19 papers · ranked by Valyu relevance
Sonia García, Ana L. Gil, Alejandro Cisterna, Federico Jurado + 5 more
Gene co-expression networks ^1,2^ are a powerful type of analysis to construct genome wide gene groupings based on expression profiling. Co-expression networks allow discovery of groups of genes whose mRNA levels are highly correlated. Subsequent annotation of those modules often reveals biological functions and…
John Lee, Manthan Shah, Sara Ballouz, Megan Crow + 1 more
Co-expression analysis has provided insight into gene function in organisms from Arabidopsis to zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties or by finding alternative model systems where…
John Lee, Manthan Shah, Sara Ballouz, Megan Crow + 1 more
Co-expression analysis has provided insight into gene function in organisms from Arabidopsis to Zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties, or by finding alternative model systems where…
Fei He, Sergei Maslov
Genome-wide gene expression experiments have been performed using the model plant Arabidopsis during the last decade. Some studies involved construction of coexpression networks, a popular technique used to identify groups of co-regulated genes, to infer unknown gene functions. One approach is to construct a single…
Elise A. R. Serin, Harm Nijveen, Henk W. M. Hilhorst, Wilco Ligterink
'Wilco Ligterink'] Plants are fascinating and complex organisms. A comprehensive understanding of the organization, function and evolution of plant genes is essential to disentangle important biological processes and to advance crop engineering and breeding strategies. The ultimate aim in deciphering complex biological…
Swarup Roy, Dhruba K Bhattacharyya, Jugal K Kalita
Background Biological networks connect genes, gene products to one another. A network of co-regulated genes may form gene clusters that can encode proteins and take part in common biological processes. A gene co-expression network describes inter-relationships among genes. Existing techniques generally depend on…
Sonia García-Ruiz, Ana L. Gil-Martínez, Alejandro Cisterna, Federico Jurado-Ruiz + 5 more
'Federico Jurado-Ruiz' 'Regina H. Reynolds' '' 'Mark R. Cookson' 'John Hardy' 'Mina Ryten' 'Juan A. Botía'] Gene co-expression networks are a powerful type of analysis to construct gene groupings based on transcriptomic profiling. Co-expression networks make it possible to discover modules of genes whose mRNA levels…
Oren Tzfadia, Tim Diels, Sam De Meyer, Klaas Vandepoele + 2 more
'Asaph Aharoni' 'Yves Van de Peer'] Motivation: Comparative transcriptomics is a common approach in functional gene discovery efforts. It allows for finding conserved co-expression patterns between orthologous genes in closely related plant species, suggesting that these genes potentially share similar function and…
Lyuba V. Bozhilova, Javier Pardo-Diaz, Gesine Reinert, Charlotte M. Deane
Gene co-expression networks can be constructed in multiple different ways, both in the use of different measures of co-expression, and in the thresholds applied to the calculated co-expression values, from any given dataset. It is often not clear which co-expression network construction method should be preferred.…
Megan Crow, Hamsini Suresh, John Lee, Jesse Gillis
What makes a mouse a mouse, and not a hamster? The answer lies in the genome, and more specifically, in differences in gene regulation between the two organisms: where and when each gene is expressed. To quantify differences, a typical study will either compare functional genomics data from homologous tissues, limiting…
Satwik Acharyya, Xiang Zhou, Veerabhadran Baladandayuthapani
The analysis of spatially-resolved transcriptome enables the understanding of the spatial interactions between the cellular environment and transcriptional regulation. In particular, the characterization of the gene-gene co-expression at distinct spatial locations or cell types in the tissue enables delineation of…
Deisy Morselli Gysi, Tiago Miranda Fragoso, Eivind Almaas, Katja Nowick
'Katja Nowick'] Biomedical sciences are increasingly recognising the relevance of gene co-expression-networks for analysing complex-systems, phenotypes or diseases. When the goal is investigating complex-phenotypes under varying conditions, it comes naturally to employ comparative network methods. While approaches for…
Amanda K. Hund, Peter Tiffin, Jean-Gabriel Young, Daniel I. Bolnick
- 1. University of Minnesota, Department of Ecology, Evolution, and Behavior, St. Paul, Minnesota, USA - 2. University of Minnesota, Department of Plant and Microbial Biology, St. Paul, Minnesota, USA - 3. University of Vermont, Department of Computer Science, Burlington, Vermont, USA - 4. University of Connecticut…
Mingyu Qi, Tianxi Li, Wen Zhou
In this paper, we study the characterization of a network population by analyzing a single observed network, focusing on the counts of multiple network motifs or their corresponding multivariate network moments. We introduce an algorithm based on node subsampling to approximate the nontrivial joint distribution of the…
Maxwell A. Bertolero, Ann S. Blevins, Graham L. Baum, Ruben C. Gur + 4 more
'Raquel E. Gur' 'David R. Roalf' 'Theodore D. Satterthwaite' 'Danielle S. Bassett'] For much of biology, the manner in which genotype maps to phenotype remains a fundamental mystery. The few maps that are known tend to show modular pleiotropy: sets of phenotypes are determined by distinct sets of genes. One key map…
Junyao Kuang, Caterina Scoglio
—A multilayer network depicts different types of interactions among the same set of nodes. For example, protease networks consist of five to seven layers, where different layers represent distinct types of experimentally confirmed molecule interactions among proteins. In a multilayer protease network, the co-expression…
Stephen T. A. Rush, Dirk Repsilber
Background Molecular profiles change in response to perturbations. These changes are coordinated into functional modules via regulatory interactions. The genes and their products within a functional module are expected to be differentially expressed in a manner coherent with their regulatory network. This perspective…
Laura Cantini, Enzo Médico, Santo Fortunato, Michele Caselle
We propose a new multi-network-based strategy to integrate different layers of genomic information and use them in a coordinate way to identify driving cancer genes. The multinetworks that we consider combine transcription factor co-targeting, microRNA co-targeting, protein-protein interaction and gene co-expression…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…