Results 41 to 50 of about 48,393 (270)

A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. [PDF]

, 2018
Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative analysis of 930 tumor whole genomes and matched transcriptomes, identifying a network of 193 ...
Bojorquez-Gomez, Ana, Carter, Hannah, Chen, Kevin, Farley, Emma K, Fraley, Stephanie I, Huang, Justin K, Ideker, Trey, Kreisberg, Jason F, Licon, Katherine, Melton, Collin, Olson, Katrina M, Sanchez, Kyle S, Shen, John Paul, Snyder, Michael, Velez, Daniel Ortiz, Xu, Guorong, Yu, Michael Ku, Zhang, Wei   +17 more
core   +1 more source

DNA methylation modulated genetic variant effect on gene transcriptional regulation

Genome Biology, 2023
Background Expression quantitative trait locus (eQTL) analysis has emerged as an important tool in elucidating the link between genetic variants and gene expression, thereby bridging the gap between risk SNPs and associated diseases.
Yong Zeng, Rahi Jain, Magnus Lam, Musaddeque Ahmed, Haiyang Guo, Wenjie Xu, Yuan Zhong, Gong-Hong Wei, Wei Xu, Housheng Hansen He   +9 more
doaj   +1 more source

RNA-Seq optimization with eQTL gold standards. [PDF]

, 2013
BackgroundRNA-Sequencing (RNA-Seq) experiments have been optimized for library preparation, mapping, and gene expression estimation. These methods, however, have revealed weaknesses in the next stages of analysis of differential expression, with results ...
Arking, Dan E, Ashar, Foram N, Bader, Joel S, Ellis, Shannon E, Gupta, Simone, West, Andrew B   +5 more
core   +2 more sources

Transcriptome-wide association study and eQTL colocalization identify potentially causal genes responsible for human bone mineral density GWAS associations

eLife, 2022
Genome-wide association studies (GWASs) for bone mineral density (BMD) in humans have identified over 1100 associations to date. However, identifying causal genes implicated by such studies has been challenging.
B. Al-Barghouthi, Will T. Rosenow, Kangping Du, J. Heo, R. Maynard, L. Mesner, G. Calabrese, Aaron Nakasone, Bhavya Senwar, L. Gerstenfeld, J. Larner, Virginia Ferguson, C. Ackert-Bicknell, E. Morgan, D. Brautigan, C. Farber   +15 more
semanticscholar   +1 more source

PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types [PDF]

Nucleic Acids Research, 2017
Expression quantitative trait locus (eQTL) analysis, which links variations in gene expression to genotypes, is essential to understanding gene regulation and to interpreting disease-associated loci. Currently identified eQTLs are mainly in samples of blood and other normal tissues. However, no database comprehensively provides eQTLs in large number of
Gong, Jing, Mei, Shufang, Liu, Chunjie, Xiang, Yu, Ye, Youqiong, Zhang, Zhao, Feng, Jing, Liu, Renyan, Diao, Lixia, Guo, An-Yuan, Miao, Xiaoping, Han, Leng   +11 more
openaire   +2 more sources

Molecular Relationships between Bronchial Asthma and Hypertension as Comorbid Diseases

Journal of Integrative Bioinformatics, 2018
Comorbidity, a co-incidence of several disorders in an individual, is a common phenomenon. Their development is governed by multiple factors, including genetic variation.
Bragina Elena Yu., Goncharova Irina A., Garaeva Anna F., Nemerov Evgeniy V., Babovskaya Anastasija A., Karpov Andrey B., Semenova Yulia V., Zhalsanova Irina Z., Gomboeva Densema E., Saik Olga V., Zolotareva Olga I., Ivanisenko Vladimir A., Dosenko Victor E., Hofestaedt Ralf, Freidin Maxim B.   +14 more
doaj   +1 more source

Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits

Genetics Selection Evolution, 2021
Background Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is
Zehu Yuan, Bolormaa Sunduimijid, Ruidong Xiang, Ralph Behrendt, Matthew I. Knight, Brett A. Mason, Coralie M. Reich, Claire Prowse-Wilkins, Christy J. Vander Jagt, Amanda J. Chamberlain, Iona M. MacLeod, Fadi Li, Xiangpeng Yue, Hans D. Daetwyler   +13 more
doaj   +1 more source

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease. [PDF]

, 2019
The MHC region is highly associated with autoimmune and infectious diseases. Here we conduct an in-depth interrogation of associations between genetic variation, gene expression and disease.
Aguiar, Assis, Auton, Bijvelds, Blackwell, Bonder, D'Antonio, D'Antonio-Chronowska, DeBoever, Dechecchi, DeGiorgio, Dendrou, Diwakar, Dobin, Eguchi, Ernst, Fehrmann, Freudenberg, Gambino, Gensterblum-Miller, Giambartolomei, González-Galarza, Gough, Graffelman, Guo, Hardy, Harrow, Herrmann, Holoshitz, Huang, Jakubosky, Jakubosky, Jensen, Jia, Kilpinen, Kilpinen, Klein, Kontakioti, Kundaje, Laki, Lam, Lee, Leung, Li, Li, Li, Li, Li, Lyczak, Mahdi, Mall, Matzaraki, Mayba, McNicholas, Miretti, Morison, Munder, Nariai, Norman, Oldstone, Panopoulos, Panousis, Pier, Robinson, Sondo, Stegle, Stoltz, Streeter, Tan, Tomati, Trowsdale, Van der Auwera, Vicente, Wilke, Yin, Zhang, Zheng   +76 more
core   +2 more sources

Optimizing expression quantitative trait locus mapping workflows for single-cell studies

Genome Biology, 2021
Background Single-cell RNA sequencing (scRNA-seq) has enabled the unbiased, high-throughput quantification of gene expression specific to cell types and states.
Anna S. E. Cuomo, Giordano Alvari, Christina B. Azodi, single-cell eQTLGen consortium, Davis J. McCarthy, Marc Jan Bonder   +5 more
doaj   +1 more source

kruX: matrix-based non-parametric eQTL discovery [PDF]

BMC Bioinformatics, 2014
The Kruskal-Wallis test is a popular non-parametric statistical test for identifying expression quantitative trait loci (eQTLs) from genome-wide data due to its robustness against variations in the underlying genetic model and expression trait distribution, but testing billions of marker-trait combinations one-by-one can become computationally ...
Qi, Jianlong, Asl, Hassan, Björkegren, Johan L. M., Michoel, Tom   +3 more
openaire   +5 more sources