Nature Cardiovascular Research, Journal Year: 2023, Volume and Issue: 2(1), P. 58 - 75
Published: Jan. 16, 2023
Language: Английский
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
3313
Genome biology, Journal Year: 2018, Volume and Issue: 19(1)
Published: Aug. 24, 2018
We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D tracks, allowing users to combine various data types, synchronize multiple modalities, share fully customizable views with others. demonstrate its utility in exploring different experimental conditions, comparing the results analyses, creating interactive snapshots collaborators broader public. HiGlass is accessible online at http://higlass.io also available as containerized application can be run any platform.
Language: Английский
Citations
1620
Bioinformatics, Journal Year: 2019, Volume and Issue: 36(1), P. 311 - 316
Published: July 10, 2019
Abstract Motivation Most existing coverage-based (epi)genomic datasets are one-dimensional, but newer technologies probing interactions (physical, genetic, etc.) produce quantitative maps with two-dimensional genomic coordinate systems. Storage and computational costs mount sharply data resolution when such stored in dense form. Hence, there is a pressing need to develop storage strategies that handle the full range of useful resolutions multidimensional by taking advantage their sparse nature, while supporting efficient compression providing fast random access facilitate development scalable algorithms for analysis. Results We developed file format called cooler, based on model, can support genomically labeled matrices at any resolution. It has flexibility accommodate various descriptions axes (genomic coordinates, tracks bin annotations), resolutions, density patterns metadata. Cooler HDF5 supported Python library command line suite create, read, inspect manipulate cooler collections. The been adopted as standard NIH 4D Nucleome Consortium. Availability implementation cross-platform, BSD-licensed be installed from package index or bioconda repository. source code maintained Github https://github.com/mirnylab/cooler. Supplementary information available Bioinformatics online.
Language: Английский
Citations
1509
Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 47(D1), P. D729 - D735
Published: Nov. 5, 2018
The Cistrome Data Browser (DB) is a resource of human and mouse cis-regulatory information derived from ChIP-seq, DNase-seq ATAC-seq chromatin profiling assays, which map the genome-wide locations transcription factor binding sites, histone post-translational modifications regions accessible to endonuclease activity. Currently, DB contains approximately 47,000 samples with about 24,000 newly collected datasets compared previous release two years ago. Furthermore, has new Toolkit module several features that allow users better utilize large-scale DNase-seq, data. First, can query factors are likely regulate specific gene interest. Second, facilitates searches for binding, modifications, accessibility in any given genomic interval shorter than 2Mb. Third, determine most similar terms overlaps user-provided sets. user-friendly, up-to-date, well maintained resource, tools will greatly benefit biomedical research community. database freely available at http://cistrome.org/db, http://dbtoolkit.cistrome.org.
Language: Английский
Citations
723
Genome biology, Journal Year: 2018, Volume and Issue: 19(1)
Published: Oct. 4, 2018
Here, we introduce the 3D Genome Browser, http://3dgenome.org , which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. We design a new binary format for Hi-C that reduces file size by at least magnitude visualize interactions millions base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with potential target genes. Users can seamlessly integrate thousands other omics gain comprehensive view regulatory landscape genome structure.
Language: Английский
Citations
463
Nucleic Acids Research, Journal Year: 2020, Volume and Issue: 49(D1), P. D1046 - D1057
Published: Nov. 19, 2020
Abstract For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to research community. As field of grows become available, new modes display are required accommodate technologies. New features released this past year include a Hi-C heatmap display, phased family trio for VCF files, various track improvements. Striving keep up-to-date, updates gene GENCODE Genes, NCBI RefSeq Ensembl Genes. tracks added human mouse genomes ENCODE registry candidate cis-regulatory elements, promoters from Eukaryotic Promoter Database, Select Matched Annotation EMBL-EBI (MANE). Within weeks learning about outbreak coronavirus, browser, with detailed annotation tracks, SARS-CoV-2 RNA reference assembly.
Language: Английский
Citations
450
Cell Systems, Journal Year: 2018, Volume and Issue: 6(2), P. 256 - 258.e1
Published: Feb. 1, 2018
Language: Английский
Citations
412
Nucleic Acids Research, Journal Year: 2019, Volume and Issue: 47(W1), P. W158 - W165
Published: June 1, 2019
The WashU Epigenome Browser (https://epigenomegateway.wustl.edu/) provides visualization, integration and analysis tools for epigenomic datasets. Since 2010, it has provided the scientific community with data from large consortia including Roadmap Epigenomics ENCODE projects. Recently, we refactored codebase, redesigned user interface, developed various novel features. New features include: (i) visualization using virtual reality (VR), which implications in biology education study of 3D chromatin structure; (ii) expanded public hubs, 4DN, ENCODE, Epigenomics, TaRGET, IHEC TCGA consortia; (iii) a more responsive interface; (iv) history interactions, enables undo redo; (v) feature call Live Browsing, allows multiple users to collaborate remotely on same session; (vi) ability visualize local tracks hubs. Amazon Web Services also hosts redesign at https://epigenomegateway.org/.
Language: Английский
Citations
269
Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)
Published: July 23, 2018
Temozolomide (TMZ) was used for the treatment of glioblastoma (GBM) over a decade, but its benefits are limited by acquired resistance, process that remains incompletely understood. Here we report an enhancer, located between promoters marker proliferation Ki67 (MKI67) and O6-methylguanine-DNA-methyltransferase (MGMT) genes, is activated in TMZ-resistant patient-derived xenograft (PDX) lines recurrent tumor samples. Activation enhancer correlates with increased MGMT expression, major known mechanism TMZ resistance. We show forced activation cell low expression results elevated expression. Deletion this high leads to dramatic reduction lesser extent sensitivity, impaired proliferation. Together, these studies uncover regulates confers potentially
Language: Английский
Citations
229
Nature Genetics, Journal Year: 2019, Volume and Issue: 51(11), P. 1652 - 1659
Published: Nov. 1, 2019
Language: Английский
Citations
220