GPCR expression in TPM are gene-level estimates calculated via RSEM (Li and Dewey, 2011) and generated by the TOIL project, whereas CPM values were calculated by us using EdgeR (Robinson et al, 2010) with TMM normalization. Input for EdgeR were curated files, containing gene-level RSEM estimated counts, downloaded from Xena here.
The ‘raw’ download file linked above contains counts for all TCGA samples and genes together. We have provided curated files for each tumor type at here.
Gene expression in TPM provides an estimate of the relevant abundance of different genes within the same sample or set of replicates. These data may be used for estimating which GPCR is highest expressed in a given tumor type/subtype and for ranking GPCRs based on magnitude of expression in an individual sample or a specific tumor type/subtype.
Do not use expression in TPM for differential expression / fold change calculations and avoid using expression in TPM for any between-sample or between-group comparisons.
Gene expression in CPM will allow comparison of expression of the same gene across different samples and groups. Hence, if comparing expression between groups, performing survival analysis, cluster analysis etc., use the data in CPM. Do not use expression in CPM for ranking genes in terms of magnitude of expression. To estimate fold changes, use either the fold-change calculations already provided or re-analyze the data using the raw counts via edgeR.
Download the spreadsheet in the link below; enter the GPCR gene symbol in the highlighted cell and plots will be produced showing median, upper and lower quartiles of expression of the queried GPCR in 45 tumor types/subtypes and corresponding normal tissue, normalized in CPM (counts per million).
Each file contains expression in TPM for all endo-GPCRs in the respective tumor types, further divided into subtypes as applicable. For example, the esophageal cancer file provides expression for squamous cell carcinomas and adenocarcinomas as distinct groups. For each GPCR, expression is shown as median for the tumor subtype, as well as expression in each individual tumor sample. Where applicable, data for (tumor-matched) normal samples are also shown.
In addition, on the second sheet of each file is corresponding GPCR expression in GTEX ‘normal’ samples from corresponding normal tissue.
Certain samples highlighted in yellow were not included for other analyses (such as DE analysis) due to issues such as unclear metadata or classification into subtypes with very few (<10) replicates. These highlighted samples will therefore not appear in the accompanying files with GPCR expression in CPM.
The same files as above, with ready-made plots like the one shown above comparing GPCR expression in TCGA tumors vs GTEX normal tissues can be found here
Each file contains GPCR expression in CPM for every GPCR gene in every sample, grouped together based on tumor subtype or as normal samples. Median expression of GPCRs in tumor subtypes are also provided.