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How to cite this record FAIRsharing.org: BEDgraph; BEDgraph; DOI: https://doi.org/10.25504/FAIRsharing.vttygv; Last edited: Jan. 8, 2019, 1:33 p.m.; Last accessed: Sep 22 2020 2 a.m.
Record updated: Oct. 24, 2016, 7:09 p.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.vttygv' by 'The FAIRsharing Team' at 19:09, 24 Oct 2016 (approved): 'description' has been modified: Before: "BEDgraph" is a standard, specialising in the fields described under "scope and data types", below. Until this entry is claimed, more information on this project can be found at http://genome.ucsc.edu/goldenPath/help/bedgraph.html. This text was generated automatically. If you work on the project responsible for "BEDgraph" then please consider helping us by claiming this record and updating it appropriately. After: The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. This track type is similar to the wiggle (WIG) format, but unlike the wiggle format, data exported in the bedGraph format are preserved in their original state.
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The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, nucleotide and protein motifs, non-coding RNA predictions, operon predictions, and other types of bioinformatic analyses. In addition, we display available gene expression data (microarray or high-throughput RNA sequencing). Direct contributions or notices of publication of functional genomic data or bioinformatic analyses from archaeal research labs are very welcome.
Ensembl creates, integrates and distributes reference datasets and analysis tools that enable genomics. Ensembl is a genome browser that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data.
FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge.
Eukaryotic Promoter Database
The Eukaryotic Promoter Database (EPD) provides accurate transcription start site (TSS) information for promoters of 15 model organisms, from human to yeast to the malaria parasite Plasmodium falciparum. While the original database was a manually curated database based on published experiments, new promoter collections are now produced entirely automatically (under the name “EPDnew”) based on high-throughput transcript mapping data and high-quality gene annotation resources. Corresponding functional genomics data can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats like FASTA or BED for subsequent analysis with other tools; of note, EPD is tightly integrated with two tool suites developed by our group: ChIP-Seq (https://ccg.epfl.ch/chipseq) and Signal Search Analysis (https://ccg.epfl.ch/ssa), for analysis of chromatin context and sequence motif respectively. EPD provides promoter viewers, designed with the aim of integrating and displaying information from different sources about, for instance, histone marks, transcription factor-binding sites or SNPs with known phenotypes. These viewers rely upon the UCSC genome browser as a visualization platform, which enables users to view data tracks from EPD jointly with tracks from UCSC or public track hubs.
ReMap is an integrative analysis of transcription factor ChIP-seq experiments publicly available, merged with the Encode dataset. The resource is an extensive regulatory catalogue of transcription factor binding sites from transcription factors (TFs). The data is available to browse or download either for a given transcription factor or for the entire dataset.
4DNucleome Data Portal
The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. It is a platform to search, visualize, and download nucleomics data.
InterMine was formed in 2002 at the University of Cambridge, originally as a Drosophila-dedicated resource, before expanding to become organism-agnostic, enabling a large range of organisations around the world to create their own InterMines. There are many instances of InterMine installations, relating to particular model organisms. These can be searched individually or via a cross-Mine search function.
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