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 |
545MB |
Ensembl database release 89 |
TargetScan website version 5 |
UCSC genome browser on August 2012 |
KEGG data base November 09, |
|
|
WikiPathways |
||||||
|
Sep-17 |
||||||
|
Baker's yeast |
72.2MB |
Ensembl database release 89 |
- |
- |
KEGG data base November 09, |
|
|
WikiPathways |
||||||
|
Sep-17 |
||||||
|
S. pombe |
72.3MB |
Ensembl database release 36 |
- |
- |
KEGG data base November 09, |
|
|
|
||||||
|
|
||||||
|
Listeria monocytosenes EGD-e |
1.74MB |
Not available |
- |
- |
KEGG data base November 09 |
|
|
Mouse |
419MB |
Ensembl database release 89 |
TargetScan website version 5 |
UCSC genome browser on August 2012 |
KEGG data base November 09, |
|
|
WikiPathways |
||||||
|
Sep-17 |
||||||
|
Rat |
262MB |
NCBI (May 2017) |
Ensembl database release 89 |
- |
UCSC genome browser on Mar 2012 |
KEGG data base November 09, |
|
WikiPathways |
||||||
|
Sep-17 |
||||||
|
Fly |
235MB |
NCBI (May 2017) |
Ensembl database release 89 |
TargetScan website version 5 |
UCSC genome browser on Mar 2012 |
KEGG data base November 09, |
|
WikiPathways |
||||||
|
Sep-17 |
||||||
|
C-elegans |
278Mb |
Ensembl database release 89 |
TargetScan website version 5 |
UCSC genome browser on Mar 2012 |
KEGG data base November 09, |
|
|
WikiPathways |
||||||
|
Sep-17 |
||||||
|
Arabidopsis |
345MB |
Ensembl database release 36 |
- |
- |
KEGG data base November 09, |
|
|
WikiPathways |
||||||
|
Sep-17 |
||||||
|
Zebra Fish |
333Mb |
Ensembl database release 89 |
- |
UCSC genome browser on August 2012 |
KEGG data base November 09, |
|
|
WikiPathways |
||||||
|
Sep-17 |
||||||
|
Chicken |
90.4Mb |
Ensembl database release 89 |
- |
- |
KEGG data base November 09, |
|
|
WikiPathways |
||||||
|
Sep-17 |
||||||
|
347Mb |
SGN database on June 2017 |
Ensembl database release 36 |
- |
UCSC genome browser on August 2012 |
- |
|
|
A.Fumigatus |
79.3Mb |
Kevin |
- |
- |
KEGG data base November 09 |
|
|
Verstrepen's lab (via private communication with Nir |
||||||
|
Osherov) |
||||||
|
E. coli |
32MB |
UCSC microbes |
- |
- |
- |
|
|
Rice |
360MB |
Ensembl database release 36 |
- |
- |
KEGG data base Jan 11 |
|
|
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/) |
|
Human |
ppi.IntAct.sif |
IntAct database (2017) |
|
Mouse |
Expander.mmu.IntAct.sif |
IntAct database (http://www.ebi.ac.uk/intact/) |
|
Mouse |
ppi.IntAct.sif |
IntAct database (2017) |
|
Rat |
Expander.rno.IntAct.sif |
IntAct database (http://www.ebi.ac.uk/intact/) |
|
Rat |
ppi.IntAct.sif |
IntAct database (2017) |
|
Zebrafish |
ppi.IntAct.sif |
IntAct database (2017) |
|
C.elegans |
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) |
|
C.elegans |
ppi.IntAct.sif |
IntAct database (2017) |
|
Fly |
ppi.IntAct.sif |
IntAct database (2017) |
|
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) |
|
Yeast |
ppi.IntAct.sif |
IntAct database (2017) |
|
S.pombe |
ppi.IntAct.sif |
IntAct database (2017) |
|
Arabidopsis |
Expander.ath.TAIR.sif |
TAIR database (http://www.arabidopsis.org/) |
|
Arabidopsis |
ppi.IntAct.sif |
IntAct database (2017) |
|
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) |
|
E. coli |
ppi.IntAct.sif |
IntAct database (2017) |
|
Rice |
ppi.IntAct.sif |
IntAct database (2017) |