Question: Comparing RNAseq expressions in cancer cell lines to patient population in order to pick cell lines to work with
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gravatar for shaban.hiba8
6 months ago by
shaban.hiba810
shaban.hiba810 wrote:

I would like to be able to pick cancer cell lines that have "high", "medium" and "low" expressions of certain genes based on what the high, medium, and low expressions of those genes are in cancer patient populations. Would need to know the distribution of expressions in patients before determining what my high, medium, and low cutoffs will be.

I've gathered RNAseq data on cell lines from DepMap.org and I also have RNAseq data on The Cancer Genome Atlas (TCGA) patient populations from cBioPortal, the problem is DepMap.org's RNAseq units are log2(tpm+1) and TCGA RNAseq units are RSEM. Is there a way to be able to compare those numbers (convert one unit into the other or another source with same units??)

Description of one of my TCGA files (for adenoid cystic carcinoma - ACC) called meta_RNA_Seq_v2_expression_median.txt:

cancer_study_identifier: acc_tcga

genetic_alteration_type: MRNA_EXPRESSION

datatype: CONTINUOUS

data_filename: data_RNA_Seq_v2_expression_median.txt

stable_id: rna_seq_v2_mrna

show_profile_in_analysis_tab: false

profile_description: Expression levels for 20532 genes in 79 acc cases (RNA Seq V2 RSEM)

profile_name: mRNA expression (RNA Seq V2 RSEM)
tcga cancer cell lines • 272 views
ADD COMMENTlink modified 6 months ago by ATpoint23k • written 6 months ago by shaban.hiba810
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