The following files can be downloaded from the Expander download page, and
include gene info files: Gene ID conversion files, GO annotation files, TF
fingerprint files, promoter sequences, miRNA target scan files,
chromosomal position files, and biological pathway files, taken from the KEGG
database*. These files should be extracted into "Expander/organisms"
directory.
|
Organism |
Size after extraction |
Origin of GO annotations | Origin of sequences used for generating TF-fingerprint files | Origin of miRNA targets data files: | Origin of chromosomal location data files | Origin of pathway data files |
|
Human |
431MB |
NCBI - Oct 2009, GOA@EBI - Nov 2008 | Ensembl release 53 | TargetScan website version 5 | UCSC genome browser Jan 09 | KEGG data base November 09 |
|
Baker's yeast |
30.6MB |
NCBI - October 2009 | SGD database 1.01 | - | - | KEGG data base November 09 |
|
S. pombe |
15.7MB |
NCBI - November 2008 | Sanger GeneDB - October 2008 | - | - | KEGG data base November 09 |
|
Listeria monocytosenes EGD-e |
1.74MB |
Blast2GO - February 2009 | Not available | - | - | KEGG data base November 09 |
|
Mouse |
338MB |
NCBI - Oct 2009 | Ensembl release 53 | TargetScan website version 5 | UCSC genome browser Jan 09 | KEGG data base November 09 |
|
Rat |
280MB |
NCBI - Oct 2009 | Ensembl release 56 | - | UCSC genome browser Jan 09 | KEGG data base November 09 |
|
Fly |
218MB |
NCBI - Oct 2009 | Ensembl release 53 | TargetScan website version 5 | UCSC genome browser Jan 09 | KEGG data base November 09 |
|
C-elegans |
278Mb |
NCBI - Oct 2009 | Ensembl release 56 | TargetScan website version 5 | UCSC genome browser Jan 09 | KEGG data base November 09 |
|
Arabidopsis |
267MB |
NCBI - Oct 2009 | TAIR - December 2006 | - | - | KEGG data base November 09 |
| Zebra Fish (for version 5.08 and higher) | 254Mb | NCBI - Oct 2009 | Ensembl release 53 | - | UCSC genome browser Jan 09 | KEGG data base November 09 |
| chickenData5.08.zip">Chicken (for version 5.08 and higher) | 205Mb | NCBI - Oct 2009 | Ensembl release 56 | - | - | KEGG data base November 09 |
| Tomato | 1.7Mb | EBI - March 2009 | - | - | - | - |
| A. Fumigatus | 72.5Mb | EBI - Jan 2010 | Kevin Verstrepen's lab (via private communication with Nir Osherov) |
- | - | KEGG data base November 09 |
|
E. coli |
1.25MB |
EBI - April 2008 | Not available yet | - | - | - |
* Users of this product may not download large quantities of KEGG Data.
Gene ID conversion files:
The following table contains gene Id conversion files for several Affymetrix chips. The files map each probe ID into the corresponding gene IDs depending on the analyzed organism (for further details refer to the supplied files section in the user manual), and should be loaded via the "Conversion File" field in the data load dialog, or by selecting Data>>Load Conversion File from the Expander menu.
|
Organism |
Chip name |
|
Human |
HG-Focus |
|
Human |
HGU1332 |
|
Human |
HG-U95E |
|
Human |
HG-U133A |
|
Human |
HT_HG-U133A |
|
Human |
HG-U133Plus2 |
|
Human |
Hu-35KsubB |
|
Human |
HuGene-1_0-ST |
|
Human |
HuEx-1_0-ST-v2 |
| Human | Agilent 014850 |
|
Mouse |
MGU74Av2 |
|
Mouse |
MGU430_2 |
|
Mouse |
MG430A2 |
|
Mouse |
MoGene-1_0-ST |
|
Listeria |
TIGR oligos |
|
Rat |
RGU34A |
|
Rat |
Rat230_2 |
|
Rat |
Agilent |
|
Rat |
RatGene-1_0-ST |
|
C-elegans |
C. elegans Genome Chip |
|
Arabidopsis |
ATH1 |
|
Zebra-Fish |
GeneChip Zebrafish Genome Array |
|
Chicken |
Affymetrix Chicken Genome Chip |
|
E. coli |
Affymetrix E. coli Antisense Genome Array |
|
E. coli |
Affymetrix E. coli Genome 2.0 Array |
|
Baker's yeast |
Affymetrix S. cerevisiae Genome 2.0 Array |