Question: Annotating RNA-seq gene ids (differentially expressed)
0
gravatar for David_emir
4.9 years ago by
David_emir360
India
David_emir360 wrote:

Hello All,
 

I have Differentially expressed gene list from RNA-seq data, i have compared Drug treated v/s Untreated And i have got differentially expressed gene list which i have pasted in the following table.

My question is, when i use R/Bioconductor package "cummeRbund" to inspect the number of genes and transcript that are differentially expressed b/w two sample, i have loaded the results of cuffdiff's analysis , which reports the number of differentially expressed genes. The differentially expressed genes is not annotated (XLOC_000007), is their any way to annotate gene_id with actual gene names?

 

Control vs Treated Data

<caption>Differentially expressed Genes</caption>
gene_id sample_1 sample_2 status value_1 value_2 log2_fold_change test_stat p_value q_value significant
XLOC_000007 treated control OK 2.35097    1.35961 -0.790057 -3.82466 .00005 9.84048E-005 yes
XLOC_000009 treated control OK 5.11344     0.0453474 -6.81713 0.00005    9.84048E-005     9.84048E-005 yes
XLOC_000010 treated control OK 8.49633 1.21619 -0.564379 -32.2551 0.00005     9.84048E-005 yes
XLOC_000011 treated control OK 100.369 8.49633 -0.564379 0.00005    9.84048E-005     9.84048E-005 yes
XLOC_000012 treated control OK 206.885     0.0453474 -6.81713 0.00005    0.00005     9.84048E-005
XLOC_000013 treated control OK 9.63649 1.21619 -0.564379 0.00005    9.84048E-005     9.84048E-005 yes
XLOC_000017 treated control OK 18.764 8.49633 -0.564379 -32.2551 0.00005     9.84048E-005 yes
XLOC_000018 treated control OK 0.878346     0.0453474 -6.81713 0.00005    9.84048E-005     9.84048E-005 yes
XLOC_000019 control control OK 1.21619 1.21619 -0.564379 0.00005    0.00005 9.84048E-005
XLOC_000019 treated control OK 1.21619     0.0453474 -6.81713 -32.2551 9.84048E-005     9.84048E-005 yes


Thanks a Lot ...

-Ateeq Khaliq

rna-seq • 2.7k views
ADD COMMENTlink modified 4.9 years ago by geek_y9.9k • written 4.9 years ago by David_emir360
1

Did you include a GFF/GTF file in the Cuffdiff run? the XLOC ids are that appear if gene annotation is missing.. 

ADD REPLYlink written 4.9 years ago by roy.granit800

Hi Roy , yes i have included the file and it looks the following, it has got gen name with Id but couldn't get the same if i am running cummRband... i used the following command

> gene_diff_data <- diffData(genes(cuff_data))

> sig_gene_data <- subset(gene_diff_data, (significant == 'yes'))

My cuffdiff output looks like this

test_id gene_id gene
XLOC_000001 XLOC_000001 DDX11L1
XLOC_000002 XLOC_000002 OR4F5
XLOC_000003 XLOC_000003 LOC100132062,LOC100133331
ADD REPLYlink written 4.9 years ago by David_emir360

Did you try to remove the first two columns is the cuffdiff output and then run cummRband?

ADD REPLYlink written 4.9 years ago by roy.granit800

Yes i tried doing that, but no change, its showing the same !!! :(

ADD REPLYlink written 4.9 years ago by David_emir360
1
gravatar for geek_y
4.9 years ago by
geek_y9.9k
Barcelona
geek_y9.9k wrote:

Use the annotation file (GTF) while running the cuffdiff. If you have multiple GTF files, e.g one from cufflinks and other from standard annotation, use cuffmerge to generate the final version of GTF and use it while running cuffdiff.

If you use GTF file, the gene names will be printed to one of the columns in the final output.

e.g: Cuffdiff output ran with GTF file

test_id gene_id gene    locus   sample_1        sample_2        status  value_1 value_2 log2(fold_change)       test_stat       p_value q_value significant

ENSMUST00000000001      ENSMUSG00000000001      Gnai3   3:107910197-107949064   SB      AB      OK      14.2736 14.5269 0.0253732       0.112543        0.8671  0.999385        no

ENSMUST00000000003      ENSMUSG00000000003      Pbsn    X:75083239-75098962     SB      AB      NOTEST  0       0       0       0       1       1       no

ENSMUST00000000010      ENSMUSG00000020875      Hoxb9   11:96132770-96137909    SB      AB      NOTEST  0       0       0       0       1       1       no

ENSMUST00000000028      ENSMUSG00000000028      Cdc45   16:18780539-18835354    SB      AB      OK      0.872629        0.902901        0.0492005       0.0316144       0.9662  0.999385        no

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by geek_y9.9k
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