BINGO custom annotation files

[h.l....@liv.ac.uk]

I am having problems setting up custom annotation files to check for
GO enrichment within a network (2000 genes). I am working with micro-
array data and have approximately 10,000 genes detected on the
affymetrix chip.

I need to set these 10,000 genes as my custom annotation file, so I
can check for over-representation of GO terms in the network (2000
genes).

The problem is the format the annotation file needs to be in:
(I have a list of Entrez gene IDs so.....)

Entrez Gene ID = GO Identifier

But a lot of the Entrez Gene IDs do not have go annotations!

Is there an alternative file format I can introduce my annotation file
in?

Thanks in advance,
Helen

[swaraj basu]

As far as I know u cant do much like that. Its is not necessary to gv
all in the input, for those u dnt hv GO annotations, get their
sequences in fasta format, name the sequences after Entrez IDs, thn
try to get their GO using BLAST2GO. add up the results and make
complete file. Still if some are left out no problems,the program will
run smoothly.

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[Maital Ashkenazi]

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