What is the state of multi-omics dataset ?

Question

[tevlon84]

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 ?

[Jean-Karim Heriche]

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.

Answer 1

[Amitm]

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.

Answer 2

[ypriverol]

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