Question: Finding gene expression from TCGA pan cancer
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gravatar for mikemakaveli1
5 months ago by
mikemakaveli10 wrote:

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 • 547 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by mikemakaveli10

Thank you, but using the mRNA expression I can find out my interest gene expression from the 366 mRNA expression,?

ADD REPLYlink written 5 months ago by mikemakaveli10

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.

ADD REPLYlink written 5 months ago by ahmad mousavi410

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

ADD REPLYlink written 5 months ago by genomax65k

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

ADD REPLYlink written 5 months ago by mikemakaveli10

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

ADD REPLYlink written 5 months ago by mikemakaveli10

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

ADD REPLYlink written 5 months ago by mikemakaveli10

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

ADD REPLYlink written 5 months ago by Santosh Anand4.7k
1
gravatar for ahmad mousavi
5 months ago by
ahmad mousavi410
Royan Institute, Tehran, Iran
ahmad mousavi410 wrote:

In TCGA you just have cancer data not normal data.

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

ADD COMMENTlink written 5 months ago by ahmad mousavi410
5

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

ADD REPLYlink written 5 months ago by genomax65k
1

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.

ADD REPLYlink modified 5 months ago • written 5 months ago by ATpoint15k
1
gravatar for Santosh Anand
5 months ago by
Santosh Anand4.7k
Santosh Anand4.7k wrote:

You may use GEPIA, http://gepia.cancer-pku.cn/detail.php?gene=TP53

ADD COMMENTlink written 5 months ago by Santosh Anand4.7k
1
gravatar for lsp03yjh
5 months ago by
lsp03yjh750
China
lsp03yjh750 wrote:

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.).

ADD COMMENTlink modified 5 months ago • written 5 months ago by lsp03yjh750
0
gravatar for mikemakaveli1
5 months ago by
mikemakaveli10 wrote:

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

ADD COMMENTlink written 5 months ago by mikemakaveli10
1

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/.

ADD REPLYlink written 5 months ago by lsp03yjh750
0
gravatar for mikemakaveli1
5 months ago by
mikemakaveli10 wrote:

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?

ADD COMMENTlink written 5 months ago by mikemakaveli10
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