Ran WGCNA! Interpretation and next steps?

[aspencoyle]

Alright, so I was able to complete running WGCNA on my ambient-temperature crabs over days 0, 2, and 17. These libraries are aligned to cbai_transcriptomev2.0, which is not filtered by taxa, and thus it examines both C. bairdi and Hematodinium genes together

To speed the process up, I rejected genes with counts below 30 in all samples (recommendation is below 10), so these aren't perfect, but they'll be decent!

The heat map is particularly interesting - seems to not show any significant relationships with day (if we set the p-value bar at 0.05), but some interesting relationships with individual crab.

I could really use some help both interpreting these results and deciding where to go next.

• Recreate this with Day 0/2 Elevated crabs

• Recreate this with Day 2 Ambient/Day 2 Elevated crabs

• Continue by performing GO-MWU on each WGCNA module

Any thoughts on what the best way to go from here would be?

Sample dendrogram

Sample dendrogram with condition

Cluster dendrogram with original and merged eigengenes

Clustering of module eigengenes

Gene clustering on TOM-based dissimilarity

Gene dendrogram with module colors. NOTE: Didn't work at first, as of time of posting this link is broken - will re-run soon, thus hopefully fixing the link

Mean connectivity

Heat map of module-treatment relationships

Scale independence

Specific gene lists for each eigengene

[sr320]

sorry if I am missing but is there a image showing expression patterns over 3 days?

[aspencoyle]

Shoot, no there isn't - I based my analysis off a script that didn't look at expression patterns over time, but one of the tutorials I finished earlier did do that. I'll start on that next - hopefully should be relatively quick!

[aspencoyle]

Hmm, update - apparently I misremembered, there weren't any tutorials that dealt with time series data or graphing single-gene differences in expression patterns (which is what I assumed you were asking for)

If you're just looking for an image that shows expression patterns in each eigengene cluster over time, this might be what you're looking for - the heat map.

It only shows differences in expression over time, without differentiating between day 0/2/17. However, I believe I could separate the days out - like in the graph at the bottom of this page if that's what you mean!

Furthermore, I ran WGCNA again, this time changing the bar from "must be >30 counts in 1+ of our 9 samples" to "must be >10 counts in 2+ of our 9 samples", as it seemed closer to the recommendation (must be >10 counts in 2+ of 10+ samples).

That produced a heat map that isn't too different, but thought I'd mention it!

[sr320]

Note you can put images in posts 😄

I was thinking something more like