Question: What is the state of multi-omics dataset ?
0
gravatar for tevlon84
3.2 years ago by
tevlon8430
tevlon8430 wrote:

Hi there,

i am implementing a multi-omics workflow that includes analysis of transcriptomics (RNA-seq) , proteomics ( Mass spec ) and metabolomics ( Mass spec ) data. While i am able to test and analyse each data seperately ( meaning from different sources, therefore different experiments). I have a hard time to test the whole system with a dataset where data of all 3 domains are collected.

My question is :

Does such data even exist ?

ADD COMMENTlink modified 2.4 years ago by ypriverol0 • written 3.2 years ago by tevlon8430

There are multiple examples of multi-omics data integration in the literature. The way you approach the problem usually depends on the question you're asking.

ADD REPLYlink written 3.2 years ago by Jean-Karim Heriche18k
0
gravatar for Amitm
3.2 years ago by
Amitm1.6k
UK
Amitm1.6k wrote:

Yes! At least one that I know of - 

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32874

http://snyderome.stanford.edu/

 

I am pretty sure that apart from above, such multi-omics approach has been employed in some cancer studies as well. Can't remember any now.

But, I hope you have heard of TCGA. Though no Mass-spec data but it has RPPA (low throughput protein array capturing phosphorylation state) and methylation profile along with RNA-seq and mut. status (tumor vs normal) and miRNA sequencing as well. These datasets are per patient-wise and there are scores of cancer types studied with thousands of samples in between.

ADD COMMENTlink written 3.2 years ago by Amitm1.6k
0
gravatar for ypriverol
2.4 years ago by
ypriverol0
ypriverol0 wrote:

You can look for multiomics datasests in this new resource www.omicsdi.org here one example:

http://www.omicsdi.org/search?q=:%20AND%20omics_type:%22Multi-Omics%22%20AND%20omics_type:%22Proteomics%22

Regards Yasset

ADD COMMENTlink written 2.4 years ago by ypriverol0
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