UCSC Genome Browser enters 20th year

Abstract

The University of California Santa Cruz Genome Browser website (https://genome.ucsc.edu) enters its 20th year of providing high-quality genomics data visualization and genome annotations to the research community. In the past year, we have added a new option to our web BLAT tool that allows search against all genomes, a single-cell expression viewer (https://cells.ucsc.edu), a 'lollipop' plot display mode for high-density variation data, a RESTful API for data extraction and a custom-track backup feature. New datasets include Tabula Muris single-cell expression data, GeneHancer regulatory annotations, The Cancer Genome Atlas Pan-Cancer variants, Genome Reference Consortium Patch sequences, new ENCODE transcription factor binding site peaks and clusters, the Database of Genomic Variants Gold Standard Variants, Genomenon Mastermind variants and three new multi-species alignment tracks.

Figure 1.

The GeneHancer track set and the interaction track format with hills instead of the default valleys. The GeneHancer track relates enhancer and promoters to their interactions with nearby genes. In this display, a highlighted GH01J209814 enhancer is associated with the gene IRF6 (interferon regulatory factor 6) located about 10 kb upstream.

Figure 2.

The TCGA Pan-Cancer track at the TP53 locus. The lollipop display showcases SNPs found in cancers that were not present in normal tissue. Lollipops are shaded according to their score relative to the other SNPs in the current view. The tall yellow and gray lollipops stand out to reveal hotspots indicated across ∼120 people and multiple cancers.

Figure 3.

The single-cell browser. The left-hand panel shows the default view upon loading the Tabula Muris dataset in the cell browser. Cells are shaded according to which tissue cluster they belong to, and each tissue cluster is labeled accordingly. Hovering the mouse pointer over an individual cell populates the fields on the left-hand panel with the metadata associated with each cell. The right-hand panel shows the result of filtering all of the cells for Pax9 gene expression.

Figure 4.

The BLAT All search results for a chunk of dolphin DNA show that the majority of potential hits apply only to the source turTru2 (Tursiops truncatus) dolphin assembly, but also suggest interesting matches to minke whale.