22 papers · ranked by Valyu relevance
Takeshi Obayashi, Shun Kodate, Himiko Hibara, Yuki Kagaya + 1 more
'Kengo Kinoshita'] Title: Abstract Gene coexpression is synchronization of gene expression across many cellular and environmental conditions and is widely used to infer the biological function of genes. Gene coexpression information is complex, comprising a complete graph of all genes in the genome, and requires…
Diogo M. Ribeiro, Chaymae Ziyani, Olivier Delaneau
Most human genes are co-expressed with a nearby gene. Yet, previous studies only reported this extensive local gene co-expression using bulk RNA-seq. Here, we leverage single cell datasets in >85 individuals to identify gene co-expression across cells, unbiased by cell type heterogeneity and benefiting from the…
Diogo M. Ribeiro, Simone Rubinacci, Anna Ramisch, Robin J. Hofmeister + 2 more
'Robin J. Hofmeister' 'Emmanouil T. Dermitzakis' 'Olivier Delaneau'] 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…
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%…
Georg Kustatscher, Piotr Grabowski, Juri Rappsilber
Genes are not randomly distributed in the genome. In humans, 10% of protein-coding genes are transcribed from bidirectional promoters and many more are organised in larger clusters. Intriguingly, neighbouring genes are frequently coexpressed but rarely functionally related. Here we show that coexpression of…
Mario Huerta, Oriol Casanova, Roberto Barchino, Jose Flores + 2 more
'Enrique Querol' 'Juan Cedano'] Organisms simplify the orchestration of gene expression by coregulating genes whose products function together in the cell. The use of clustering methods to obtain sets of coexpressed genes from expression arrays is very common; nevertheless there are no appropriate tools to study the…
Simonida Zehr, Sebastian Wolf, Thomas Oellerich, Matthias S. Leisegang + 3 more
Extraction of meaningful biological insight from gene expression profiling often focuses on the identification of statistically enriched terms or pathways. These methods typically use gene sets as input data, and subsequently return overrepresented terms along with associated statistics describing their enrichment.…
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…
Chuan Gao, Shiwen Zhao, Ian C. McDowell, Christopher D. Brown + 1 more
'Barbara E. Engelhardt'] Identifying latent structure in large data matrices is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are locally co-regulated by shared biological…
Lingfei Wang, Tom Michoel
Genetic differences between individuals associated to quantitative phenotypic traits, including disease states, are usually found in non-coding genomic regions. These genetic variants are often also associated to differences in expression levels of nearby genes (they are "expression quantitative trait loci" or eQTLs…
Haim Bar, Seojin Bang
In the early days of gene expression data, researchers have focused on gene-level analysis, and particularly on finding differentially expressed genes. This usually involved making a simplifying assumption that genes are independent, which made likelihood derivations feasible and allowed for relatively simple…
Authors not listed
Bioinformatics and microarrays have given scientists powerful new tools to investigate the structure and activity of genes on a global scale. Rather than studying just a few genes, scientists can analyze tens of thousands within and across species. Microarrays flag which genes are expressed under particular cellular…
Ben-Yang Liao, Andrew Ying-Fei Chang, Jo-Ann L. Stanton
Coexpression has been frequently used to explore modules of functionally related genes in eukaryotic genomes. However, we found that genetically interacting mammalian genes identified through radiation hybrid (RH) genotypes tend not to be coexpressed across tissues. This pattern remained unchanged after controlling for…
Piotr Grabowski, Georg Kustatscher, Juri Rappsilber
Genes are often coexpressed with their genomic neighbors, even if these are functionally unrelated. For small expression changes driven by genetic variation within the same cell type, non-functional mRNA coexpression is not propagated to the protein level. However, it is unclear if protein levels are also buffered…
Dan Kaptijn, Corinna Losert, Maryna Korshevniuk, Roy Oelen + 12 more
Genes act within complex regulatory networks, and genetic variants can perturb these networks by altering gene co-expression. Here, we performed co-expression quantitative trait locus (co-eQTL) mapping using single-cell RNA-seq from the sc-eQTLGen consortium (1,330 donors, >2 million cells), enabling sensitive…
Kaijie Xu, Witold Pedrycz, Zhiwu Li, Yinghui Quan + 1 more
Traditional clustering methods are limited when dealing with huge and heterogeneous groups of gene expression data, which motivates the development of bi-clustering methods. Bi-clustering methods are used to mine bi-clusters whose subsets of samples (genes) are co-regulated under their test conditions. Studies show…
Om Prakash
Identification of possibility of co-expression or co-performance directly from set of bio-strings as protein sequences represents an important problem of bridging between genotype to phenotype. This algorithm presents above bridging. Algorithm was implemented with proteins known from human hormone signaling system.…
Radwa Adel, Erçan E. Kuruoğlu
—Complex gene interactions play a significant role in cancer progression, driving cellular behaviors that contribute to tumor growth, invasion, and metastasis. Gene co-expression networks model the functional connectivity between genes under various biological conditions. Understanding the system-level evolution of…
Boel Brynedal, Towfique Raj, Barbara E. Stranger, Robert Bjornson + 3 more
'Benjamin M. Neale' 'Benjamin F. Voight' 'Chris Cotsapas'] Genetic variation affecting gene regulation is a central driver of phenotypic differences between individuals and can be used to uncover how biological processes are organized in a cell. Although detecting cis-eQTLs is now routine, trans-eQTLs have proven more…
Indra Roux, Simon Bowles, John A. Kalaitzis, Daniel Vuong + 3 more
Chemical exploration of the recently described Australian fungus, Aspergillus burnettii, uncovered a new metabolite, burnettiene A. Here, we characterise the structure of burnettiene A as a polyene-decalin polyketide. Bioinformatic analysis of the genome of A. burnettii identified a putative biosynthetic gene cluster…
Giuseppe Faudone, Whitney Kilu, Xiaomin Ni, Apirat Chaikuad + 7 more
The orphan nuclear receptor TLX is expressed almost exclusively in neural stem cells. TLX acts as an essential factor for neural stem cell survival and is hence considered as a promising drug target in neurodegeneration. However, few studies have characterized the roles of TLX due to a lack of ligands and limited…
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…