GC Analysis Follow Up

[mwang87]

We can explore several things:

1. What molecules are significantly differentially expressed between MERS and MOCK
2. What molecules are increasing over time.

[mwang87]

@aaksenov1 will do statistical significance and merge with network and upload to github @helenamrusso will analyze the cytoscape file for biological insights

[aaksenov1]

Network uploaded: https://github.com/mwang87/MassSpec-Coronavirus-Project-Docs/tree/master/docs/data

[mwang87]

Am linking on main page

[aaksenov1]

The differences are quite pronounced: https://docs.google.com/document/d/1nd4N5hm9tEpkG33zOASEfUforoYQPebT7XdtlRHzRTI/edit?usp=sharing

[aaksenov1]

Sugars are down, phosphate and alanine are up - some kind of basic metabolism disregulation

[aaksenov1]

Library search with cos 0.5 https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=8cdcf51214c546ce82b73c875c4edff2

[aaksenov1]

Network with networking cos 0.5 is is uploaded: https://github.com/mwang87/MassSpec-Coronavirus-Project-Docs/tree/master/docs/data

[helenamrusso]

Sugars are down, phosphate and alanine are up - some kind of basic metabolism disregulation

Evidences that support this theory: "A large proportion of the recovered SARS patients reported glucose metabolic disorders, including hyperinsulinemia, insulin resistance, hyperglycemia, and type 1 or 2 diabetes, a few years prior to this study" - Paper here

"...Although limited numbers of metabolites from the glycolysis/gluconeogenesis pathways were detected, the reduced levels of glucose 6-phosphate (G6P), dihydroxyacetone phosphate (DHAP), and 3-phospho-D-glycerate (3PG) further support theidea of a decrease in activity of this central pathway..." - Paper here

[mwang87]

Very cool. If possible, lets go ahead and add these links to this page:

https://github.com/mwang87/MassSpec-Coronavirus-Project-Docs/blob/master/docs/metabolomics.md

[chasemc]

I haven't done a deep dive into the data, but when I was looking at the metabolomics (LC-based I think) I noticed features with high quant in most replicates but then were 0 in one replicate (replicate varied). Just something to watch out for

[mabelgon88]

The differences between MERS and MOCK, and sampling times are statistically supported by the PLS-DA analysis in 3 dimensions, but not very much in the PCA analysis. I have included 3D figures for visualization of each Phenotype-time in the doc and PERMANOVA analysis showing the significance of the differentiation based on the phenotype, phenotype-time simultaneously, MHAE, and sampling time.

Here is the link: https://docs.google.com/document/d/1nd4N5hm9tEpkG33zOASEfUforoYQPebT7XdtlRHzRTI/edit