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RNA Seq V2 RSEM Data

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
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updated by Zhenyu Zhang Zhenyu Zhang • written by archana.katta9000 • archana.katta9000

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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written by archana.katta9000 • archana.katta9000

It would be better to contact cBioPortal.

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written by Kevin Blighe Kevin Blighe

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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written by Zhenyu Zhang Zhenyu Zhang

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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written by archana.katta9000 • archana.katta9000

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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written by Kevin Blighe Kevin Blighe

1 answer

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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updated by Ram Ram • written by Kevin Blighe Kevin Blighe

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