[Feedback] Site Feedback: go annotation of maize

[feedback at gramene.org]

URL         : http://www.gramene.org/

Subject     : Site Feedback: go annotation of maize

Name        : Gorliver

Email       : gorliverz at yahoo.com

Organization: UW

Comments    : 

We find GO enrichment analysis using gramene GO annotation (release 30) and other source of GO annotation ( http://structuralbiology.cau.edu.cn/PlantGSEA) generate different results. We then developed a GO annotation by mapping maize genes to TAIR10 gene models and get similar results to the other source of GO annotation (http://structuralbiology.cau.edu.cn/PlantGSEA).
Due to the roughness of our GO annotation, we cannot determine what is the reason of the differences. By manual check, it seems gramene GO annotation over represents some GO term, like  "response to stimulus".  It is highly appreciated if this problem could be inspected.

Below is the gene list used to do the GO enrichment analysis:
GRMZM5G841142
GRMZM2G025855
GRMZM2G075637
GRMZM2G074317
GRMZM2G124715
GRMZM2G073860
GRMZM2G153541
GRMZM2G133173
GRMZM5G800723
GRMZM2G118731
GRMZM2G079127
GRMZM2G132971
GRMZM2G078839
GRMZM2G074404
GRMZM2G389173
GRMZM2G114793
GRMZM2G130018
GRMZM2G130548
GRMZM2G127609
GRMZM2G072909
GRMZM2G055936
GRMZM2G025441
GRMZM2G460406
GRMZM2G097289
GRMZM2G072071
GRMZM2G166646
GRMZM2G147500
GRMZM2G062210
GRMZM2G155253
GRMZM2G044557
GRMZM2G113349
GRMZM2G036765
GRMZM2G112336
GRMZM2G010328
GRMZM2G155329
GRMZM2G400156
GRMZM2G144042
GRMZM2G037140
GRMZM2G029107
GRMZM2G007795
GRMZM2G135877
GRMZM2G086258
GRMZM5G864335
GRMZM2G098643
GRMZM2G078781
GRMZM2G152194
GRMZM2G009808
GRMZM2G415007
GRMZM2G160452
GRMZM2G056068
GRMZM2G392101
GRMZM2G020216
GRMZM2G113033
GRMZM5G890190
GRMZM2G102499
GRMZM2G027756
GRMZM2G057408
GRMZM2G036609
GRMZM2G308687
GRMZM5G845755
GRMZM2G351977
AC215244.3_FG002
GRMZM5G895313
GRMZM5G855672
GRMZM2G171507
GRMZM5G826714
GRMZM2G027821
GRMZM2G079200
GRMZM2G032252
GRMZM2G040095
GRMZM2G049418
GRMZM2G132929
GRMZM2G133986
GRMZM2G038388
GRMZM2G413897
GRMZM2G061969
GRMZM2G051974
GRMZM2G396397
GRMZM2G162434
GRMZM2G091155
GRMZM5G813892
GRMZM2G120579
GRMZM2G056732
GRMZM2G453805
GRMZM2G034575
GRMZM5G851753
GRMZM2G445602
GRMZM2G165567
GRMZM2G352415
GRMZM2G131907
GRMZM5G818431
GRMZM2G342856
GRMZM2G110328
GRMZM2G452142
GRMZM2G086496
GRMZM2G101004
GRMZM2G016511
GRMZM2G159399
GRMZM2G036921
GRMZM2G035749
GRMZM2G176085
GRMZM2G040736
GRMZM2G125969
GRMZM2G027479
GRMZM2G098577
GRMZM2G058954
GRMZM2G086801
GRMZM2G062373
GRMZM2G148904
GRMZM2G122337
GRMZM2G421279
GRMZM2G159237
GRMZM2G017045
GRMZM2G061950
GRMZM2G021331
GRMZM2G363801
GRMZM2G030523
GRMZM2G129428
GRMZM2G128880
GRMZM2G080178
GRMZM2G151726
GRMZM2G063363
GRMZM2G134396
GRMZM2G347280
GRMZM2G040627
GRMZM2G099305
GRMZM2G019317
GRMZM2G352159
GRMZM2G138230
GRMZM2G447151
GRMZM2G149768
GRMZM2G163877
GRMZM2G358059
GRMZM2G050714
GRMZM2G117746
GRMZM2G427954
GRMZM2G457699
AC213521.3_FG005
GRMZM2G003385
GRMZM2G180328
GRMZM2G027451
GRMZM2G056870
GRMZM2G137839
GRMZM2G052336
GRMZM2G050305
GRMZM2G048313
GRMZM2G069208
GRMZM2G062914
GRMZM2G033885
GRMZM2G049811
GRMZM2G156174
GRMZM2G019121
GRMZM2G114707
GRMZM2G154735
GRMZM2G365374
GRMZM5G878558
GRMZM2G035417
GRMZM2G027282
GRMZM2G133937
GRMZM2G044132
GRMZM5G879178
GRMZM2G178517
GRMZM2G420801
GRMZM2G031802
GRMZM2G114739
GRMZM2G061900
GRMZM2G109130
GRMZM2G383088
GRMZM2G027723
GRMZM2G126821
GRMZM2G009719
GRMZM2G167520
GRMZM2G181269
GRMZM5G881803
GRMZM2G060257
GRMZM2G012966
GRMZM2G100652
GRMZM2G124532
GRMZM2G146280
GRMZM2G058910
GRMZM2G173647
GRMZM2G303465
GRMZM2G471357
GRMZM5G853245
GRMZM2G118485
GRMZM2G063875
GRMZM2G375504
GRMZM2G030784
GRMZM2G477741
GRMZM2G036880
GRMZM2G080001
GRMZM5G870176
GRMZM2G091276
GRMZM2G075081
GRMZM2G048616
GRMZM2G064988
GRMZM2G092008
GRMZM2G107114
GRMZM2G092174
GRMZM2G452630
GRMZM2G143008
GRMZM2G147014
AC217358.3_FG005
GRMZM2G052821
GRMZM2G015967
GRMZM5G898471
GRMZM2G117707
GRMZM2G020721
GRMZM2G071970
GRMZM2G300135
GRMZM2G075870
GRMZM2G025014
GRMZM2G033208
GRMZM5G801949
GRMZM5G884600
GRMZM2G178958
GRMZM2G150098
GRMZM2G083689
GRMZM2G329144
GRMZM2G028736
GRMZM2G134806
GRMZM2G045243
GRMZM2G098298
GRMZM2G176707
GRMZM5G853513
GRMZM2G037177
GRMZM2G028516
GRMZM2G157018
GRMZM2G075002
GRMZM2G024668
GRMZM2G178892
GRMZM2G020631
GRMZM2G306679
GRMZM2G056569
GRMZM2G176029
GRMZM2G084958
GRMZM2G009359
GRMZM2G157760
GRMZM2G437460
GRMZM2G130953
GRMZM2G027219
GRMZM5G829894
GRMZM2G301647
GRMZM2G006791

Thanks,

http://www.warelab.org/bugs/view.php?id=5329