Post ingestion, data will be represented in Base.
Select BASE
from the ICA left-navigation and click Query
.
Under the New Query window, a list of tables is displayed. Expand the Shared Database for Project \<your project name\>
.
Cohorts tables will be displayed.
To preview the table and fields click each view listed.
Clicking any of these views then selecting PREVIEW
on the right-hand side will show you a preview of the data in the tables.
Note: If your ingestion includes Somatic variants, there will be two molecular tables: ANNOTATED_SOMATIC_MUTATIONS and ANNOTATED_VARIANTS. All ingestions will include a PHENOTYPE table.
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Note: The PHENOTYPE table includes a harmonized set that is collected across all data ingestions and is not representative of all data ingested for the Subject or Sample. Sample information is also displayed in this table, if applicable. Sample information drives the annotation process if molecular data is included in the ingestion. That data is stored in the PHENOTYPE table.
This table will be available for all projects with ingested molecular data
This table will only be available for data sets with ingested Somatic molecular data.
This table will only be available for data sets with ingested CNV molecular data.
This table will only be available for data sets with ingested SV molecular data. Note that ICA Cohorts stores copy number variants in a separate table.
These tables will only be available for data sets with ingested RNAseq molecular data.
Table for gene quantification results:
The corresponding transcript table uses TRANSCRIPT_ID instead of GENE_ID and GENE_HGNC.
These tables will only be available for data sets with ingested RNAseq molecular data.
Table for differential gene expression results:
The corresponding transcript table uses TRANSCRIPT_ID instead of GENE_ID and GENE_HGNC.