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4.6 years ago
mathavanbioinfo
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90
Hello All, I am doing gene expression analysis using the network analyst tool, I followed their standard instructions, the output of DEGs analysis using limma showed 5000 significant genes. How do I interpret these high gene counts? Please share the valuable suggestions
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Without context no advice possible. There are for sure experiments where one expects that many significant genes, yes, e.g. knockout of a master regulator transcription factor. Still, given that no code is shared (not sure if the tool provides this) and the post lacks any details on the experiment it is hard to tell if this number is trustworthy or not.
Thank you for your reply, It is virus-infected human macrophage (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93861), the samples as following groups, Control, severe1, Critical, Severe2, fair, outpatient. In this analysis I compared Control vs Severe2 (i.e control 30 samples GSM464170-199 - Severe28 sample GSM2464227-234)
So a dedicated immune cell that is activated, I would guess it is definitely possible that the transcriptome undergoes a massive activation wave towards immune-related genes and genes that supports this action (metabolism, protein synthesis etc). The replicate number is also large so high numbers of DEG can be expected.