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I am working on pathway analysis using GAGE and Pathview. I can determine up-regulated and down-regulated pathways and get corresponding heatmaps, but I have a question on the "type" of counts I should be using. When I did differential gene expression analysis I generated a DGElist that has pseudo.counts which if I understand correctly are transformed and normalized. I also have a Counts Per Million list that was generated after quality filtering of raw counts. I get similar differentially regulated pathways while using either counts but I do not know which one is more appropriate to use. If anyone can help me I would very much appreciate the help. Thanks!
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The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM -
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM
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