A GCT file (.gct) is a tab-delimited text file that contains gene expression data. The GCT file format is described on the GenePattern web site: http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/gct.

The GCT format is used for gene expression and RNAi data.

Example: example.gct

Gene Expression Data

Before IGV can display gene expression data, it must map the probes named in the file to genomic locations. Unless you specify loci for a probe in the file, IGV uses annotations and mapping files to look up the locations. For information on how gene expression data is mapped, see Genomic Locations for Probes.

To specify loci for a probe in the file, enter the data into the second column as follows:

 Name  Description  Sample 1  Sample 2
  100_g_at na|@chr6:1950428-1950681,chr6:2304548-2304574,
 215.37  132.94
  101_g_at na |@RABGGTA| 211.3 90.56
  • To specify one locus, use this format: |@chr6:1950428-1950681|.  A gene symbol can also be used: |@RABGGTA|

     Name  Description  Sample 1  Sample 2
      100_g_at  na |@chr6:1950428-1950681|  215.37  132.94
  • To specify more than one locus, use a comma delimited list: |@chr6:1950428-1950681,chr6:2304548-2304574|


RNAi Data

GCT files for RNAi data must use the .rnai.gct extension.

To display the RNAi data, IGV maps the hairpin names to gene names, determines the gene locus, and displays the data at that location. The hairpin-to-gene mappings used by IGV are based on work published by Luo, Cheung, Subramanian et al. (PNAS, 2008, 105:51:20380-20385) and available at http://broadinstitute.org/cancer/software/rnai/data/Luo_Cheung_Subramanian_PNAS_2008.chip. The mappings used by IGV are different only where a gene name has been modified to match one used in a genome on the genome server.