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Search · four archives
26 papers · ranked by Valyu relevance
Jigang Zhang, Jian Li, Hong-Wen Deng, I. King Jordan
Gene set analysis allows the inclusion of knowledge from established gene sets, such as gene pathways, and potentially improves the power of detecting differentially expressed genes. However, conventional methods of gene set analysis focus on gene marginal effects in a gene set, and ignore gene interactions which may…
Andreas Hahn, Jörg Rahnenführer, Priti Talwar, Thomas Lengauer
Background With microarray technology the expression of thousands of genes can be measured simultaneously. It is well known that the expression levels of genes of interacting proteins are correlated significantly more strongly in Saccharomyces cerevisiae than those of proteins that are not interacting. The objective of…
Katrin Sameith, Saman Amini, Marian J. A. Groot Koerkamp, Dik van Leenen + 11 more
'Dik van Leenen' 'Mariel Brok' 'Nathalie Brabers' 'Philip Lijnzaad' 'Sander R. van Hooff' 'Joris J. Benschop' 'Tineke L. Lenstra' 'Eva Apweiler' 'Sake van Wageningen' 'Berend Snel' 'Frank C. P. Holstege' 'Patrick Kemmeren'] Background Genetic interactions, or non-additive effects between genes, play a crucial role in…
Saman Amini, Annika Jacobsen, Olga Ivanova, Philip Lijnzaad + 4 more
Genetic interactions, a phenomenon whereby combinations of mutations lead to unexpected effects, reflect how cellular processes are wired and play an important role in complex genetic diseases. Understanding the molecular basis of genetic interactions is crucial for deciphering pathway organization as well as…
Saman Amini, Annika Jacobsen, Olga Ivanova, Philip Lijnzaad + 5 more
Genetic interactions, a phenomenon whereby combinations of mutations lead to unexpected effects, reflect how cellular processes are wired and play an important role in complex genetic diseases. Understanding the molecular basis of genetic interactions is crucial for deciphering pathway organization as well as…
Orr Levy, Shubham Tripathi, Scott D. Pope, Yang Y. Liu + 1 more
'Ruslan Medzhitov'] The diversity of gene expression plays a critical role in cellular specialization, adaptation to environmental changes, and overall cell functionality. This diversity varies dramatically across different cell types and is orchestrated by intricate, dynamic, and cell type-specific gene regulatory…
Bernd Fischer, Thomas Sandmann, Thomas Horn, Maximilian Billmann + 4 more
'Varun Chaudhary' 'Wolfgang Huber' 'Michael Boutros' 'Christopher Glass'] Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules. However…
David Angeles-Albores, Carmie Puckett Robinson, Brian A. Williams, Paul W. Sternberg
RNA-seq is commonly used to identify genetic modules that respond to a perturbation. Although transcriptomes have been mainly used for target gene discovery, their quantitative nature makes them attractive structures with which to study genetic interactions. To understand whether whole-organism RNA-seq is suitable for…
Khalid Raza, Mahish Kohli
Inferring gene interaction network from gene expression data is an important task in systems biology research. The gene interaction network, especially key interactions, plays an important role in identifying biomarkers for disease that further helps in drug design. Ant colony optimization is an optimization algorithm…
Sofie Demeyer, Tom Michoel
Transcriptional regulation of gene expression is one of the main processes that affect cell diversification from a single set of genes. Regulatory proteins often interact with DNA regions located distally from the transcription start sites (TSS) of the genes. We developed a computational method that combines open…
Siddhant Kalra, Guadalupe Sanchez, Alexandra Stubin, Anya Le + 20 more
Gene-by-environment (GxE) interactions play a major role in shaping both phenotypic and molecular variation, with important implications for human health and disease. In this study, we used the Doxycycline (Dox) regulated, tetracycline-responsive (Tet-Off) promoter system to sequentially reduce or titrate gene…
Ira Horecka, Matej Ušaj, Myra P.D. Masinas, Henry N. Ward + 8 more
Genetic interaction networks map functional connections between genes and their corresponding pathways and complexes. We previously developed TheCellMap.org as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) analysis in the…
Laurence Calzone, Emmanuel Barillot, Andreï Zinovyev
Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model. Experimentally characterized genetic interaction networks in model organisms…
Arkadiusz Gladki, Piotr Zielenkiewicz, Szymon Kaczanowski
In this study, we used genetic interaction (GI) and gene-chemical interaction (GCI) data to compare mutations with different dominance phenotypes. Our analysis focused primarily on Saccharomyces cerevisiae, where haploinsufficient genes (HI; genes with dominant loss-of-function mutations) were found to be participating…
Gernot Wolf, Philipp Leippe, Svenja Onstein, Ulrich Goldmann + 5 more
Solute carriers (SLCs), the largest superfamily of transporter proteins in humans with about 450 members, control the movement of molecules across membranes. A typical human cell expresses over 200 different SLCs, yet their collective influence on cell phenotypes is not well understood due to overlapping substrate…
Jorge Fernández‐de‐Cossio, Jorge Fernández-de-Cossio-Díaz, Yasser Perera
'Yasser Perera'] We derive a general statistical model of interactions, starting from probabilistic principles and elementary requirements. Prevailing interaction models in biomedical researches diverge both mathematically and practically. In particular, genetic interaction inquiries are formulated without an obvious…
Ryan C. Vignogna, Sean W. Buskirk, Gregory I. Lang
Understanding how genes interact is a central challenge in biology. Experimental evolution provides a useful, but underutilized, tool for identifying genetic interactions, particularly those that involve non-loss-of-function mutations or mutations in essential genes. We previously identified a strong positive genetic…
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…
J. Javier Díaz-Mejía, Joseph C. Mellor, Atina Coté, Attila Balint + 16 more
Condition-dependent genetic interactions can reveal functional relationships between genes that are not evident under standard culture conditions. State-of-the-art yeast genetic interaction mapping, which relies on robotic manipulation of arrays of double mutant strains, does not scale readily to multi-condition…
Carles Pons
Genetic interactions are essential to decipher the complex relationship between genotype and phenotype, which is key to addressing fundamental biology questions and developing therapies for human diseases. However, the scarcity of genetic interaction data in most species hinders research progress. Understanding the…
Lin Xu, Brandon Barker, Zhenglong Gu
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including pathway organization, evolution of sexual reproduction, mutational load, ploidy…
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…
Sunit Pal, Ilja Gordijenko, Stefan Schmeing, Somarghya Biswas + 3 more
The removal of poly(A) tail from mRNA sequences reduces their stability and translational activity. The deadenylation process is mainly regulated by the CCR4-NOT complex for which potent chemical inhibitors are rare. The subunit NOT9 binds various RNA binding proteins (RBPs) which recruit mRNA in a sequence-specific…
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…
Authors not listed
RNA droplets assembled from co-transcriptionally folded nanostructures have recently emerged as a promising platform for constructing protocells and minimal synthetic cell models. In these systems, a custom-designed DNA template encodes an RNA nanostar, which is produced by transcription and self-assembles into…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…