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External Requests
NetworkAnalyst now accepts gene lists generated from other tools or databases. Please use the API defined below:
dataType: "html",
type: "POST",
url: 'http://www.networkanalyst.ca/NetworkAnalyst/faces/NAER_LIST',
data: {
organism: org.code,
idtype: id.code,
genes: gene.list
}
organism: the three letters org.code:
hsa - H. sapiens (human)
mmu - M. musculus (mouse)
rno - R. norvegicus (rat)
cel - C. elegans (roundworm)
dme - D. melanogaster (fruitfly)
dre - D. rerio (zebrafish)
sce - S. cerevisiae (yeast)
bta - B. taurus (cow)
gga - G. gallus (chicken)
cjo - C. japonica (japanese quail)
eco - E. coli
bsu - B. subtilis
pae - P. aeruginosa
mtb - M. tuberculosis
tbr - T. brucei (trypanosoma)
pfa - P. falciparum (malaria)
ath - A. thaliana (Arabidopsis)
idtype: entrez is the primary ID in NetworkAnalyst. Generic and organism-specific id.code are given below:
Human gene IDs:
entrez - Entrez ID
refseq - RefSeq ID
genbank - Genbank ID
symbol - Official Gene Symbol
emblgene - Ensembl Gene ID
embl_transcript - Ensemble Transcript ID
emblprotein - Ensembl Protein ID
hgu95a - Affymetrix Human Genome U95 (chip hgu95a)
hgu95av2 - Affymetrix Human Genome U95 (chip hgu95av2)
hgu95b - Affymetrix Human Genome U95 (chip hgu95b)
hgu95c - Affymetrix Human Genome U95 (chip hgu95c)
hgu95d - Affymetrix Human Genome U95 (chip hgu95d)
hgu95e - Affymetrix Human Genome U95 (chip hgu95e)
hgu133a - Affymetrix Human Genome U133 (chip hgu133a)
hgu133b - Affymetrix Human Genome U133 (chip hgu133b)
hgu133plus2 - Affymetrix Human Genome U133plus2 (hgu133plus2)
hgu133plus2pm - Affymetrix Human Genome U133plus2_PM (hgu133plus2pm)
lumiht12v3 - Illumina HumanHT-12 V3 BeadArray
lumiht12v4 - Illumina HumanHT-12 V4 BeadArray
lumiref8v2 - Illumina HumanRef-8 V2 BeadArray
lumiref8v3 - Illumina HumanRef-8 V3 BeadArray
lumiwg6v2 - Illumina HumanWG-6 V2 BeadArray
lumiwg6v3 - Illumina HumanWG-6 V3 BeadArray
agi4100a - Agilent Human 1 cDNA Microarray (4100A)
agi4101a - Agilent Human 2 cDNA Microarray (4101A)
agi4110b - Agilent Human 1A cDNA Microarray (4110B)
agi4111a - Agilent Human 1B cDNA Microarray (4111A)
agi4112a - Agilent Human Genome Whole Microarray (4x44k/4112)
agi4845a - Agilent Human AMADID 026652 Microarray (4845A)
Mouse gene IDs:
entrez - Entrez ID
refseq - RefSeq ID
genbank - Genbank ID
symbol - Official Gene Symbol
emblgene - Ensembl Gene ID
embl_transcript - Ensemble Transcript ID
emblprotein - Ensembl Protein ID
lumiwg6v1 - Illumina MouseWG-6 v1.0 Bead Array
lumiwg6v2 - Illumina MouseWG-6 v2.0 Bead Array
lumiref8v1 - Illumina MouseRef-8 v1.0 Bead Array
lumiref8v2 - Illumina MouseRef-8 v2.0 Bead Array
mgu74a - Affymetrix Murine Genome U74v2 (chip mgu74a)
mgu74av2 - Affymetrix Murine Genome U74v2 (chip mgu74av2)
mgu74b - Affymetrix Murine Genome U74v2 (chip mgu74b)
mgu74bv2 - Affymetrix Murine Genome U74v2 (chip mgu74bv2)
mgu74c - Affymetrix Murine Genome U74v2 (chip mgu74c)
mgu74cv2 - Affymetrix Murine Genome U74v2 (chip mgu74cv2)
moe430a - Affymetrix Mouse Expression Set 430 (chip moe430a)
moe430b - Affymetrix Mouse Expression Set 430 (chip moe430b)
moe430_2 - Affymetrix GeneChip Mouse Genome 430 2.0
mgi_st1 - Affymetrix Mouse Gene 1.0 ST Array
mgu4101a - Agilent Mouse Array (chip mgug4104a)
mgu4120a - Agilent Mouse Array (chip mgug4120a)
mgu4121a - Agilent Mouse Array (chip mgug4121a)
mgu4122a - Agilent Mouse Array (chip mgug4122a)
Generic IDs:
entrez - Entrez ID
emblgene - Ensembl Gene ID
embl_transcript - Ensembl Transcript ID
uniprot - Uniprot Protein ID
symbol - Official Gene Symbol
In addition to the generic IDs, the specific id.code are supported for the organisms below:
Fruitfly: flybase - Flybase ID
Yeast: orfid - Open Reading Frame Identifiers
Arabidopsis: tair - Tair ID
P. aeruginosa: paelocus - Locus Tag
E. coli: ecogene - Ecocyc Gene ID
genes: same format as NetworkAnalyst gene list input. A small example data is shown below
(first column: Entrez ID, second column: fold change):
5743 24.25
3552 21.85
6364 14.64
3553 13.07
10148 10.87
6349 9.19
3620 -8.38
50486 -7.25
2919 -6.96
3557 -6.4
629 -6.07
27074 -6.02
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