Question: How To Get Mirna-Mrna Expression In Same Sample From Tcga ?
2
gravatar for jack
5.4 years ago by
jack450
jack450 wrote:

Hi all,

I want to get miRNA-mRNA expression measured in same sample from TCGA. for example I've looked at BRCA at TCGA, it gives the miRNA and mRNA expressions. but it's does not belong to same sample( what I need is both miRNA-mRNA expression are measured in the same biopsy sample, not mRNA measured in one biopsy sample and miRNA measured in other biopsy sample) .

Does anybody knows how can I retrive this kind of data (miRNA-mRNA expression is same biopsy sample) from TCGA ? as I searched in TCGA, apprently TCGA does not put this filter in data searching.

tcga genomic bioinformatician • 3.6k views
ADD COMMENTlink modified 5.4 years ago by zhxq09140 • written 5.4 years ago by jack450
2
gravatar for zhxq09
5.4 years ago by
zhxq09140
China
zhxq09140 wrote:

starBase has constructed Pan-Cancer miRNA-mRNA interaction maps from TCGA matched miRNA-Seq and RNA-Seq data. starBase provided pearsion correlations between miRNA and target expression profiles.

For example: hsa-miR-21-5p and its target gene PDCD4 and mir-200 and its target gene ZEB2

In addition, starBase also provides Pan-Cancer miRNA-lncRNA, protein-lncRNA and protein-mRNA interactions and ceRNA networks.

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by zhxq09140

@zhxq09,

that's not what I want.

ADD REPLYlink written 5.4 years ago by jack450

@zhxq09,

that's not what I want.

ADD REPLYlink written 5.4 years ago by jack450

you can find that starBase really provides expression values of miRNAs and mRNAs from same person. Tutorial of starBase shows the expression values of miRNAs and mRNAs from same person. You can get their tutorial with following website: http://starbase.sysu.edu.cn/downloads/starBase_Pan-Cancer_Platform.pdf

For more details, you may ask starbase developers how to get miRNA-mRNA expression in same sample from TCGA.

ADD REPLYlink written 5.4 years ago by zhxq09140
2
gravatar for zhxq09
5.4 years ago by
zhxq09140
China
zhxq09140 wrote:

you can find that starBase really provides expression values of miRNAs and mRNAs from same person.

For example: hsa-miR-141-3p:ZEB1 interactions (http://starbase.sysu.edu.cn/pcMirTargetInfo.php?database=hg19&name=hsa-miR-141-3p&targetGene=ZEB1&autoId=179263#expTabs) You move mouse on the circles of scatterplot figure, you can find the expression values of miRNAs and miRNAs from same person. Tutorial of starBase also give detail descritpion for all Pan-Cancer analysis. You can get their tutorial with following website: http://starbase.sysu.edu.cn/downloads/starBase_Pan-Cancer_Platform.pdf

For more details, you may ask starbase developers how to get miRNA-mRNA expression in same sample from TCGA.

ADD COMMENTlink written 5.4 years ago by zhxq09140
0
gravatar for Danielk
5.4 years ago by
Danielk570
Karolinska Institutet, Stockholm, Sweden
Danielk570 wrote:

It was my belief that they extracted DNA/RNA/proteins from the same tissue pieces so they should come from the same piece of tissue. Are you sure that's not the case?

ADD COMMENTlink written 5.4 years ago by Danielk570

Yes, The same tissue, but they are not measured in same sample at same time. in other word, I need miRNA-mRNA expression data for same tissue at same sample (which means at the same time, they measured mRNA-miRNA expression in specific sample/experiment)

ADD REPLYlink written 5.4 years ago by jack450

Oh I see. So total RNA (incl small RNA) extracted and then sequenced together? Don't think that's available as miRNA and RNA-seq were two separate analyses. Emphasis on think

ADD REPLYlink written 5.4 years ago by Danielk570

no, for example, for lung cancer, they measured miRNA in person X and mRNA in person Y. I want to have data that both measurments belong to same person, which means that, miRNA in person X and mRNA in person X.

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by jack450

I you go to http://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm and select LUAD under disease and under Data Type select miRNAseq, RNAseqV2 and RNAseq you get a long list of samples where both data types are available in the same sample. You should be able to get the expression data for both types using "Build Archive".

ADD REPLYlink written 5.4 years ago by Danielk570
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