Hello everybody,

I have a table with some microarray experiments which look like that:
my "genelist.txt"
Probe Id    NAME    FC_set1    FC_set2    FC_set3    FC_set4
A_51_P100021    Hivep3    1.048368    -1.085207    -1.013457    1.032816
A_51_P100034    Mif4gd   -1.049719    -1.077773    -1.084012    -1.004941
A_51_P100052    Slitrk2   1.339832    1.063053    -1.157675    -1.003128
A_51_P100063    Lnx1    1.073604    1.010892    -1.058375    1.063377
A_51_P100084    Unknown   1.084544    -1.258876    -1.092571    -1.058791
...

the Probe Ids are from the Agilent expression arrays. I extracted the names
using BiomaRt and now I would like to find whether there are some
overrepresented gene sets in the differentially regulated genes.
For once I would like to see if there are any GO terms which are
overrepresented in these gene lists for each of the columns (gene sets).
Secondly i would like to search for accumulations of other gene sets of
differentially regulated genes in these lists (for example kinases,
transcription factors, but also localization, protein domain etc.)

I would like your help in creating the gene sets of either GO terms or the
other parameters.

I know I can extract the data from BiomaRt to each and every gen. for
example:

mart <- useMart("ensembl")
ensembl <- useDataset("mmusculus_gene_ensembl", mart = mart)

test <- read.delim("genelist.txt")
geneset1 <- read.delim("geneset1_all_signal.txt")
genes <- as.character(geneset1[,1])

geneNames <- getBM(attributes = c("go_biological_process_id", "name_1006",
"agilent_wholegenome", "external_gene_id", "ensembl_gene_id", "entrezgene"),
filter = c("agilent_wholegenome"), values = geneset1, mart = ensembl)

> geneNames

go_biological_process_id
name_1006
1
GO:0007409
axonogenesis
2               GO:0006511                               ubiquitin-dependent
protein catabolic process
3               GO:0051260
protein homooligomerization
4               GO:0042787 protein ubiquitination during ubiquitin-dependent
protein catabolic process
5               GO:0006417
regulation of translation
6
GO:0016070                                                       RNA
metabolic process
7
GO:0016070                                                       RNA
metabolic process
  agilent_wholegenome external_gene_id    ensembl_gene_id entrezgene
1        A_51_P100052          Slitrk2 ENSMUSG00000036790     245450
2        A_51_P100063             Lnx1 ENSMUSG00000029228      16924
3        A_51_P100063             Lnx1 ENSMUSG00000029228      16924
4        A_51_P100063             Lnx1 ENSMUSG00000029228      16924
5        A_51_P100034           Mif4gd ENSMUSG00000020743      69674
6        A_51_P100034           Mif4gd ENSMUSG00000020743      69674
7        A_51_P100034           Mif4gd ENSMUSG00000020743         NA

Now I would like to create the gene sets according to these GO categories. I
would like to get something like that:

GO:0007409 A_51_P100052 ... the rest of the genes from this category in the
list on one line
GO:0016070 A_51_P100034 ...
GO:0006417 A_51_P100034 ...

THX for the help

Assa

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