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Search · four archives
21 papers · ranked by Valyu relevance
Yu-Ting Tseng, Wenyuan Li, Ching-Hsien Chen, Shihua Zhang + 3 more
'Jeremy JW Chen' 'Xianghong Jasmine Zhou' 'Chun-Chi Liu'] Background Protein-protein interactions (PPIs) are key to understanding diverse cellular processes and disease mechanisms. However, current PPI databases only provide low-resolution knowledge of PPIs, in the sense that "proteins" of currently known PPIs…
Tülay Karakulak, Damian Szklarczyk, Cemil Can Saylan, Holger Moch + 2 more
Alternative splicing, as an essential regulatory mechanism in normal mammalian cells, is frequently disturbed in cancer and other diseases. Switches in the expression of most dominant alternative isoforms can alter protein interaction networks of associated genes giving rise to a disease or disease progression. Here…
Abdullah Kahraman, Christian von Mering
Under normal conditions, cells of almost all tissues types express the same predominant canonical transcript isoform at each gene locus. In cancer, however, splicing regulation is often disturbed, leading to cancer-specific switches in the most dominant transcripts (MDT). But what is the pathogenic impact of these…
Weidi Wang, Yucan Chen, Jingjing Zhao, Liang Chen + 3 more
'Li Li' 'Guan Ning Lin'] Nuclear receptor SET domain protein (NSD2) plays a fundamental role in the pathogenesis of Wolf-Hirschhorn Syndrome (WHS) and is overexpressed in multiple human myelomas, but its protein-protein interaction (PPI) patterns, particularly at the isoform/exon levels, are poorly understood. We…
Hong-Dong Li, Rajasree Menon, Ridvan Eksi, Aysam Guerler + 3 more
Functional relationship networks, which reveal the collaborative roles between genes, have significantly accelerated our understanding of gene functions and phenotypic relevance. However, establishing such networks for alternatively spliced isoforms remains a difficult, unaddressed problem due to the lack of systematic…
Mohamed Ali Ghadie, Luke Lambourne, Marc Vidal, Yu Xia + 1 more
'Andrey Rzhetsky'] Alternative splicing is known to remodel protein-protein interaction networks (“interactomes”), yet large-scale determination of isoform-specific interactions remains challenging. We present a domain-based method to predict the isoform interactome from the reference interactome. First, we construct…
Hong-Dong Li, Rajasree Menon, Ridvan Eksi, Aysam Guerler + 3 more
'Yang Zhang' 'Gilbert S. Omenn' 'Yuanfang Guan'] The laboratory mouse is the primary mammalian species used for studying alternative splicing events. Recent studies have generated computational models to predict functions for splice isoforms in the mouse. However, the functional relationship network, describing the…
Gaurav Kandoi, Julie A. Dickerson
Alternative Splicing produces multiple mRNA isoforms of genes which have important diverse roles such as regulation of gene expression, human heritable diseases, and response to environmental stresses. However, little has been done to assign functions at the mRNA isoform level. Functional networks, where the…
Marina Uhart, Diego M. Bustos, Peter Csermely
The 14-3-3 protein family interacts with more than 700 different proteins in mammals, in part as a result of its specific phospho-serine/phospho-threonine binding activity. Upon binding to 14-3-3, the stability, subcellular localization and/or catalytic activity of the ligands are modified. Seven paralogs are strictly…
Wei Zhang, Jae-Woong Chang, Lilong Lin, Kay Minn + 6 more
'Jeremy Chien' 'Jeongsik Yong' 'Hui Zheng' 'Rui Kuang' 'Xianghong Jasmine Zhou'] High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we…
Wei Zhang, Kay Minn, Lilong Lin, Baolin Wu + 3 more
'Hui Zheng' 'Rui Kuang'] High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as…
Randa Mahran, Jonas N. Kapp, Salla Valtonen, Allison Champagne + 8 more
Mutated KRAS proteins are frequently expressed in some of the most lethal human cancers, thus having been a target of intensive drug discovery efforts for decades. Lately, KRAS(G12C) switch-II pocket (SII-P)-targeting covalent small molecule inhibitors have finally reached the clinical practice. Sotorasib (AMG-510) was…
Ying Cai, Bernard J. Fendler, Gurinder S. Atwal
—An important challenge in cancer systems biology is to uncover the complex network of interactions between genes (tumor suppressor genes and oncogenes) implicated in cancer. Next generation sequencing provides unparalleled ability to probe the expression levels of the entire set of cancer genes and their transcript…
Alexander Vergara, Tamara Hernández-Verdeja, Pedro Ojeda-May, Leonor Ramirez + 3 more
Alternative splicing (AS) plays a key role in numerous cellular processes by enabling the existence of different protein isoforms with potentially different functions and fine-tuning isoform abundance. However, despite its biological importance, tools to compare the domain composition of AS-derived protein isoforms…
Péter Csermely, Tamás Korcsmáros, Huba Kiss, Gábor London + 1 more
'Ruth Nussinov'] Abstract: Despite considerable progress in genome- and proteome-based high-throughput screening methods and in rational drug design, the increase in approved drugs in the past decade did not match the increase of drug development costs. Network description and analysis not only give a systems-level…
Dariia Yehorova, Rory Crean, Peter Kasson, Shina Caroline Lynn Kamerlin
Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction…
Wei Sun, Yufeng Liu, James J. Crowley, Ting‐Huei Chen + 13 more
'Haitao Chu' 'Shun‐Ping Huang' 'Pei Fen Kuan' 'Yuan Li' 'Darla R. Miller' 'Ginger D. Shaw' 'Yichao Wu' 'Vasyl Zhabotynsky' 'Leonard McMillan' 'Fei Zou' 'Patrick F. Sullivan' 'Fernando Pardo‐Manuel de Villena'] We have developed a statistical method named IsoDOT to assess differential isoform expression (DIE) and…
Authors not listed
Protein-protein interactions are at the heart of biological processes. Understanding how proteins interact is key for deciphering their roles in health and disease, and for therapeutic interventions. However, identifying protein interaction sites, especially for intrinsically disordered proteins, is challenging. Here…
Sara Ghazanfari, Ali Rasteh, Seyed Abolfazl Motahari, Mahdieh Soleymani Baghshah
'Mahdieh Soleymani Baghshah'] Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA sequence, They may have a systematic effect on cell…
Authors not listed
Water structure is crucially important to protein function and catalysis and can be conserved throughout related proteins despite differences in sequence. The complex hydrogen bonding networks formed by water molecules and protein residues has been studied extensively, with graph theory-based methods frequently used to…
Alex J. Cornish, Florian Markowetz
Linking networks of molecular interactions to cellular functions and phenotypes is a key goal in systems biology. Here, we adapt concepts of spatial statistics to assess the functional content of molecular networks. Based on the guilt-by-association principle, our approach (called SANTA) quantifies the strength of…