![]() You will need to examine with care if these are paralog transcripts or alternates at one locus, that can also have divergent expression. members of many Nearly Identical Paralogs families also exhibit differential expressionĢ003: Divergence in the Spatial Pattern of Gene Expression Between Human Duplicate Genes These results quantitatively and mechanistically establish enrichment of paralogs with diversifying expression patterns as genomic and evolutionary basis of multicellularity.Ģ009: Increased Expression and Protein Divergence in Duplicate Genes Is Associated with Morphological DiversificationĢ006: Nearly Identical Paralogs: Implications for Maize (Zea mays L.) Genome Evolution gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication.Ģ010: Duplicate gene enrichment and expression pattern diversification in multicellularity: Īll 100 NDGs were transcribed and under functional constraints, while 24% of the NDGs have differential expression patterns compared to their parental genes.Ģ011: The Ecoresponsive Genome of Daphnia pulex new duplicate genes (NDGs) play a functional role in the evolution and adaption. High identity paralogs often have divergent expression patterns, and they can be protein-identical so have the same GO/orthology annotations.Ģ013: Divergent Evolutionary and Expression Patterns between Lineage Specific New Duplicate Genes and Their Parental Paralogs in Arabidopsis thaliana ![]() No no no, you are about to throw away the stuff of evolution. One more thing is that I won't be able to use cuffdiff for the DGE test (or as you suggested, isoforms tracking) just use CLC GW. Transcript | GO object name | fold changeĮvg_4430 | sodium-coupled neutral amino acid transporter 9-like | 3.946997356Įvg_2502 | sodium-coupled neutral amino acid transporter 9-like | -4.507410413 one is showing + fold change, and another one is. My situation is 2 different transcripts having the same annotation. By the way, it is not the *same transcript* having both + and - fold change. If you have the *same transcript* with both + and - regulation then I would suggest this is a problem with your annotation/genome build, or worse, a bug in the software.Thanks for the reply. The fold changes of the transcripts may be relatively unimportant to the gene level expression value, depending on how abundant your transcripts are. RPKMs from transcripts are summed to make a gene level expression value. Gene upregulation is almost a nonsense in an RNA-Seq world (of sufficient read depth), a hangover from microarray experiements where you had no idea which transcripts you may or may not be detecting. Genes may switch isoforms under certain conditions, there are specific tests for this in the cuffdiff package. Your question title 'genes found to have + and - fold change' morphs into 'transripts' in the text.Īre you saying that some transcripts from a gene are downregulated, whilst others are upregulated between conditions? That's perfectly possible.
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