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sr320 / LabDocs

Roberts Lab Documents
http://sr320.github.io/LabDocs/
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Sneak peak at possible proteins indicative of mortality #598

Closed Ellior2 closed 7 years ago

Ellior2 commented 7 years ago

I am starting down the rabbit hole of figuring out which proteins are indicative of mass mortality events. Here is my first annotated comparison of sample 27 (Silo 2-23C at Day 9) and sample 32 (Silo 9-29C at Day 9). We saw a large divergence occurring between the samples in the NMDS plot. These proteins are sorted from largest to smallest absolute values of z statistic and logfoldchange values (Most differentially abundant proteins are located on top!) Exciting stuff here. Anyone care to take a look and let me know what you think?@sr320 @emmats @kubu4

Here are some of the questions I plan on tackling in the coming days/weeks...

emmats commented 7 years ago

I see a lot of cytoskeletal proteins and cell adhesion proteins. You should definitely try to figure out if these pathways are showing greater or lesser abundance. Ubiquitin is interesting because it can be sign of protein degradation (among other things). Maybe make two lists of differentially abundant proteins (zstat > |2|, log fold change > |0.5|): proteins that are at higher or lower abundance. Your questions should keep you busy for a while!

Ellior2 commented 7 years ago

Good idea. Here are ones highly expressed in dying seed Silo 2-23C and surviving seed Silo 9-29C

Ellior2 commented 7 years ago

Highly expressed proteins in 23C (high mortality) compared to 29C (low mortality) image

VIRUS??

emmats commented 7 years ago

Before you make any assumptions, look at what those proteins actually are and think about whether or not you think they come from a virus. It would be odd to pick up that many viral proteins using DDA.