I have transcriptome data of resistant and susceptible genotypes in 3 biological replicates. I have a list of significantly differentially expressed transcripts. I also have their functional annotations. But when I check the fold change value of specific genes (multiple transcripts), one transcript show upregulation, the other shows down-regulation but the gene is the same. What should I do? Ex. Gene Transcript Log2FC PAL Contig108 +2.5 PAL Contig1113 -3.6
Hey,
if there are multiple transcript variants of one gene it could be that a specific variation is effected by treatment/trait in one way and the other in the other. Meaning, that in a particular circumstance different gene variants are differentially effected. You should check your probe sequences if they are specific to one variant.
Best regards
Soner
Lot of genes produce some transcripts different from their rules and regulations. Escaping from these regulation and implicating them in the genesis of the pathology, it's easy to understand those type of data.
Try using pubmed with the pathology you're interested in and transcripts dysregulation purposes, a lot of papers you can find.
fred
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