Gene Name nomenclature

ronaldrcutler

Member

Join Date: May 2016
Posts: 80

Gene Name nomenclature

07-07-2016, 06:51 AM

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

Tags: deseq, gfold, hisat2, rna-seq, tophat

Previous template Next

Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems

by SEQadmin2

Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...
- Channel: Articles
07-09-2026, 11:10 AM
Cancer Drug Resistance: The Lingering Barrier to Rising Survival

by SEQadmin2

Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
- Channel: Articles
07-08-2026, 05:17 AM
Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by GATTACAT

Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
- Channel: Articles
07-01-2026, 11:43 AM

Topics	Statistics	Last Post
UC San Diego Bioengineers Map Gene Function in Human Stem Cells by SEQadmin2 Started by SEQadmin2, Today, 10:26 AM	0 responses 9 views 0 reactions	Last Post by SEQadmin2 Today, 10:26 AM
New Analysis Splits Leukemia Into 16 Epigenomic Subgroups by SEQadmin2 Started by SEQadmin2, 07-09-2026, 10:04 AM	0 responses 24 views 0 reactions	Last Post by SEQadmin2 07-09-2026, 10:04 AM
Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2 Started by SEQadmin2, 07-08-2026, 10:08 AM	0 responses 16 views 0 reactions	Last Post by SEQadmin2 07-08-2026, 10:08 AM
Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2 Started by SEQadmin2, 07-07-2026, 11:05 AM	0 responses 33 views 0 reactions	Last Post by SEQadmin2 07-07-2026, 11:05 AM

Unconfigured Ad

Gene Name nomenclature

Latest Articles

ad_right_rmr

News