Overlapping genes between gene modules in WGCNA
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@shresthavivek18-22711
Last seen 20 months ago

Hello, I did a WGCNA analysis on around ~ 4000 genes with 30 samples. WGCNA created 5 gene modules based on their coexpression but I found that there are numbers of genes (ranges from 1- 40) that overlap with one or other modules. Is this overlapping of genes between two modules are Ok? If not what might be the issue and how can I solve this? Please let me know. Thank you

WGCNA • 377 views
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Could you please post the code you used? It will make it easier to suggest changes to avoid this. Also 4000 genes seems like a low number, did you filter the genes before using WGCNA?

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Here is the code, (also the original data had ~8000 genes, after filtering the poor quality it has around ~4000). Thank you

zmnet = blockwiseModules(zmdatExpr, power = 18,corType = "pearson", TOMType = "signed", minModuleSize = 30, reassignThreshold = 0, mergeCutHeight = 0.25, numericLabels = TRUE, pamRespectsDendro = FALSE, saveTOMs = TRUE, saveTOMFileBase = "B73maizepower18TOM2", verbose = 3)

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It is strange that you needed such a high power. Could you show more code?

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for soft threshold power, https://drive.google.com/open?id=1ZyZlRWW0O9s7F0YaLJIxeHzVXKN7MiKV Let me know if you have any comments? Shoud I have stick to B=12?

I did not know any simple code to extract genes within each modules, so did this,

zmmodules_overlap <- overlapTableUsingKME( zmdatExpr, zmdatExpr, moduleColors, moduleColors, MEs1 = NULL, MEs2 = NULL, name1 = "MM1", name2 = "MM2", cutoffMethod = "assigned", cutoff = 0.5, omitGrey = TRUE, datIsExpression = TRUE)

genesMM1 <- zmmodulesoverlap$GenesMM1

and then manually extract the genes in each modules. Is there any simple code after module construction to extract genes within each modules?

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For a "signed" network, power 18 is not exceptionally high. Especially for lower numbers of samples (below say 30) it may be entirely appropriate.

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Ok great, thank you! I think I figured out there were some problems during the filtration process where I did not remove all of the duplicated genes. Thank you Lluis and Peter for taking the time to answer my question. I appreciate your help. However, still if you know any code that can directly generate/extract the gene list within each module; that would be great! Thanks a lot.

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