RNA Seq V2 RSEM Data
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23 months ago

I am unable to download the mRNA Expression z-Scores (RNA Seq V2 RSEM) for single gene from the cBioPortal website. I tried but it is showing, HTTP Status 500 – Internal Server Error.

RNA-Seq • 1.2k views
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Which gene and dataset?

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Thank you so much for responding to my question, I need TCGA Combined Studies mRNA Expression z-Scores (RNA Seq V2 RSEM) for single mutation in a gene.

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It would be better to contact cBioPortal.

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Thank you for suggestion, I will contact cBioPortal

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Btw, be careful when using z-scores

  • they are normalized in a particular project, and thus not comparable across projects
  • they are normalized to SD of each gene, so a small change in a very consistently expressed gene could have a very large z-score (in absolute value)

cBioPortal uses z-scores for their visualization purpose. If you are interested in doing analysis, I strongly suggest you to download raw count or rsem data and do your own normalization.

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Thank you for your response, I should download a data of mutations expression for several genes but individually. Examples likeEGFR, ERBB2...Here am attaching a link where we will get an box plot for mutations expression, if we click on the bubble, we will get the expression data of single mutation. so could you please suggest me, how can we download the data for all mutations? Please Find the Following Link. https://www.cbioportal.org/results/expression?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=laml_tcga_pan_can_atlas_2018%2Cacc_tcga_pan_can_atlas_2018%2Cblca_tcga_pan_can_atlas_2018%2Clgg_tcga_pan_can_atlas_2018%2Cbrca_tcga_pan_can_atlas_2018%2Ccesc_tcga_pan_can_atlas_2018%2Cchol_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018%2Cdlbc_tcga_pan_can_atlas_2018%2Cesca_tcga_pan_can_atlas_2018%2Cgbm_tcga_pan_can_atlas_2018%2Chnsc_tcga_pan_can_atlas_2018%2Ckich_tcga_pan_can_atlas_2018%2Ckirc_tcga_pan_can_atlas_2018%2Ckirp_tcga_pan_can_atlas_2018%2Clihc_tcga_pan_can_atlas_2018%2Cluad_tcga_pan_can_atlas_2018%2Clusc_tcga_pan_can_atlas_2018%2Cmeso_tcga_pan_can_atlas_2018%2Cov_tcga_pan_can_atlas_2018%2Cpaad_tcga_pan_can_atlas_2018%2Cpcpg_tcga_pan_can_atlas_2018%2Cprad_tcga_pan_can_atlas_2018%2Csarc_tcga_pan_can_atlas_2018%2Cskcm_tcga_pan_can_atlas_2018%2Cstad_tcga_pan_can_atlas_2018%2Ctgct_tcga_pan_can_atlas_2018%2Cthym_tcga_pan_can_atlas_2018%2Cthca_tcga_pan_can_atlas_2018%2Cucs_tcga_pan_can_atlas_2018%2Cucec_tcga_pan_can_atlas_2018%2Cuvm_tcga_pan_can_atlas_2018%2Cmsk_impact_2017&case_set_id=all&data_priority=0&gene_list=EGFR&geneset_list=%20&tab_index=tab_visualize.

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Mutation data for all samples for a particular cohort (LUSC, BRCA, et cetera) is availalble in MAF format at the Genomic Data Commons (GDC) Data Portal.

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5 weeks ago

This is now in their FAQ: https://docs.cbioportal.org/1.-general/faq#how-is-tcga-rnaseqv2-processed-what-units-are-used

How is TCGA RNASeqV2 processed? What units are used?

RNASeqV2 from TCGA is processed and normalized using RSEM. Specifically, the RNASeq V2 data in cBioPortal corresponds to the rsem.genes.normalized_results file from TCGA. A more detailed explanation of RSEM output can be found here. cBioPortal then calculates z-scores as described above in What are mRNA and microRNA Z-Scores?

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