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  • Gene Name nomenclature

    Hello all. I have a set of DE genes from a single replicate as identified by the GFOLD package. Though I am getting results which have the same gene ID but different suffixes at the end of the name and different GFOLD levels. I used a .bed file for the annotation. Usually I use a .gff3 file with HTSeq-count.


    It looks like this:

    Code:
    #GeneSymbol	                                                             GeneName  GFOLD(0.005)
    42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1	 NA	-4.50996
    42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds1	 NA	-3.62531
    42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds2	 NA	-2.81447
    42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds3	 NA	-3.38619
    42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds4	 NA	-2.05015
    42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds5	 NA	-1.9145
    42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds6	 NA	-2.44262
    42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds7	 NA	-3.6937
    42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds8	 NA	-1.33762
    42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.cds9	 NA	-3.64182
    42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+.mrna1.exon1 NA	-3.62531
    Can anybody clarify to me the differences between these Gene Symbols? I am used to Gene names looking something like this:

    Code:
    42SP43|c.Taira201203kidney_X008044|JGIv7b.000075417_5391788-5397899+__chr9_10L
    42SP50|c.XenBase_133737005|JGIv7b.000220448_3999398-4005758+__chr6L
    A1CF|c.Taira201203intestine_X005935|JGIv7b.000079772_4581973-4609884+__chr7L
    Thanks

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