21 papers · ranked by Valyu relevance
Judy C. Keen, Helen M. Moore, Lori A. Orlando
Evaluation of how genetic mutations or variability can directly affect phenotypic outcomes, the development of disease, or determination of a tailored treatment protocol is fundamental to advancing personalized medicine. To understand how a genotype affects gene expression and specific phenotypic traits, as well as the…
Pietro Hiram Guzzi, Ugo Lomoio, Pierangelo Veltri, Can Alkan
Becoming older or ageing represents the accumulation of phenotype changes in humans over time (). Ageing may be explained as a set of ageing clocks, identifying a subset of modifications for molecules which could be considered age evolution predictors. Observing these changes might determine a measure of biological age…
Kuo-Feng Tung, Chao-Yu Pan, Chao-Hsin Chen, Wen-chang Lin
With considerable accumulation of RNA-Seq transcriptome data, we have extended our understanding about protein-coding gene transcript compositions. However, alternatively compounded patterns of human protein-coding gene transcripts would complicate gene expression data processing and interpretation. It is essential to…
Biao Cai, Jingfei Zhang, Hongyu Li, Chang Su + 1 more
There is a growing interest in cell-type-specific analysis from bulk samples with a mixture of different cell types. A critical first step in such analyses is the accurate estimation of cell-type proportions in a bulk sample. Although many methods have been proposed recently, quantifying the uncertainties associated…
D. Jothi
GTEx_Pro is a Nextflow-based pipeline for preprocessing GTEx v8 transcriptomic data, enhancing multi-tissue comparability. It integrates TMM + CPM normalization and SVA batch effect correction to improve biological signal recovery while reducing systematic variations across 54 GTEx tissues. Designed for scalability and…
Margaret K. R. Donovan, Agnieszka D’Antonio-Chronowska, Matteo D’Antonio, Kelly A. Frazer
The Genotype-Tissue Expression (GTEx) resource has contributed a wealth of novel insights into the regulatory impact of genetic variation on gene expression across tissues, however thus far has not been utilized to study how variation acts at the resolution of the different cell types composing the tissues. To address…
Kuo-Jen Wu, Ming-Tsuen Hsieh, Chi-Rei Wu, W. Gibson Wood + 1 more
'Yuh-Fung Chen'] Ischemic stroke results in brain damage and behavioral deficits including memory impairment. Protective effects of green tea extract (GTex) and its major functional polyphenol (−)-epigallocatechin gallate (EGCG) on memory were examined in cerebral ischemic rats. GTex and EGCG were administered 1 hr…
Jianfeng Ke, Tingjian Ge, Rachel D. Melamed
Uncovering genes dysregulated in neuropsychiatric diseases promises to put forward therapeutic targets. By linking disease risk variants to tissue-specific gene regulation, the Genotype-Tissue Expression (GTEx) project has enabled discovery of disease genes and the brain tissues where these pathogenic effects occur.…
Tim O. Nieuwenhuis, Avi Z. Rosenberg, Matthew N. McCall, Marc K. Halushka
'Marc K. Halushka'] The extracellular matrix (ECM) has historically been explored through proteomic methods. Whether or not global transcriptomics can yield meaningful information on the human matrisome is unknown. Gene expression data from 17,382 samples across 52 tissues, were obtained from the Genotype-Tissue…
Tim O. Nieuwenhuis, Avi Z. Rosenberg, Matthew N. McCall, Marc K. Halushka
The extracellular matrix (ECM) has historically been explored through proteomic methods. Whether or not global transcriptomics can yield meaningful information on the human matrisome is unknown. Gene expression data from 17,382 samples across 52 tissues, were obtained from the Genotype-Tissue Expression (GTEx) project.…
Jianfeng Ke, Tingjian Ge, Rachel D. Melamed
Uncovering genes dysregulated in neuropsychiatric diseases promises to put forward therapeutic targets. By linking disease risk variants to tissue-specific gene regulation, the Genotype-Tissue Expression (GTEx) project has enabled discovery of disease genes and the brain tissues where these pathogenic effects occur.…
Wenjia Wang, Yi‐Hui Zhou
Classical canonical correlation analysis (CCA) requires matrices to be low dimensional, i.e. the number of features cannot exceed the sample size. Recent developments in CCA have mainly focused on the high-dimensional setting, where the number of features in both matrices under analysis greatly exceeds the sample size.…
Gen Li, Sungkyu Jung
In modern biomedical research, it is ubiquitous to have multiple data sets measured on the same set of samples from different views (i.e., multi-view data). For example, in genetic studies, multiple genomic data sets at different molecular levels or from different cell types are measured for a common set of individuals…
William Zeng, Benjamin S. Glicksberg, Yangyan Li, Bin Chen
Normal tissue samples are often employed as a control for understanding disease mechanisms, however, collecting matched normal tissues from patients is difficult in many instances. In cancer research, for example, the open cancer resources such as TCGA and TARGET do not provide matched tissue samples for every cancer…
Fei Xue, Hongzhe Li
The Genotype-Tissue Expression (GTEx) project collects samples from multiple human tissues to study the relationship between genetic variation or single nucleotide polymorphisms (SNPs) and gene expression in each tissue. However, most existing eQTL analyses only focus on single tissue information. In this paper, we…
Gen Li, Dereje D. Jima, Fred A. Wright, Andrew B. Nobel
Background: Expression quantitative trait loci (eQTL) analysis identifies genetic markers associated with the expression of a gene. Most existing eQTL analyses and methods investigate association in a single, readily available tissue, such as blood. Joint analysis of eQTL in multiple tissues has the potential to…
Abhishek Singh
Univariate and multivariate methods for association of the genomic variations with the end-or-endo phenotype have been widely used for genome wide association studies. In addition to encoding the SNPs, we advocate usage of clustering as a novel method to encode the structural variations, SVs, in genomes, such as the…
Yizhen Zhong, Tanima De, Cristina Alarcon, C. Sehwan Park + 3 more
'Bianca Lec' 'Minoli A. Perera' 'Christopher R. Gignoux'] African Americans (AAs) are disproportionately affected by metabolic diseases and adverse drug events, with limited publicly available genomic and transcriptomic data to advance the knowledge of the molecular underpinnings or genetic associations to these…
W. Zabołotny, A.P. Byszuk, D. Dementev, D. Emschermann + 7 more
'Marek Gumiński' 'Michał Kruszewski' 'Piotr Miedzik' 'K. Późniak' 'Ryszard S. Romaniuk' 'C. Schmidt' 'M. Shitenkov'] Abstract: The GBTX ASIC is a standard solution for providing fast control and data readout for radiation detectors used in HEP experiments. However, it is subject to export control restrictions due to…
Authors not listed
Glutathione S-transferase theta 1 (GSTT1) is essential for metastatic tumour cell dissemination, making it a promising anti-cancer target. This study employed reaction-based de novo design to generate novel competitive GSTT1 inhibitors optimised for both target binding and synthetic accessibility. Using the Synopsis…
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…