniel Stetson, Brian Dougherty, J Carl Barrett, Justin H Johnson
Sensitivity of short read DNA-sequencing for gene fusion detection is improving, but is hampered by the significant amount of noise composed of uninteresting or false positive hits in the data. In this paper we describe a tiered prioritisation approach to extract high impact gene fusion events from existing structural variant calls. Using cell line and patient DNA sequence data we improve the annotation and interpretation of structural variant calls to best highlight likely cancer driving fusions. We also considerably improve on the automated visualisation of the high impact structural variants to highlight the effects of the variants on the resulting transcripts...
2017: PeerJ
https://www.readbyqxmd.com/read/28392843/validation-of-the-methylationepic-beadchip-for-fresh-frozen-and-formalin-fixed-paraffin-embedded-tumours
#13
Teresia Kling, Anna Wenger, Stephan Beck, Helena Carén
DNA methylation is the most studied epigenetic modification due to its role in regulating gene expression, and its involvement in the pathogenesis of cancer and several diseases upon aberrations in methylation. The method of choice to evaluate genome-wide methylation has been the Illumina HumanMethylation450 BeadChip (450K), but it was recently replaced with the MethylationEPIC BeadChip (EPIC). We therefore sought to validate the EPIC array in comparison to the 450K array for both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tumours...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28391524/intron-retention-as-a-component-of-regulated-gene-expression-programs
#14
REVIEW
Aishwarya G Jacob, Christopher W J Smith
Intron retention has long been an exemplar of regulated splicing with case studies of individual events serving as models that provided key mechanistic insights into the process of splicing control. In organisms such as plants and budding yeast, intron retention is well understood as a major mechanism of gene expression regulation. In contrast, in mammalian systems, the extent and functional significance of intron retention have, until recently, remained greatly underappreciated. Technical challenges to the global detection and quantitation of transcripts with retained introns have often led to intron retention being overlooked or dismissed as "noise"...
April 8, 2017: Human Genetics
https://www.readbyqxmd.com/read/28389569/parallel-adaptive-evolution-of-geographically-distant-herring-populations-on-both-sides-of-the-north-atlantic-ocean
#15
Sangeet Lamichhaney, Angela P Fuentes-Pardo, Nima Rafati, Nils Ryman, Gregory R McCracken, Christina Bourne, Rabindra Singh, Daniel E Ruzzante, Leif Andersson
Atlantic herring is an excellent species for studying the genetic basis of adaptation in geographically distant populations because of its characteristically large population sizes and low genetic drift. In this study we compared whole-genome resequencing data of Atlantic herring populations from both sides of the Atlantic Ocean. An important finding was the very low degree of genetic differentiation among geographically distant populations (fixation index = 0.026), suggesting lack of reproductive isolation across the ocean...
April 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28387726/rethinking-the-epigenetic-framework-to-unravel-the-molecular-pathology-of-schizophrenia
#16
REVIEW
Ariel Cariaga-Martinez, Raúl Alelú-Paz
Schizophrenia is a complex mental disorder whose causes are still far from being known. Although researchers have focused on genetic or environmental contributions to the disease, we still lack a scientific framework that joins molecular and clinical findings. Epigenetic can explain how environmental variables may affect gene expression without modifying the DNA sequence. In fact, neuroepigenomics represents an effort to unify the research available on the molecular pathology of mental diseases, which has been carried out through several approaches ranging from interrogating single DNA methylation events and hydroxymethylation patterns, to epigenome-wide association studies, as well as studying post-translational modifications of histones, or nucleosomal positioning...
April 7, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28379537/tasic-determining-branching-models-from-time-series-single-cell-data
#17
Sabrina Rashid, Darrell N Kotton, Ziv Bar-Joseph
Motivation: Single cell RNA-Seq analysis holds great promise for elucidating the networks and pathways controlling cellular differentiation and disease. However, the analysis of time series single cell RNA-Seq data raises several new computational challenges. Cells at each time point are often sampled from a mixture of cell types, each of which may be a progenitor of one, or several, specific fates making it hard to determine which cells should be used to reconstruct temporal trajectories...
April 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28379479/experimental-design-and-data-analysis-of-ago-rip-seq-experiments-for-the-identification-of-microrna-targets
#18
Diana Tichy, Julia Maria Anna Pickl, Axel Benner, Holger Sültmann
The identification of microRNA (miRNA) target genes is crucial for understanding miRNA function. Many methods for the genome-wide miRNA target identification have been developed in recent years; however, they have several limitations including the dependence on low-confident prediction programs and artificial miRNA manipulations. Ago-RNA immunoprecipitation combined with high-throughput sequencing (Ago-RIP-Seq) is a promising alternative. However, appropriate statistical data analysis algorithms taking into account the experimental design and the inherent noise of such experiments are largely lacking...
March 31, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28371780/pca-based-on-graph-laplacian-regularization-and-p-norm-for-gene-selection-and-clustering
#19
Chunmei Feng, Ying-Lian Gao, Jin-Xing Liu, Chun-Hou Zheng, Jiguo Yu
In modern molecular biology, the hotspots and difficulties of this field are identifying characteristic genes from gene expression data. Traditional reconstruction-error- minimization model Principal Component Analysis (PCA) as a matrix decomposition method uses quadratic error function, which is known sensitive to outliers and noise. Hence it is necessary to learn a good PCA method when outliers and noise exist. In this paper, we develop a novel PCA method enforcing P-norm on error function and graph-Laplacian regularization term for matrix decomposition problem, which is called as PgLPCA...
March 31, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28369256/entropy-based-consensus-clustering-for-patient-stratification
#20
Hongfu Liu, Rui Zhao, Hongsheng Fang, Feixiong Cheng, Yun Fu, Yang-Yu Liu
Motivation: Patient stratification or disease subtyping is crucial for precision medicine and personalized treatment of complex diseases. The increasing availability of high-throughput molecular data provides a great opportunity for patient stratification. Many clustering methods have been employed to tackle this problem in a purely data-driven manner. Yet, existing methods leveraging high-throughput molecular data often suffers from various limitations, e.g., noise, data heterogeneity, high dimensionality or poor interpretability...
March 24, 2017: Bioinformatics
keyword
keyword
11793
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"