Expression Data

File Formats

For expression data, use the GCT file format. This a tab-delimited format that contains a row for each probe set ID (or gene), a column for each sample, and expression values for each feature in each sample.

Display Notes

• By default, IGV displays expression data as a blue-to-red heatmap where the data range is -1.5 to 1.5. If loaded expression data appears in tracks colored all red, check the data values and modify the data range as necessary.
• To change track display options, use the track pop-up menu. The commands that appear in the pop-up menu are those relevant to any data track.

Genomic Locations for Probes

To display expression data, IGV must first map the probe set IDs named in the expression data file to their genomic locations. IGV displays data for all of the probes that it can map to genomic locations. If none of the probes in the file can be mapped, IGV displays an error message.

IGV determines the genomic locations for probes as follows:

1. If you use the delimiters |@ and | to specify the probe loci in the file (see the GCT file format), IGV uses the specified loci. Otherwise, it goes to the next step.
2. IGV searches all loaded annotation tracks for each probe. (This is the same as entering the ID in the first column [the Name column] of the file into the search box on the IGV tool bar and clicking Go.) If a probe is found, IGV displays the data at that location. Otherwise, it goes to the next step.
3. IGV searches its probe mapping files for each probe. If a probe is found, IGV determines the probe locus and displays the data at that location. Otherwise, it goes to the next step.
4. IGV uses its gene mapping files to map each probe ID to a gene symbol, determines the gene locus, and displays the data at that location.

Choose preferred mapping: By default, IGV uses its probe mapping files before its gene mapping files. If you prefer to map probes to genes, select the Map probes to genes radio button on the Probes tab of the Preferences window.

Probe Mapping Files

Probe mapping files map probe identifiers to chromosomal locations. They are compiled from source files provided by Affymetrix, Agilent, and Illumina. The Affymetrix and Agilent mapping files are split by species due to their large size. Separate mapping files are provided for human, mouse, and other (non-mouse, non-human) species. Human probe identifiers are mapped to hg18. Depending on the vendor, mouse probe identifiers are mapped to mm9 (Affymetrix), mm5 (Agilent) or mm8 (Illumina).

Following are links to the probe mapping files:

• http://data.broadinstitute.org/igvdata/probes/affy/affy_human_mappings.txt.gz
• http://data.broadinstitute.org/igvdata/probes/affy/affy_mouse_mappings.txt.gz
• http://data.broadinstitute.org/igvdata/probes/affy/affy_other_mappings.txt.gz
• http://data.broadinstitute.org/igvdata/probes/agilent/agilent_human_mappings.txt.gz
• http://data.broadinstitute.org/igvdata/probes/agilent/agilent_mouse_mappings.txt.gz
• http://data.broadinstitute.org/igvdata/probes/agilent/agilent_other_mappings.txt.gz
• http://data.broadinstitute.org/igvdata/probes/illumina/illumina_allMappings.txt.gz

Gene Mapping Files

Gene mapping files map probe identifiers to gene identifiers. Following are links to the gene mapping files:

• http://data.broadinstitute.org/igvdata/probes/affy/affy_probe_gene_mapping.txt.gz
• http://data.broadinstitute.org/igvdata/probes/agilent/agilent_probe_gene_mapping.txt.gz
• http://data.broadinstitute.org/igvdata/probes/illumina/illumina_probe_gene_mapping.txt.gz

Sources for the Mapping Files

The probe and gene mapping files are compiled from source files provided by Affymetrix, Agilent, and Illumina. A list of the source files is available at http://data.broadinstitute.org/igvdata/probes/data_sources_for_mapping.txt.