Tracks Description

We constructed a comprehensive vervet gene set by merging gene transcripts from NCBI Chlorocebus sabaeus Annotation Release 100 (Pruitt et al. 2012) and ENSEMBL Chlorocebus sabaeus v.1.82 (Aken et al. 2016) , excluding pseudogenes. The merged set is non-redundant at the protein level, that is, if two transcripts from NCBI and ENSEMBL translate to the same sequence, only the NCBI transcript is included. The gene set contains 23,250 non-coding transcripts and 67,175 protein-coding transcripts (59,868 NCBI and 7,307 ENSEMBL) that represent 20,533 protein-coding genes.

Based on location in the gene region and type of nucleotide change, detected SNVs were classified into the following categories: stop-gain, stop-loss, splice-site (donor, acceptor), missense (damaging, benign, unknown), synonymous, UTR exon, non-coding gene exon, gene flank (upstream, downstream), intron. Annotation is non-redundant, that is, if a variant has conflicting annotations in different transcripts of the same gene, the earlier one in the list above is assigned. Indels were classified into the same prioritized categories, excluding stop-gain, stop-loss, missense and synonymous types, replaced by the general “coding exon indel” type.

Our definition of PTVs (protein-truncating variants) follows that implemented in the LOFTEE software ( Loss-Of-Function Transcript Effect Estimator): stop gain SNVs, splice site disrupting SNVs or indels, frameshifting indels. PTVs do not include indels with length being multiple of 3 (non-frameshifting, or inframe, indels), variants in the last 5% of a transcript, variants in non-canonical and NAGNAG splice sites or surrounding short exons (<15bp). Of 13,777 coding exon indel, splice site or stop gain alleles, 9,574 alleles in 5,668 protein-coding genes pass the PTV criteria above and were used in this study.

Chip-seq H3K27 track shows genomic profiles of H3K27 acetylation based on chromatin immunoprecipitation sequencing in the vervet liver based on three healthy adult individuals (Villar et al. 2015). H3K4me3 marks are associated with promoters.

Chip-seq H3K4 track shows genomic profiles of H3K4 trimethylation marks based on chromatin immunoprecipitation sequencing in the vervet liver based on three healthy adult individuals (Villar et al. 2015). H3K27ac marks are associated with promoters or enhancers.

Villar, Diego, Camille Berthelot, Sarah Aldridge, Tim F. Rayner, Margus Lukk, Miguel Pignatelli, Thomas J. Park, et al. 2015. “Enhancer Evolution across 20 Mammalian Species.” Cell 160 (3): 554–66.

  • MedRPKM legend image
    MedRPKM track

    Median gene expression RPKM values in 7 vervet tissues from RNA-seq of 58 samples. Gene expression bar plots are aligned to left-most coordinate of NCBI gene it represents. The tissue RNA-seq data sets are deposited in the Gene Expression Omnibus (GEO) repository under project PRJNA219198.

    Jasinska AJ, Zelaya I, Service SK, et al. Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate. Nat Genet. 2017 Dec;49(12):1714-1721. doi: 10.1038/ng.3959. PubMed PMID: 29083405.

  • Guide to Using JBrowse
    Search Feature

    Gene search under Home page is done against NCBI-GeneInfo data and in JBrowse search is done against 3 tracks i.e NCBI-GeneInfo, Ensemble-1.9 & Ensembl-1.8 and user is given an option to choose chromosome coordinates.

    • Search by gene image
      JBrowse Search Box

      The JBrowse search box is located between the lines for the chromosome-level position and the detail-level position in the consolidated header region. Autocomplete, which offers suggestions based on what you have already typed, is included for object symbols. For example, typing Ascl results in a list which includes the gene symbols ASCL1, ASCL2, ASCL3, ASCL4 and ASCL5.

    • Search by chromosome image

      Alternatively, the position may be entered as Chr#:start..stop, for example Chr1:171,707,625..171,713,991. Commas can be used as thousands separators in the start and stop nucleotide position numbers but they are not required.

      Selecting a different chromosome number in the dropdown to the left moves the selection to the same nucleotide position on a different chromosome.

    • Navigation image
      The upper grey bar in the tool header gives the chromosomal position being shown in the detail display as a red vertical line or box. The lower gray bar at the bottom of the header region gives the chromosomal positions of the detail display below it. Light blue shading connects the ends of the outlined area in the chromosome view to the ends of the detail view below.

    • Available tracks image
      Selecting Tracks
      Click the check box to the left of the track name to turn that track on. Click again (i.e. uncheck the box) to turn it off. As tracks are turned on, they will appear at the bottom of the browser display. Tracks in the browser display can be reordered by dragging the name of the track in the display (not in the list of available tracks) to the desired location and “dropping” the track there.

    • Highlighting a Region
      Highlighting a Region
      JBrowse supports highlighting a region and if you know the position of the object you are interested in you can use the View–>Set Highlight function in the dark blue menu bar at the top of the page. Enter the position in the popup window as Chr#:start..stop just as you would enter a region in the JBrowse search box. Click the button labeled “Highlight” and the region you entered will be highligted in yellow across all the open tracks. If the position you enter is not in the region that is being shown in the browser, the region you specify will be highlighted but you will not see it (i.e. the browser will not move to the highlighted region). If, however, you navigate to that region it will be displayed with the yellow highlight.
    • Highlighting a Region
      You can also highlight a region in the browser using the “Highlight a region” button to the right of the search box. Click this button, then click and drag in the browser window to select the region to highlight. Do not click and drag on the position bar for this function. Doing so will cause the browser to zoom to that region, not highlight it. Once a region is highlighted, it will remain highlighted through movements, zooming, etc. To clear the highlighting, go to View–>Clear Highlight to remove the yellow highlighting. Only one region may be highlighted at a time. Selecting a second region to highlight removes the highlight from the first region rather than adding to it.