Statistics

General
Species Numbers 15
Map Numbers 724 in total
Metabolic Maps 436
Gene Family Maps 288
Compound Numbers 37751 in total
KEGG Compound 16957
KEGG Glycan 10980
KEGG Drug 9814
Reaction Numbers 26944 in total
KEGG Reaction 9229 (R00*****. ***** is the number part of KEGG REACTION ID)
KEGG ORTHOLOGY 16435 (R10*****. ***** is the number part of KEGG ORTHOLOGY ID)
Others
1280 (R20*****. ***** is sequentially assinged number. It will alter by data updating)

* KaPPA-View KEGG Reaction IDs:
The description about the origin of R10***** and R02***** written above is right, and it is different from the supplemental file of KaPPA-View4 paper (Sakurai et al 2011, NAR 39: 677-).

Genes
Animals
Homo sapiens (human) 8706 on the maps, 26232 in the database (KEGG hsa)
Mus musculus (mouse) 9499 on the maps, 23119 in the database (KEGG mmu)
Rattus norvegicus (rat) 9628 on the maps, 23180 in the database (KEGG rno)
Caenorhabditis elegans (nematode) 2584 on the maps, 44504 in the database (KEGG cel)
Drosophila melanogaster (fruit fly) 3462 on the maps, 14982 in the database (KEGG dme)
Plants
Arabidopsis thaliana (thale cress) 5746 on the maps, 27464 in the database (KEGG ath)
Oryza sativa (Japanese rice) 4711 on the maps, 28524 in the database (KEGG osa)
Populus trichocarpa (black cottonwood, poplar) 6176 on the maps, 40529 in the database (KEGG pop)
Ricinus communis (castor bean) 4160 on the maps, 31412 in the database (KEGG rcu)
Sorghum bicolor (sorghum) 4561 on the maps, 33079 in the database (KEGG sbi)
Vitis vinifera (wine grape) 4733 on the maps, 22733 in the database (KEGG vvi)
Zea mays (maize) 4382 on the maps, 22421 in the database (KEGG zma)
Physcomitrella patens subsp. patens 4350 on the maps, 35996 in the database (KEGG ppp)
Bacteria
Escherichia coli K-12 MG1655 2159 on the maps, 4496 in the database (KEGG eco)
Saccharomyces cerevisiae (budding yeast) 2548 on the maps, 6331 in the database (KEGG sce)
Correlation Data (gene-to-gene)
Arabidopsis thaliana Ath: ATTED-II c4.1 (1388 chips) MR <= 100
Ath: ATTED-II c4.1 (1388 chips) PCC >= 0.6
Ath: ATTED-II c4.1 (1388 chips) PCC <= -0.6
Ath: CoP (5257 chips) CCC Co-expressed Genes
Oryza sativa Osa: ATTED-II c1.0 (208 chips) MR <= 100
Osa: CoP (432 chips) CCC Co-expressed Genes
Homo sapiens Hsa: COXPRESdb c3.1 (4401 chips) MR <= 100
Hsa: COXPRESdb c3.1 (4401 chips) PCC >= 0.6
Hsa: COXPRESdb c3.1 (4401 chips) PCC <= -0.5
Mus musculus Mmu: COXPRESdb c2.1 (2226 chips) MR <= 100
Mmu: COXPRESdb c2.1 (2226 chips) PCC >= 0.6
Mmu: COXPRESdb c2.1 (2226 chips) PCC <= -0.6
Rattus norvegicus Rno: COXPRESdb c1.1 (632 chips) MR <= 100
Rno: COXPRESdb c1.1 (632 chips) PCC >= 0.6
Rno: COXPRESdb c1.1 (632 chips) PCC <= -0.6
PCC: Pearson's Correlation Coefficient
CCC: Cosign theta Correlation Coefficient
MR: Mutual Rank
Co-expressed Genes: Gene-to-gene relationships evaluated as significant co-expressions in CoP
Gene and Probe Infromation
Species Gene ID Probe ID / Sample Array Type Abbr.
Animals
Homo sapiens (human) KEGG Entry ID KEGG Entry ID / 9081
(= NCBI Entrez Gene ID)
KEGG hsa Hsa
Mus musculus (mouse) KEGG Entry ID KEGG Entry ID / 620017
(= NCBI Entrez Gene ID)
KEGG mmu Mmu
Rattus norvegicus (rat) KEGG Entry ID KEGG Entry ID / 297970
(= NCBI Entrez Gene ID)
KEGG rno Rno
Caenorhabditis elegans (nematode) KEGG Entry ID KEGG Entry ID / W10C8.2
NCBI Entrez Gene ID / 171849
KEGG cel * Cel
Drosophila melanogaster (fruit fly) KEGG Entry ID KEGG Entry ID / Dmel_CG33116
NCBI Entrez Gene ID / 326259
KEGG dme * Dme
Plants
Arabidopsis thaliana (thale cress) KEGG Entry ID KEGG Entry ID / AT2G17870
NCBI Entrez Gene ID / 816297
KEGG ath * Ath
Oryza sativa (Japanese rice) KEGG Entry ID KEGG Entry ID / 4326813
(= NCBI Entrez Gene ID)
KEGG osa Osa
Affymetrix Rice GeneChip probe ID / Os.1.1.S1_s_at Affy Rice Probe ID
Populus trichocarpa (black cottonwood, poplar) KEGG Entry ID KEGG Entry ID / POPTR_706161
NCBI Entrez Gene ID / 7485705
KEGG pop * Pop
Ricinus communis (castor bean) KEGG Entry ID KEGG Entry ID / RCOM_0524530
NCBI Entrez Gene ID / 8258020
KEGG rcu * Rcu
Sorghum bicolor (sorghum) KEGG Entry ID KEGG Entry ID / SORBI_02g029460
NCBI Entrez Gene ID / 8054797
KEGG sbi * Sbi
Vitis vinifera (wine grape) KEGG Entry ID KEGG Entry ID / 100262800
(= NCBI Entrez Gene ID)
KEGG vvi Vvi
Nimblegen's Grape Microarray / VitusP00052349 NimbleGen vvi
Zea mays (maize) KEGG Entry ID KEGG Entry ID / 542476
(= NCBI Entrez Gene ID)
KEGG zma Zma
Physcomitrella patens subsp. patens KEGG Entry ID KEGG Entry ID / PHYPADRAFT_158468
NCBI Entrez Gene ID / 5914413
KEGG ppp * Ppp
Bacteria
Escherichia coli K-12 MG1655 KEGG Entry ID KEGG Entry ID / b0001
NCBI Entrez Gene ID / 944742
KEGG eco * Eco
Saccharomyces cerevisiae (budding yeast) KEGG Entry ID KEGG Entry ID / YAL068C
NCBI Entrez Gene ID / 851229
KEGG sce * Sce

The gene information file and probe information file for each species are available from "Download" function after log-in. Check on "Information" for Data Type and press "Search" button. Then all the information files used in the KaPPA-View4 system will be listed. Please see the files named Abbr_geneInfo_DATE.csv for gene information (File Type: Gene) and Abbr_featureGene_DATE.csv for probe information (File Type: Feature).Quantitative gene expression data should be described with the proper probe IDs and should be uploaded as corresponding Array Type.

* In addition to the KEGG Entry ID, the NCBI Entrez Gene ID (If it exists) can be accepted by the Array Type. When two quantitative data for the same gene are described in both KEGG Entry ID and NCBI Entrez Gene ID in the data file, the quantitative value will be averaged when it represented on the pathway maps.