ClueGO: Missing genes for Mycoplasma Genitalium G37

[oc1...@bristol.ac.uk]

Hi,

Below is a list of genes that can't be found. They are classed as "classified" within the WholeCell model and so thought it was strange to not have any GO matches. Can you help me with this? Are the gene names wrong or is GO just not up to date enough perhaps?

All the best,
Oli

Gene IDs not found (no annotation or wrong ids) in Cluster#1:

MG471

MG472

MG475

MG479

MG483

MG484

MG485

MG486

MG487

MG488

MG489

MG490

MG492

MG493

MG495

MG496

MG497

MG499

MG500

MG501

MG502

MG503

MG504

MG506

MG507

MG508

MG509

MG510

MG511

MG512

MG513

MG514

MG518

MG519

MG520

MG523

MG_0001

MG_0003

MG_0004

MG_288

MG_333

MGrrnA16S

MGrrnA23S

MGrrnA5S

[bernhard]

Hi Oli,
your IDs are either not the official MG IDs or they were discontinued.
e.g. are official ids but were discontinued in NCBI:
MG_288 -> http://www.ncbi.nlm.nih.gov/gene/875403
MG_333 -> http://www.ncbi.nlm.nih.gov/gene/875441

e.g.:

MG_0001

MG_0003

MG_0004

MGrrnA16S

MGrrnA23S

MGrrnA5S

are not official EnsemblGeneIDs
rename them to

MG_001

MG_003

MG_004

and it should work (as long they have a GO/KEGG annotation)

all the other missing IDs are also not official EnsemblGeneIDs

MG471 MG472 MG475 MG479 MG483 MG484 MG485 MG486

etc...

MG518 MG519 MG520 MG523 MGrrnA16S MGrrnA23S MGrrnA5S

they should be: MG_471 MG_472 MG_475 MG_479 MG_483 MG_484 MG_485 MG_486

etc...

MG_518 MG_519 MG_520 MG_523

MG_rrnA16S MG_rrnA23S MG_rrnA5S

I added an AlternativeID column removing the "_" from the IDs so it should work also with e.g. MG518, but the official ID should be MG_518. I put the update organism data on the webserver and you can downloading it again in the "Download Organism" section. Best