Repo for transposon-element expression in bladder cancer samples in TCGA (TCGA-BLCA).
A 2020 review on the topic by Sophie Lanciano & Gael Cristofari which has been published in Nature Reviews Genetics provides fair amount of details on the methods for quantifying TE in RNA-seq data. For gene expression analysis , the method explained in Yu Kong et al. (Nature Communications volume 10, Article number: 5228 (2019)), which they called it "REdiscoverTE" was used. More details on how this tool works can be find here.
Diffrent kind of expression data( raw count, normalized and ...) were generated for 433 TCGA-BLCA cases and here is short description on each files(adapted from the "REdiscoverTE" software manual):
GENE: Transcript-level expression values:
- GENE_1_raw_counts.RDS: raw counts DGEList data object.
- GENE_2_counts_normalized.RDS: normalized counts (by total gene counts) DGEList data object.
- GENE_3_TPM.RDS: TPM (transcripts per million) for each gene/transcript. DGEList data object.
Repetitive elements
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RE all: Repetitive elements found anywhere in the genome. Granularity for all RE reporting is at repName level (where the three levels we use are name, family, and class, in increasing order of generality).
- RE_all_1_raw_counts.RDS: raw counts DGEList data object.
- RE_all_2_counts_normalized.RDS: note that counts are normalized by total gene counts
- RE_all_3_TPM.RDS: TPM (transcripts per million) for each repetitive element ‘repName’. DGEList data object.
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RE exon: Subset of RE all: only repetitive elements found at least partially within an annotated exon.
- RE_exon_1_raw_counts.RDS: raw counts DGEList data object.
- RE_exon_2_counts_normalized.RDS: counts are normalized by total gene counts
- RE_exon_3_TPM.RDS: TPM (transcripts per million) for each repetitive element ‘repName’. DGEList data object.
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RE intron: Subset of RE all: only repetitive elements that do not have any overlap with an exon, and have some overlap with an intron.
- RE_intron_1_raw_counts.RDS: raw counts DGEList data object.
- RE_intron_2_counts_normalized.RDS:counts are normalized by total gene counts
- RE_intron_3_TPM.RDS: TPM (transcripts per million) for each repetitive element ‘repName’. DGEList data object.
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RE intergenic: Subset of RE all: only repetitive elements that have no overlap with annotated introns or exons.
- RE_intergenic_1_raw_counts.RDS: raw counts DGEList data object.
- RE_intergenic_2_counts_normalized.RDS: counts are normalized by total gene counts
- RE_intergenic_3_TPM.RDS: TPM (transcripts per million) for each repetitive element ‘repName’. DGEList data object.
Expression datasets can be download from Google drive here. In those files column names are UUID code and need to be map to TCGA barcodes. To do so, gdc-manifest file (click here) and a table for id conversion is needed (click here). Both can be find in the files directory, as well.