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Question: GAGE for non model organism
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gravatar for melkile26
7 months ago by
melkile260
melkile260 wrote:

Dear All,


I have a non model reference genome which is not found in in public databases, as it is mentioned in GAGE vingnatte, I used the following commands to generate the KEGG gene set

kg.ko=kegg.gsets("ko")
kegg.gs=kg.ko$kg.sets[kg.ko$sigmet.idx]

and found the following results,

$`ko00970 Aminoacyl-tRNA biosynthesis`
 [1] "K00604" "K01042" "K01866" "K01867" "K01868" "K01869" "K01870" "K01872" "K01873" "K01874" "K01875" "K01876" "K01878" "K01879" "K01880"
[16] "K01881" "K01883" "K01884" "K01885" "K01886" "K01887" "K01889" "K01890" "K01892"

$`ko02024 Quorum sensing`
  [1] "K00494" "K01114" "K01218" "K01318" "K01342" "K01364" "K01399" "K01497" "K01580" "K01626" "K01635" "K01657" "K01658" "K01728" "K01897"
 [16] "K01995" "K01996" "K01997" "K01998" "K01999" "K02031" "K02032" "K02033" "K02034" "K02035" "K02052" "K02053" "K02054" "K02055" "K02250"

My reference genome has annotation file as shown below for 24232 genes

Gene_ID                                     KO
XP_010995747.1                        K18401
ENSBTAP00000034638              K18400
ENSBTAP00000016466              K18200
XP_010977173.1-D14                K17914
ENSBTAP00000027125              K17846
ENSP00000248071                    K17845
ENSBTAP00000053440-D3        K17843

 

I tried to convert the KEGG gene set  to my gene ID, I tried 'eg2sym' but this function is only for human and it only convert enternez to symbol. Any help is appreciated

 

Many Thanks
 

gage gage package • 139 views
ADD COMMENTlink written 7 months ago by melkile260
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