Annotation and TF-fingerprint files are currently supplied with EXPANDER for yeast, human, mouse, rat, fly, zebrafish and c-elegans and are updated on a regular basis.
The following conventional gene IDs are used in the annotation and TF-fingerprint files:
|
Organism |
ID type |
|
Human |
Entrez / Locus Link |
|
Mouse |
Entrez / Locus Link |
|
Rat |
Entrez / Locus Link |
|
Yeast |
ORF codes |
|
Fly |
Ensembl |
|
c-elegans |
Ensembl |
|
Arabidopsis |
AGI IDs |
|
Zebrafish |
Ensembl |
Gene ID conversion files:
The following gene ID conversions files for Affymetrix chips can be downloaded from the Expander download page. The files map each Affy Id into the corresponding Entrez/LocusLink Id:
|
Organism |
Chip name |
|
Human |
HG-Focus |
|
Human |
HGU1332 |
|
Human |
HG-U95E |
|
Human |
HG-U133A |
|
Human |
HT_HG-U133A |
|
Human |
HG-U133Plus2 |
|
Human |
Hu-35KsubB |
|
Mouse |
MGU74Av2 |
|
Mouse |
MGU430_2 |
|
Mouse |
MG430A2 |
|
Rat |
RGU34A |
|
C-elegans |
C. elegans Genome Chip |
|
Arabidopsis |
ATH1 |
|
Zebra-Fish |
GeneChip Zebrafish Genome Array |
Gene ontology and annotation files:
The gene ontology and annotation files supplied with Expander are based on data that was downloaded from the GO website.
The following table specifies the database from which these files are derived for each of the organisms that we support, and the date of download from GO site:
|
Organism |
Extracted from |
Updated on |
|
Human |
May 2007 |
|
|
Mouse |
May 2007 |
|
|
Rat |
October 2007 |
|
|
Yeast |
October 2007 |
|
|
Fly |
January 2005 |
|
|
c-elegans |
October 2007 |
|
|
Arabidopsis |
TAIR (The Arabidopsis information resource) |
October 2007 |
|
Zebrafish |
May 2007 |
TF fingerprint files:
The following TF fingerprint files can be downloaded from our web download page (as part of the zip supplied for each organism):
|
Organism |
Promoter sequences range |
Promoter sequences origin |
TF Models origin |
|
Human |
3000 bp upstream the TSS to 200 bp downstream the TSS. |
Ensembl web-site (v27, December '04) |
TRANSFAC (version 8.2) |
|
Mouse |
3000 bp upstream the TSS to 200 bp downstream the TSS. |
Ensembl web-site (v27, December '04) |
TRANSFAC (version 8.2) |
|
Rat |
3000 bp upstream the TSS to 200 bp downstream the TSS. |
Ensembl web-site (v27, December '04) |
TRANSFAC (version 8.2) |
|
Yeast |
600 bp upstream CDS to CDS |
SGD database |
TRANSFAC (version 8.2) & Harbison et al. 2004 (see References) |
|
Fly |
3000 bp upstream the TSS to 200 bp downstream the TSS. |
Ensembl web-site (v27, December '04) |
TRANSFAC (version 8.2) |
|
C-elegans |
3000 bp upstream the TSS to 200 bp downstream the TSS. |
Ensembl web-site (v27, December '04) |
TRANSFAC (version 8.2)
|
|
Arabidopsis |
1000 bp upstream the TSS to 200 bp downstream the TSS. |
TAIR: The Arabidopsis Information Resource ( February '06) |
TRANSFAC (version 8.2)
|
|
Zebrafish |
1000 bp upstream the TSS to 200 bp downstream the TSS. |
Ensembl web-site (v27, December '04) |
TRANSFAC (version 8.2) |
Sequence files (For viewing TF binding sites):
The following sequence files can be downloaded from our web download page (as part of the zip supplied for each organism):
|
Organism |
Promoter sequences range |
sequences |
|
Human |
3000 bp upstream the TSS to 200 bp downstream the TSS. |
Ensembl web-site (v27, December '04) |
|
Mouse |
3000 bp upstream the TSS to 200 bp downstream the TSS. |
Ensembl web-site (v27, December '04) |
|
Rat |
3000 bp upstream the TSS to 200 bp downstream the TSS. |
Ensembl web-site (v27, December '04) |
|
Yeast |
600 bp upstream CDS to CDS |
SGD database |
|
Fly |
3000 bp upstream the TSS to 200 bp downstream the TSS. |
Ensembl web-site (v27, December '04) |
|
C-elegans |
3000 bp upstream the TSS to 200 bp downstream the TSS. |
Ensembl web-site (v27, December '04) |
|
Arabidopsis |
1000 bp upstream the TSS to 200 bp downstream the TSS. |
TAIR ( February '06) |
|
Zebrafish |
1000 bp upstream the TSS to 200 bp downstream the TSS. |
Ensembl web-site (v27, December '04) |