Nature Reviews Genetics, Journal Year: 2019, Volume and Issue: 20(8), P. 467 - 484
Published: May 8, 2019
Language: Английский
Nucleic Acids Research, Journal Year: 2016, Volume and Issue: 44(W1), P. W160 - W165
Published: April 13, 2016
We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users perform complete bioinformatic workflows ranging from quality controls normalizations of aligned reads integrative analyses, including clustering visualization approaches. Since we first described deepTools Galaxy in 2014, have implemented new solutions many requests the community users. Here, introduce significant enhancements tools further improve data interpretation. continue be open all freely available as a service at deeptools.ie-freiburg.mpg.de. The deepTools2 suite can easily deployed within any framework via toolshed repository, also provide source code command line usage under Linux Mac OS X. A public documented API access functionality is available.
Language: Английский
Citations
6724
Science, Journal Year: 2015, Volume and Issue: 348(6235), P. 648 - 660
Published: May 7, 2015
Expression, genetic variation, and tissues Human genomes show extensive variation across individuals, but we have only just started documenting the effects of this on regulation gene expression. Furthermore, a few been examined per variant. In order to examine how expression varies among within Genotype-Tissue Expression (GTEx) Consortium collected 1641 postmortem samples covering 54 body sites from 175 individuals. They identified quantitative traits that affect determined which these exhibit tissue-specific patterns. Melé et al. measured transcription tissues, Rivas looked at truncated protein variants tissues. Science , issue p. 648 660 666 ; see also 640
Language: Английский
Citations
5034
Science, Journal Year: 2016, Volume and Issue: 352(6282), P. 189 - 196
Published: April 7, 2016
To explore the distinct genotypic and phenotypic states of melanoma tumors, we applied single-cell RNA sequencing (RNA-seq) to 4645 single cells isolated from 19 patients, profiling malignant, immune, stromal, endothelial cells. Malignant within same tumor displayed transcriptional heterogeneity associated with cell cycle, spatial context, a drug-resistance program. In particular, all tumors harbored malignant two states, such that characterized by high levels MITF transcription factor also contained low elevated AXL kinase. Single-cell analyses suggested microenvironmental patterns, including cell-to-cell interactions. Analysis tumor-infiltrating T revealed exhaustion programs, their connection activation clonal expansion, variability across patients. Overall, begin unravel cellular ecosystem how genomics offers insights implications for both targeted immune therapies.
Language: Английский
Citations
4272
Nature, Journal Year: 2017, Volume and Issue: 550(7675), P. 204 - 213
Published: Oct. 10, 2017
Characterization of the molecular function human genome and its variation across individuals is essential for identifying cellular mechanisms that underlie genetic traits diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize in gene expression levels diverse tissues body, many which are not easily accessible. Here we describe effects on 44 tissues. We find local affects majority genes, further identify inter-chromosomal 93 genes 112 loci. On basis identified effects, patterns tissue specificity, compare distal evaluate functional properties effects. also demonstrate multi-tissue, multi-individual data can be used pathways affected by disease-associated variation, enabling a mechanistic interpretation regulation disease.
Language: Английский
Citations
3993
Science, Journal Year: 2020, Volume and Issue: 369(6509), P. 1318 - 1330
Published: Sept. 10, 2020
The Genotype-Tissue Expression (GTEx) project dissects how genetic variation affects gene expression and splicing.
Language: Английский
Citations
3765
The American Journal of Human Genetics, Journal Year: 2017, Volume and Issue: 101(1), P. 5 - 22
Published: July 1, 2017
Language: Английский
Citations
3400
Nature Communications, Journal Year: 2017, Volume and Issue: 8(1)
Published: Nov. 22, 2017
Abstract A main challenge in genome-wide association studies (GWAS) is to pinpoint possible causal variants. Results from GWAS typically do not directly translate into variants because the majority of hits are non-coding or intergenic regions, and presence linkage disequilibrium leads effects being statistically spread out across multiple Post-GWAS annotation facilitates selection most likely variant(s). Multiple resources available for post-GWAS annotation, yet these can be time consuming provide integrated visual aids data interpretation. We, therefore, develop FUMA: an integrative web-based platform using information biological facilitate functional results, gene prioritization interactive visualization. FUMA accommodates positional, expression quantitative trait loci (eQTL) chromatin interaction mappings, provides gene-based, pathway tissue enrichment results. results aid generating hypotheses that testable experiments aimed at proving relations.
Language: Английский
Citations
3302
Nature Genetics, Journal Year: 2018, Volume and Issue: 50(5), P. 668 - 681
Published: April 26, 2018
Language: Английский
Citations
2798
Cancer Cell, Journal Year: 2016, Volume and Issue: 29(4), P. 452 - 463
Published: April 1, 2016
Language: Английский
Citations
2797
Cell, Journal Year: 2017, Volume and Issue: 169(7), P. 1177 - 1186
Published: June 1, 2017
Language: Английский
Citations
2748