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Gaspard Lequeux
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@gaspard-lequeux-3505
Last seen 10.3 years ago
Hej,
Has anybody succeeded in constructing an ecoliK12.db database with
usable
Gene Ontology annotations? topGO is an nice R package that works very
well
with the yeast genome, and I would like to use it with E. coli but
almost
no GO terms are apparently available for E. coli when using the tools
provided by AnnotationDbi.
No ecoliK12.db database exists in the repositories, but according to
the
documentation in the AnnotationDbi package, this should be very easy
with
the makeECOLICHIP_DB command from that package.
However, code didn't run. First some modifications had to be done to
the
AnnotationDbi package. I downloaded the sourcecode
(AnnotationDbi_1.6.0.tar.gz). I also made sure that ecoliK12.db0 was
installed (version ecoliK12.db0_2.2.11.tar.gz was used).
In the directory AnnotationDbi/R, the 2 following files were modified.
sqlForge_baseMapBuilder.R:
Comment out line 234:
sql <- "INSERT INTO probe2gene SELECT DISTINCT m.probe_id, u.gene_id \
FROM min_other_rank as m INNER JOIN src.unigene as u WHERE \
m.gene_id=u.unigene_id;"
and line 235:
sqliteQuickSQL(db, sql)
Otherwise one gets the error:
RS-DBI driver: (error in statement: no such table: src.unigene)
sqlForge_tableBuilder.R
Comment out line 181:
sqliteQuickSQL(db, "ANALYZE;")
and lines 3179 and 3180:
sqliteQuickSQL(db, "VACUUM probe_map;")
sqliteQuickSQL(db, "ANALYZE;")
Otherwise one gets the error:
RS-DBI driver: (RS_SQLite_exec: could not execute1: attempt to write a
readonly database)
The package was retarred and installed with:
R CMD INSTALL AnnotationDbi_1.6.0.tar.gz
I also downloaded the annotation file for the ecoli2 array from
affymetrix
(E_coli_2.na28.annot.csv).
R was started and the following commands were given (make sure the
directory 'ecoliK12.db' exist, also the path to the site-library may
vary):
library(AnnotationDbi);library(ecoliK12.db0)
makeECOLICHIP_DB(affy=TRUE,prefix='ecoliK12',fileName="E_coli_2.na28.a
nnot.csv",
baseMapType='eg',chipSrc='/usr/local/lib/R/site-
library/ecoliK12.db0/extdata/chipsrc_ecoliK12.sqlite',
chipMapSrc='/usr/local/lib/R/site-
library/ecoliK12.db0/extdata/chipmapsrc_ecoliK12.sqlite',
chipName='E_coli_2',outputDir='ecoliK12.db',version='2.2.11')
In the ecoliK12.db directory, another ecoliK12.db directory was
created by
those R commands. This directory was tarred (tar -czf
ecoliK12.db_2.2.11.tar.gz ecoliK12.db/) resulting in an installable
package that technically works with topGO.
But not many GO terms are associated with the probes; much less than
the
number of GO terms that can be found for each probe in the probe
annotation file provided by affymetrix.
The table below lists the number of GO terms found in the different
tables
for the three ontologies:
MG1655: the number of GO terms annotated to the probes of MG1655, as
found
in the affymetrix probe annotation file (that array contains also
probes
for other E. coli; they are filtered out for this table).
ecoliK12.db: the number of GO terms that are found in the database
generated by the makeECOLICHIP_DB command from above.
ecoliK12.db0: the number of GO terms that are found in the original
database that makeECOLICHIP_DB uses for generating the ecoliK12.db
database. It should be noted that also in that database, no evidence
codes
occur (the evidence column has everywhere the value '-').
GO_BP_all GO_CC_all GO_MF_all
MG1655 9899 7023 17925
ecoliK12.db 6394 2999 211
ecoliK12.db0 33526 17367 1266
(the comparison was done with the _all tables from the database, to be
able to compare with the affymetrix file)
Why are there not more GO terms found in the ecoliK12.db? Using other
baseMapType than 'eg' does not help. Only 'refseq' doesn't crash, but
even
less GO terms are obtained than with 'eg'. Furthermore, for refseq, I
think some modification has to be done to the cleanRefSeqs function in
sqlForge_baseMapBuilder.R (the line with baseMap[,2] =
sub("\\.\\d+?$",
"", baseMap[,2], perl=TRUE) should be changed to baseMap[,2] =
sub("^[^_]*_([^_]*)_.*", "\\1", baseMap[,2], perl=TRUE)).
Trying to add the GO terms of the affymetrix file afterwards to the
database, doesn't work (no better results in topGO: still only few
(less
than 10) significant nodes when comparing aerobic with anaerobic grown
cells giving more than 2000 differently expressed genes).
A possible problem might be that affymetrix provides also the
redundant GO
terms to the probes and that I added all those to the GO_XX and
GO_XX_all
tables. The GO_XX tables should normally only contain the most
specific GO
terms.
Is this a known problem? Should I give up doing GO analysis with topGO
for
E. coli? Or is there a workaround?
The R version used is R version 2.7.1 (2008-06-23) on Debian (however
for
AnnotationDbi and ecoliK12.db0 the most recent versions were
downloaded
from the bioC website, together with their dependencies) .
Thank you very much for any suggestions,
Gaspard