Finding gene expression from TCGA pan cancer
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3.2 years ago

I am using the bio portal to download liver HCC in TCGA PAN CANCER ATLAS, of the mRNA to find my gene expression, how can I find that from the 366 and compare it with normal sample?

RNA-Seq • 1.9k views
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Thank you, but using the mRNA expression I can find out my interest gene expression from the 366 mRNA expression,?

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Yes, take a look at GEO2R tool in GEO, after reading manual you could do a DEG analysis and filter the genes based on your list.

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mikemakaveli1 : Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

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Thank you, everyone, for sharing, I was thinking of putting my gene in the request and selecting from the genomic data, mRNA expression But in the genomic data, there are two mRNA expression RSEM and mRNA expression Z scores, RSEM from a batch normalized from Illumina Hi seq RNA seq V2.

Also if I am interested in doing like a comparison of three gene expression of my preference between HCC and normal samples ( i don't know which one to choose from the two mRNA expression to know the gene expression of my interest to normal sample).

Thank you guys once again, I appreciate your help

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Thank you, I was hoping to use the Cbio portal, Liver HCC TCGA pancancer atlas, and link the gene expression to the whole samples etiology , gender and so forth.

but the Pan cancer analysis platform, gene expression cancer sample is 373 different from the cbio portal 366 mRNA expresion

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Thank you, I was hoping to use the Cbio portal, Liver HCC TCGA pancancer atlas, and link the gene expression to the whole samples etiology , gender and so forth.

but the Pan cancer analysis platform, gene expression cancer sample is 373 different from the cbio portal 366 mRNA expresion

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why are you so much concerned with difference in the number of sampless?

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3.2 years ago
ahmad mousavi ▴ 550

In TCGA you just have cancer data not normal data.

For finding normal tissue RNA-SEQ you could use NCBI GEO search

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I don't think that is correct. There are matched tumor/normal samples.

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Also keep in mind that if you compare a TCGA tumor sample with a "normal" sample from a completely different lab, that was prepared with a different kit and sequenced on a different platform, there are a lot of confounding effects that may or may not be the cause for a seemingly "differentially" expressed gene.

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3.2 years ago
lsp03yjh ▴ 810

You can use Pan-Cancer Analysis Platform http://starbase.sysu.edu.cn/panCancer.php . It provided expression profiles of ncRNAs (miRNAs, lncRNAs, snoRNAs, pseudogenes, etc.) and protein-coding genes across 32 cancer types ( ~10,000 RNA-seq and ~9,900 miRNA-seq samples) integrated from TCGA project. It also provided survival, differential expression and co-expression analysis platforms for miRNAs and genes (lncRNAs, mRNAs, ncRNAs, pseudogenes, etc.).

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3.2 years ago

Because I was hoping to use the Cbio portal, Liver HCC TCGA pancancer atlas,366 mRNA expresion data for my gene expression and relate it with the whole sample etiology and gender

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cBio portal may use different version of RNA-seq data. I think it is OK for your project. You also can fetch the newest expression values from TCGA GDC website https://portal.gdc.cancer.gov/.

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3.2 years ago

If I am using RNA-seq data from Cbio portal only, since its using Illumina, is it like I can put the three genes in querying and change the genomic profile to 366 mRNA expression and only this shows mRNA Expression Z-scores, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2) Enter a z-score threshold ± 2.0. and after that I can get the gene expression of the three genes ? is my understanding correct?

if so what does z-score threshold ± 2.0 have meaning, 2?

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