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Supplied Files

 

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

NCBI - Oct 2009,GOA@EBI - Nov 2008

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

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

-

-

-

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)

 

 


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