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-   -   Gene Name nomenclature (http://seqanswers.com/forums/showthread.php?t=70168)

ronaldrcutler 07-07-2016 07:51 AM

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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