The following files 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 |
Ensembl release 53 |
TargetScan website version 5 |
UCSC genome browser Jan 09 |
KEGG data base November 09, WikiPathways March 2013 |
|
|
Baker's yeast |
30.6MB |
NCBI - October 2009 |
SGD database 1.01 |
- |
- |
KEGG data base November 09, WikiPathways March 2013 |
|
S. pombe |
15.7MB |
NCBI -November 2008 |
Sanger GeneDB - October 2008 |
- |
- |
KEGG data base November 09, WikiPathways March 2013 |
|
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, WikiPathways March 2013 |
|
Rat |
280MB |
NCBI - Oct 2009 |
Ensembl release 56 |
- |
UCSC genome browser Jan 09 |
KEGG data base November 09, WikiPathways March 2013 |
|
Fly |
218MB |
NCBI - Oct 2009 |
Ensembl release 53 |
TargetScan website version 5 |
UCSC genome browser Jan 09 |
KEGG data base November 09, WikiPathways March 2013 |
|
C-elegans |
278Mb |
NCBI - Oct 2009 |
Ensembl release 56 |
TargetScan website version 5 |
UCSC genome browser Jan 09 |
KEGG data base November 09, WikiPathways March 2013 |
|
Arabidopsis |
267MB |
NCBI - Oct 2009 |
TAIR - December 2006 |
- |
- |
KEGG data base November 09, WikiPathways March 2013 |
|
Zebra Fish |
254Mb |
NCBI - Oct 2009 |
Ensembl release 53 |
- |
UCSC genome browser Jan 09 |
KEGG data base November 09, WikiPathways March 2013 |
|
Chicken |
205Mb |
NCBI - Oct 2009 |
Ensembl release 56 |
- |
- |
KEGG data base November 09, WikiPathways March 2013 |
|
1.7Mb |
EBI - March 2009 |
- |
- |
- |
- |
|
|
A.Fumigatus |
72.5Mb |
EBI - Jan 2010 |
Kevin |
- |
- |
KEGG data base November 09 |
|
E. coli |
1.25MB |
EBI - April 2008 |
Not available yet |
- |
- |
- |
|
Rice |
170MB |
GO DB Dec 2010 |
Bioinformatics Core database Washington State University |
- |
- |
KEGG data base November 10 |
|
Leishmania |
2MB |
Zilberstein D. lab Technion - Israel Nov 2011 |
- |
- |
- |
- |
* Users of this product may not download large quantities of KEGG Data.
Gene ID conversion files:
Gene ID conversion files for many of the Affymetrix chips can be downloaded from the Expander download page. The files map each Affymetrix Id into the corresponding gene Id. Conversion files are generated and added to the download page according to user requests. If you can't find the file you need here, please look it up in the download page, and contact us if it's not there.
|
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 |
|
Mouse |
MGU74Av2 |
|
Mouse |
MGU430_2 |
|
Mouse |
MG430A2 |
|
Mouse |
MoGene-1_0-ST |
|
Rat |
RGU34A |
|
Rat |
Rat230_2 |
|
Rat |
Agilent |
|
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 |
Network files :
|
Organism |
File name |
Network origin |
|
Human |
Expander.hsa.RualNature05.sif |
Towards a proteome-scale map of the human protein-protein interaction network by Rual JF et al. Nature. 437(7062):1173-8 (2005) |
|
Human |
Expander.hsa.IntAct.sif |
IntAct database (http://www.ebi.ac.uk/intact/) |
|
Mouse |
Expander.mmu.IntAct.sif |
IntAct database (http://www.ebi.ac.uk/intact/) |
|
Rat |
Expander.rno.IntAct.sif |
IntAct database (http://www.ebi.ac.uk/intact/) |
|
Worm |
Expander.cel.SimonisNatMethods08.sif
|
Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network by Simonis N. et al. Nature Methods 6, 47 - 54 (2009) |
|
Fly |
Expander.dme.DroID.sif |
DroID database (http://www.droidb.org/) |
|
Yeast |
Expander.sce.United.sif |
1. High-Quality Binary Protein Interaction Map of the Yeast Interactome Network by Yu et al. Science 322(5898):104 – 110 (2008) 2. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae by Reguly et al. Journal of Biology 5(4):11 (2006) 3. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae by Collins SR et al. Molecular Cell Proteomics 6(3):439-50 (2007) |
|
Arabidopsis |
Expander.ath.TAIR.sif |
TAIR database (http://www.arabidopsis.org/) |
|
E. coli |
Expander.eco.Arifuzzaman06.txt |
Large-scale identification of protein–protein interaction of Escherichia coli K-12 by Arifuzzaman M et al. Genome Research 16(5):686-91. (2006) |