Search · four archives
Search · four archives
20 papers · ranked by Valyu relevance
Vasileios L. Zogopoulos, Georgia Saxami, Apostolos Malatras, Konstantinos Papadopoulos + 4 more
Simple Summary Genes whose expression levels rise and fall similarly in a large set of samples, may be considered coexpressed. Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. The type of biological networks that studies gene…
Apostolos Malatras, Ioannis Michalopoulos, Stéphanie Duguez, Gillian Butler-Browne + 2 more
Background High-throughput transcriptomics measures mRNA levels for thousands of genes in a biological sample. Most gene expression studies aim to identify genes that are differentially expressed between different biological conditions, such as between healthy and diseased states. However, these data can also be used…
Kai Silkwood, Emmanuel Dollinger, Josh Gervin, Scott Atwood + 2 more
Many approaches have been developed to overcome technical noise in single cell RNA-sequencing (scRNAseq). As researchers dig deeper into data—looking for rare cell types, subtleties of cell states, and details of gene regulatory networks—there is a growing need for algorithms with controllable accuracy and fewer ad hoc…
Yi Wang, Stephanie C. Hicks, Kasper D. Hansen
Estimates of correlation between pairs of genes in co-expression analysis are commonly used to construct networks among genes using gene expression data. Here, we show that the distribution of such correlations depend on the expression level of the involved genes, which we refer to this as a mean-correlation…
Scott Powers, Matt DeJongh, Aaron A. Best, Nathan L. Tintle
Background: Rapid growth in the availability of genome-wide transcript abundance levels through gene expression microarrays and RNAseq promises to provide deep biological insights into the complex, genome-wide transcriptional behavior of single-celled organisms. However, this promise has not yet been fully realized.…
Yong H. Woo, Michael Walker, Gary A. Churchill, Vladimir Brusic
Background Gene order in eukaryotic genomes is not random. Genes showing similar expression (coexpression) patterns are often clustered along the genome. The goal of this study is to characterize coexpression clustering in mammalian genomes and to investigate the underlying mechanisms. Methodology/Principal Findings We…
Amanda Lea, Meena Subramaniam, Arthur Ko, Terho Lehtimäki + 9 more
Correlation among traits is a fundamental feature of biological systems. From morphological characters, to transcriptional or metabolic networks, the correlations we routinely observe between traits reflect a shared regulation that remains poorly understood and difficult to study. To address this problem, we developed…
Eleni Ioanna Delatola, Émilie Lebarbier, Tristan Mary‐Huard, François Radvanyi + 2 more
'François Radvanyi' 'Stéphane Robin' 'Jennifer Wong'] 1AgroParisTech UMR518, Paris 5e, France 2 INRA UMR518, Paris 5e, France 3 Institut Curie, Centre de Recherche, Paris, F-75248 France 4CNRS UMR144, Equipe Oncologie Moleculaire, Paris, F-75248 ´ France 5 INRA, UMR 0320 / UMR 8120 Gen´ etique V ´ eg´ etale et ´…
Diogo M. Ribeiro, Simone Rubinacci, Anna Ramisch, Robin J. Hofmeister + 2 more
Nearby genes are often expressed as a group. Yet, the prevalence, molecular mechanisms and genetic control of local gene co-expression are far from being understood. Here, by leveraging gene expression measurements across 49 human tissues and hundreds of individuals, we found that local gene co-expression occurs in 13%…
Andrey Marakhonov, Nataliya Sadovskaya, Ivan Antonov, Ancha Baranova + 1 more
'Mikhail Skoblov'] Background Affymetrix microarray technology allows one to investigate expression of thousands of genes simultaneously upon a variety of conditions. In a popular U133A microarray platform, the expression of 37% of genes is measured by more than one probeset. The discordant expression observed for two…
Khalid Raza, Rajni Jaiswal
The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput data generated by microarray experiments fuelled researchers to use whole-genome…
Fatih Dikbaş
Correlation remains to be one of the most widely used statistical tools for assessing the strength of relationships between data series. This paper presents a novel compositional correlation method for detecting linear and nonlinear relationships by considering the averages of all parts of all possible compositions of…
Yedid Elbez, Shlomit Farkash-Amar, Itamar Simon
Background On most common microarray platforms many genes are represented by multiple probes. Although this is quite common no one has systematically explored the concordance between probes mapped to the same gene. Results Here we present an analysis of all the cases of multiple probe sets measuring the same gene on…
Mengyi Sun, Jianzhi Zhang
Gene expression is subject to stochastic noise, but to what extent and by which means such stochastic variations are coordinated among different genes are unclear. We hypothesize that neighboring genes on the same chromosome co-fluctuate in expression because of their common chromatin dynamics, and verify it at the…
Milton Pividori, Marylyn D. Ritchie, Diego H. Milone, Casey S. Greene
Correlation coefficients are widely used to identify patterns in data that may be of particular interest. In transcriptomics, genes with correlated expression often share functions or are part of disease-relevant biological processes. Here we introduce the Clustermatch Correlation Coefficient (CCC), an efficient…
Koudai Hirao, Atsushi J. Nagano, Akinori Awazu
Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions (called gene expression "noise" or phenotype "fluctuation"). In yeast and Escherichia coli, positive correlations have been found between such gene expression noise and "plasticity" with…
Wei Vivian Li, Yiling Elaine Chen, Jingyi Jessica Li
Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic data. An important question is to understand the conservation and differentiation…
Zahir Ali, Maged Serag, Gozde Demirer, Bruno Torre + 4 more
Efficient delivery of DNA, RNA, and genome engineering machinery to plant cells will enable efforts to genetically modify plants for global food security, sustainable energy production, synthetic biology applications, and climate change resilience. For the delivery of functional genetic units into plant cells, charged…
Zhiwen Pan, Jan Dellith, Lothar Wondraczek
Understanding the multivariate origin of physical properties is particularly complex for polyionic glasses. As a concept, the term genome has been used to describe the entirety of structure-property relations in solid materials, based on functional genes acting as descriptors for a particular property, for example, for…
Authors not listed
This paper addresses the challenges in cell line development (CLD), the lengthy and ambiguous clone screening in upstream biopharmaceutical production. Typically, only a small subset of the later stages of CLD data is used for manually selecting lead clones. Addressing this issue, we introduce a multivariate data…