21 papers · ranked by Valyu relevance
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…
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…
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…
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…
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…
Priyakshi Mahanta, Hasin A Ahmed, Dhruba K Bhattacharyya, Jugal K Kalita
'Jugal K Kalita'] Background The development of high-throughput Microarray technologies has provided various opportunities to systematically characterize diverse types of computational biological networks. Co-expression network have become popular in the analysis of microarray data, such as for detecting functional…
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.…
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…
S Cortijo, M Bhattarai, J C W Locke, S E Ahnert
Co-expression networks are a powerful tool to understand gene regulation. They have been used to identify new regulation and function of genes involved in plant development and their response to the environment. Up to now, co-expression networks have been inferred using transcriptomes generated on plants experiencing…
Dragana Stanley, Nathan S Watson-Haigh, Christopher JE Cowled, Robert J Moore
'Robert J Moore'] Background The annotation of many genomes is limited, with a large proportion of identified genes lacking functional assignments. The construction of gene co-expression networks is a powerful approach that presents a way of integrating information from diverse gene expression datasets into a unified…
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…
Teresa R. O’Meara, Matthew J. O’Meara
Functional characterization of open reading frames in non-model organisms, such as the common opportunistic fungal pathogen Candida albicans, can be labor intensive. To meet this challenge, we built a comprehensive and unbiased co-expression network for C. albicans, which we call CalCEN, from data collected from 853…
Nuno R. Nené
The increasing capacity of high-throughput genomic technologies for generating time-course data has stimulated a rich debate on the most appropriate methods to highlight crucial aspects of data structure. In this work, we address the problem of sparse co-expression network representation of several timecourse stress…
Jacob B. Spangler, Stephen P. Ficklin, Feng Luo, Michael Freeling + 2 more
'F. Alex Feltus' 'Steve Horvath'] Complex traits and other polygenic processes require coordinated gene expression. Co-expression networks model mRNA co-expression: the product of gene regulatory networks. To identify regulatory mechanisms underlying coordinated gene expression in a tissue-enriched context, ten…
M. A. H. Russell, Alber Aqil, Marie Saitou, Omer Gokcumen + 1 more
'Naoki Masuda'] With the recent availability of tissue-specific gene expression data, e.g., provided by the GTEx Consortium, there is interest in comparing gene co-expression patterns across tissues. One promising approach to this problem is to use a multilayer network analysis framework and perform multilayer…
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…
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…
Pradyumna Harlapur, Rahul Jagadeesan, Andre Sanches Ribeiro, Claus Kadelka + 1 more
How large-scale regulatory coordination in biological systems emerges from local signed and directed interactions in sparse gene regulatory networks (GRNs) remains an unanswered fundamental question. We introduce the coherence matrix, a topology-based framework that captures the consistency of regulatory influence…
Andrés López-Cortés, Patricia Guevara-Ramírez, Nikolaos C Kyriakidis, Carlos Barba-Ostria + 21 more
There is pressing urgency to better understand the immunological underpinnings of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) in order to identify potential therapeutic targets and drugs that allow treating patients effectively. To fill in…
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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…