Basic usage of genomes.jbrowse.org
2 videos in this tutorial
The tutorials target the JBrowse v5 beta, and the v4.3.0 release
on the download page lacks some of what they show. To install the
beta of JBrowse Web, run npm install -g @jbrowse/cli@next, then
jbrowse create jbrowse2 --branch v5.0.0-beta.13. Desktop beta builds are coming soon.
genomes.jbrowse.org hosts a ready-made JBrowse config for every UCSC genome, with that genome's UCSC track catalog. We open hg38, find TP53, and turn on its conservation, regulation and variant tracks from the catalog.
Opening a genome
genomes.jbrowse.org hosts a JBrowse 2 instance for every main UCSC database (hg19, hg38, hs1, mm39 and the rest) plus the UCSC GenArk assemblies, track hubs for tens of thousands of NCBI plants, animals, fungi, bacteria and viruses. Three routes lead to one, each ending at an instance with a URL you can share:
- The front page's table of main genomes, with the GenArk catalog below it
- The /ucsc page, with a filter box over every UCSC database's name, species and description
- The header search box, which takes a common name, a species, an assembly name or an accession across both catalogs
Searching for TP53 and trimming its isoforms
Open hg38. The page starts with NCBI RefSeq - RefSeq All on and the track
selector showing. Type TP53 into the location box and press Enter. The hosted
config ships a name index, so gene symbols resolve, and coordinates like
chr17:7,668,400-7,687,550 work too.
RefSeq All draws each transcript on a separate row, and TP53 has more than the track's height holds. Two controls trim the isoforms:
- Click the +19 more link beside the gene name to open that one gene
- Click the
Isoforms trimmedchip at the bottom right for Auto / All transcripts / Representative transcript. The last collapses every gene to one transcript, which the rest of this page uses
Finding the phyloP conservation track in the catalog
The track selector is the drawer down the right, which the button at the top
left of the view header closes and reopens. The selector lists the catalog under
UCSC's categories, and Filter tracks searches all of them. Type phyloP and
tick Basewise Conservation (phyloP) - 100-way vertebrate alignment, under
Comparative Genomics.
Reading the phyloP track
phyloP scores each base against the neutral rate the alignment implies. The score is signed: blue above the line marks a base that changes more slowly than neutral, and red below it one that changes faster.
Type chr17:7,674,180-7,674,290, a stretch of exon 7, into the location box.
- Tick Reference sequence, which is off by default
- At this zoom the gene track draws a codon row per transcript; pick Representative transcript from the isoform control to keep one
At this zoom phyloP draws one bar per base, and within a codon the third base's bar is the short one, since most third-position changes leave the amino acid alone. Hover a bar to read its score.
The multiple alignment behind the phyloP score
The multiple alignment behind a phyloP track is a checkbox too. UCSC publishes no bigMaf (indexed alignment file) for the 100-way, so this section switches to the 470-way pair. Tick both, under Comparative Genomics:
- Multiz Alignments - 470-way Mammal Alignment (Hiller lab)
- Basewise Conservation (phyloP) - 470 phyloP
In the alignment track, most columns are blank because every species matches human at those bases, and conserved columns give a positive score. phyloP counts substitution events on the tree:
- under S240 (serine 240), nearly every species differs from human, but all have the same base, which is one substitution on the human branch, so the score stays above the line
- under T256 and G244 (threonine 256, glycine 244), fewer rows differ and those that do disagree with each other, and the score goes red
A MAF block has a row per species, so at gene-wide zoom the alignment track asks you to confirm before fetching.
Regulatory tracks at the TP53 promoter
Zoom out to the whole gene, and tick five Regulation and Expression tracks:
- CpG Islands
- ENCODE cCREs - ENCODE4 cCREs
- Layered H3K4Me3 (hg19)
- Layered H3K27Ac (hg19)
- EPDnew Promoters - EPDnew v6
The Layered H3K4Me3 and H3K27Ac tracks each hold seven cell lines and open with all seven in one plot box, UCSC's layered arrangement. Their names include hg19 from ENCODE3's release, but the config points at the hg38 files.
Plot type → Multi-row → XY plot in the track menu gives each cell line a row.
TP53 is on the minus strand, so its promoter sits at the high-coordinate end, where every track in the figure has a call.
Filtering gnomAD's TP53 variants to predicted loss of function
The gnomAD v4.1.1 - gnomAD v4.1.1 Exomes track, under Variation and Repeats, opens as several thousand variant records over TP53, one block of color. Filter by... in the track menu takes rows of field, operator and value over the track's columns. Type a column name into the field box, which lists the file's columns with the description the file gives each. A record has to pass every row:
annotispLoFkeeps gnomAD's predicted loss-of-function consequence class (the others are missense, synonymous and other)AF≥0.001drops the rarest variants
Once a filter is in effect, the track menu's filter row opens a submenu with Edit filters... and Clear all filters.
The filter works on any column a BigBed has. ClinVar's clinical classification
is the column clinSign, so the row clinSign is Pathogenic filters that
catalog the same way. The same menus apply to a bigWig or BigBed of your own
added with Add track; the
web quickstart covers the steps.
Where the track data is read from
The config is hosted on jbrowse.org, but most UCSC track data resolves back to hgdownload, read by byte range. The track menu's About track prints the adapter, which is where to look when a track is slow or missing.
The URL is the file itself, and any program that reads a BigWig by range can
open it, such as rtracklayer in R:
library(rtracklayer)
scores <- import(
"https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP100way/hg38.phyloP100way.bw",
which = GRanges("chr17", IRanges(7668400, 7687550))
)Searching TP53 on a GenArk genome, the axolotl
The GenArk configs have a smaller track set than the UCSC database configs, and
their name indexes come from NCBI RefSeq annotation. A GCF_ accession has gene
tracks and resolves gene symbols, while a GCA_ accession generally has neither
and takes coordinates. An assembly released both ways appears under both
accessions: the axolotl Mex_15411 is GCF_040938575.1 and GCA_040938575.1.
Open GCF_040938575.1 from the site's header search for axolotl, and type
TP53 into its location box.
See also
- Tutorial: Synteny on genomes.jbrowse.org
- Tutorial: Proteins on genomes.jbrowse.org
- Tutorial: Pangenome (HPRC) part 1: the graph's alleles and the haplotypes that have them
- Tutorial: RepeatMasker as one row per class
- User guide: Gene track
- User guide: Quantitative track
- User guide: Opening track hubs by URL
- Docs: Hosted genomes and tracks for agents
External links
Citations
- Pollard KS et al. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 2010, the phyloP method
- Bouaoun L et al. TP53 variations in human cancers. Hum Mutat 2016, the mutation distribution across TP53 codons
- Cho Y et al. Crystal structure of a p53 tumor suppressor-DNA complex. Science 1994, which hotspot residues contact the DNA and which hold the structure
- Liao WW et al. A draft human pangenome reference. Nature 2023, the HPRC assemblies the pangenome callset is built from
Feedback on this tutorial is welcome: contact us.