When there are no overlapping segments, Xena displays the value and color of the copy number segment as indicated in the column legend at the bottom of the column.
When there are overlapping segments, Xena follows these steps:
Compute overlaps by slicing segments that overlap with other segments. For example if there was one segment from chr1:10000-20000 and a second segment from chr1:10050-10100, then resulting segments from this step would be chr1:10000-10050, chr1:10050-10100, and chr1:10100-20000.
For each segment defined in step 1, determine which segments in the original data overlap with this segment.
Divide data segments into those that are greater than copy number neutral (i.e. are amplifications) and those that are less than copy number neutral (i.e. are deletions). Average the segments for each of these two groups.
Find the colors corresponding to the two averages from step 3. Then pick a color that is in between those two colors on the color wheel. An example would be that if the amplifications are red and deletions are blue, the resulting color from a strong amplification and a strong deletion would be purple. Note that copy number neutral in this example would be white.
More information about how we color mutation columns
Samples that have mutation data are white with a dot or line for the mutation for where the mutation falls in relation to the gene model at the top of the column. Mutation data is colored by the functional impact:
Red - Deleterious
Blue - Missense
Orange - Splice site mutation
Green - Silent
Gray - Unknown
Samples for which there is no mutation data are gray with no dot or line, and are marked as 'null'.
Red --> Nonsense_Mutation, frameshift_variant, stop_gained, splice_acceptor_variant, splice_acceptor_variant&intron_variant, splice_donor_variant, splice_donor_variant&intron_variant, Splice_Site, Frame_Shift_Del, Frame_Shift_Ins
Blue --> splice_region_variant, splice_region_variant&intron_variant, missense, non_coding_exon_variant, missense_variant, Missense_Mutation, exon_variant, RNA, Indel, start_lost, start_gained, De_novo_Start_OutOfFrame, Translation_Start_Site, De_novo_Start_InFrame, stop_lost, Nonstop_Mutation, initiator_codon_variant, 5_prime_UTR_premature_start_codon_gain_variant, disruptive_inframe_deletion, inframe_deletion, inframe_insertion, In_Frame_Del, In_Frame_Ins
Green --> synonymous_variant, 5_prime_UTR_variant, 3_prime_UTR_variant, 5'Flank, 3'Flank, 3'UTR, 5'UTR, Silent, stop_retained_variant
Orange --> others, SV, upstreamgenevariant, downstream_gene_variant, intron_variant, intergenic_region
Note that we are case insensitive when we color for these terms.
For the gene-level mutation datasets (Somatic gene-level non-silent mutation):
Red (=1) --> indicates that a non-silent somatic mutation (nonsense, missense, frame-shif indels, splice site mutations, stop codon readthroughs, change of start codon, inframe indels) was identified in the protein coding region of a gene, or any mutation identified in a non-coding gene
White (=0) --> indicates that none of the above mutation calls were made in this gene for the specific sample
Pink (=0.5) --> some samples have two aliquots. In the event that in one aliquot a mutation was called and in the other no mutation was called, we assign a value of 0.5.
This dynamic, powerful, and flexible view is our default view into the data.
The Visual Spreadsheet allows you to add an arbitrary number of columns of any data type (mutation, copy number, expression, protein, phenotype, methylation, etc) on any number of patient's samples into a spreadsheet-like view. We line up all columns so that each row is the same sample, allowing you to easily see trends in the data. Data is always sorted left to right and sub-sorted on columns thereafter.
Get started by going to the Xena Browser and following the wizard to enter your data of interest.
The wizard on the screen will guide you to choose a study to view and TWO columns of data to view on those samples. Note that if you do not choose at least two columns, the wizard will not exit and let you interact with the data.
You can select a cohort either by choosing 'Help me select a cohort' and searching our cohorts for you cancer type, etc. or by choosing 'I know the study I want to use' and searching for the partial or full name of the cohort you are interested in.
Enter a HUGO gene name or a dataset-specific probe names (e.g. a CpG island). You can enter one gene or multiple genes. Separate multiple genes with a space, comma, tab, or new line.
To display a genomic region, enter the genomic region, choose your dataset and click 'done'. We recongize chromosomes (e.g. chr1), arms of chromosomes (e.g. chr19q), and chromosomes coordinates (e.g. chr1:100-4,000).
After entering a gene or probe name, you will need to select one or more datasets.
We have pre-selected default datasets for most cohorts. These datasets are selected based because they are the most used datasets. Typically there is a default mutation, copy number, and expression dataset.
Xena also has more datasets than those listed in the Basic Menu. Depending on the cohort, these can include DNA methylation, exon expression, thresholded CNV data and more. To access them, click on 'Show Advanced' below:
More information on basic datasets
We annotate datasets used in the basic Visual Spreadsheet wizard with a red asterisk in our datasets pages. For an example see: https://xenabrowser.net/datapages/?cohort=TCGA%20Acute%20Myeloid%20Leukemia%20(LAML)
Patient samples are on the y-axis and your columns of data are on the x-axis. We line up all columns so that each row is the same sample, allowing you to easily see trends in the data. Data is always sorted left to right and sub-sorted on columns thereafter.
If you entered a single gene, that gene will be listed at the top of the column. If there are multiple probes mapped to that gene in the dataset you selected they will be displayed as subcolumns ordered left to right in the direction of transcription.
If you selected a positional dataset, such as segmented copy number variation or mutation we will display the gene model will be displayed at the top of the column. The gene model is a composite of all transcripts of the gene. Boxes show different exons with UTR regions being short and CDS regions being tall. We display 2Kb upstream to show the promoter region. Use the column menu to toggle to show intronic regions.
If you entered multiple genes, each gene will be listed as a subcolumn for that dataset. If there are multiple probes mapped to that gene in the dataset (i.e. if you entered a single gene then you would see the probes as subcolumns), then the probes are averaged for a single value per gene.
Note that if you entered more than one gene and selected a mutation dataset, we will only show the first gene. If you wish to see multiple mutation columns, please enter each gene individually and click 'done'
When displaying a chromosome range, genes will be shown at the top of the column, with dark blue genes being on the forward strand and red genes being on the reverse strand. Hovering over a gene will display the gene name in the tooltip. Note that introns are always shown in this mode.
Individual values vary by dataset. The legend at the bottom of the dataset will tell you the units for your particular dataset, including any normalization that was performed. If a sample does not have data for a column, it will show as gray and be labeled as 'null'.
If the entire column is gray this means we did not recognize the gene, probe, or position. If you believe this to be in error, please try an alternate name.
More information about a dataset can be found in the dataset details page. To get there, click on the column menu and choose 'About'.
The Xena Browser uses the y-axis for samples and the x-axis/columns for genomic/phenotypic features. Data from a single sample is always on the same horizontal line across all columns, allowing you to see screen-wide trends. The Xena Browser orders samples left to right first by the first columns, then the second, etc. If there are multiple genes, identifiers, probes within in a column, samples is ordered from left to right by 1st sub-column, then 2nd sub-column, and so on.
Numerical data are ordered in descending order (e.g. 3.5, 1.2, ...). Categorical data (e.g. stage, tumor type, etc) are ordered by categories. CNV data is sorted by the average of the entire column. Positional mutation data is ordered by genomic coordinates (from 5'->3') and then by the predicted impact of the mutation. Both CNV and positional mutation data has the option to instead sort by the zoomed region. Click the column menu at the top of the column and choose 'Sort by zoom region avg'.
To reverse the ordering, click the column menu at the top of the column and chose 'Reverse sort'
As the sample sort order is controlled by the left most columns, it can be useful to explore the data by moving a different column to the left.
To move a column click on the column header and drag a column to the right or left.
Click and drag any where in any column to zoom in in either direction. Zoom out to all samples by clicking the 'Clear Zoom' at the top. Zoom out to the whole column by clicking the red 'x' at the top of a column.
The Tooltip at the top of the Visual Spreadsheet shows more information about the data under the mouse. Links are links to the UCSC Genome Browser to learn more about that gene or genomic position. Alt-click to freeze and unfreeze the tooltip to be able to click on the links. Click here for more information about interacting with the tooltip.
You can change the size of a column by clicking on the bottom right corner of a column and dragging to a new size.
You can add another column of data by clicking on 'Click to add column' either on the right edge of the visual spreadsheet or by hovering between columns until 'Click to insert column' displays'.
