Data format specifications and supported biological data types

There are 2 basic data formats and 2 advanced data formats. Each of these formats has one or more biological data types that it supports.

General Specifications for all data formats

We support most types of genomic and phenotype/clinical/sample annotations. For genomic data we support calls made on the raw data including but not limited to expression calls, mutation calls, etc. This is what TCGA calls ‘Level 3’ data and is typically a value on gene, transcript, probe, etc. We do not support FASTQ, BAMs, or other ‘raw’ files. Please contact us if you have any questions.

All data types must be tab-delimited. Generally files of this type have a file name ending in .tsv or .txt, though we do not require this. We do not support Excel files (.xls or .xlsx) files. You can export a Microsoft Excel file as a tab-delimited file using the 'Save as ...' function.

Please do not have any duplicate genes/probes/identifiers or samples. We will allow you to load with duplicates but will only display the first one encountered in the file.

Please use a blank or ‘NA’ for no data.

We assume you use a '.' to indicate a decimal place as opposed to a ',' , which is used in some languages.

Here is a folder with example data in addition to the examples below.

Basic Genomic data: numbers in a rectangle/matrix/spreadsheet

These are numeric data called on genomic regions (e.g. exon expression or gene-level copy number). This data is in a rectangle where samples are columns and rows are the genomic regions (e.g. HUGO gene symbol, transcript ID, probe ID, etc). We also support samples as rows and genomic regions as the columns (i.e. the opposite orientation). For supported genomic regions, please see supported gene and probe names.

Supported data types

  • RNA-seq expression (exon, transcript, gene, etc)

  • Array-based expression (probe, gene, etc)

  • Gene-level mutation

  • Gene-level copy number

  • DNA methylation

  • RPPA

  • and more ...

Contact us if you're unsure if we will support your data

An example of a genomic matrix file (in this case, expression):

Sample

TCGA-BA-4074-01

TCGA-BA-4075-01

TCGA-BA-4076-01

ACAP3

0.137

NA

0.022

CTRT2

0.024

0.805

0.256

ALK

0.098

0.805

1.87

Basic Phenotypic data: categories or non-genomic in a rectangle/matrix/spreadsheet

These are data on a sample or patient that is categorical in nature (e.g. Tumor Stage or 'wild type' or 'mutant' for a gene) or is numerical but non-genomic (e.g. age or a genomic signature). Samples can be columns and rows can be phenotype/clinical/sample orientation or vice versa. We support both orientations.

Supported data types

  • phenotype/patient/clinical data (age, weight, if there was blood drawn, etc)

  • sample/aliquot data (where it was sequenced, tumor weight, etc)

  • derived data (regulon activity for a gene, etc)

  • genomic signatures (EMT signature score, stemness score, etc)

  • other (whether a sample has an ERG-TMPRSS2 fusion, whether a sample has WGS data available, etc)

This is our most flexible data type. If you are wondering if your data is considered to be 'phenotypic' please contact us.

An example of a phenotype matrix file:

sample

ER_status

disease_status

age

TCGA-BA-4074-01

positive

complete remission

63

TCGA-BA-4082-01

positive

complete remission

54

TCGA-BA-4078-01

negative

undergoing treatment

65

Advanced Segmented data

For segmented data, we require the following 5 columns: sample, chr, start, end, and value. Note that your column headers must be these names exactly!

Supported data types

  • copy number

We currently accept hg38, hg19, hg18 coordinates.

Example segmented copy number data with required columns:

sample

chr

start

end

value

TCGA-V4-A9EL-01

chr1

61735

16815530

0.041

TCGA-V4-A9EL-01

chr1

16816090

17190862

-0.4227

TCGA-V4-A9EF-01

chr4

86979944

115173700

0.0414

Advanced Positional data

For positional data, we require 6 columns: sample, chr, start, end, reference, alt. Note that your column headers must be these names exactly!

Other columns that may follow are: gene, effect, DNA_VAF, RNA_VAF, and Amino_Acid_Change. These other columns are not required but will enhance the visualization of this data, such as the “effect” column will color the mutations by effect (the default color is gray).

Note that Xena will not call the gene, variant effect, etc for you. All metadata must be included in the file

Supported data types

  • mutation data

We currently accept hg38, hg19, hg18 coordinates.

Example mutation data with required columns:

sample

chr

start

end

reference

alt

gene

TCGA-AB-2802-03

chr2

29917721

29917721

G

A

ALK

TCGA-AB-2802-03

chr1

119270684

119270687

TTAAA

T

MYC

TCGA-AB-2867-03

chr1

150324146

150324146

T

G

PRPF3

Advanced Other data

We support a number of other specialty data types such as structural variants. Please contact us if you have this data so we can help you load it.