Statistics

General
Species Numbers 16
Map Numbers 707 in total
Metabolic Maps 456
Gene Family Maps 251
Compound Numbers 38243 in total
KEGG Compound 17176
KEGG Glycan 10985
KEGG Drug 10082
Reaction Numbers 28367 in total
KEGG Reaction 9522 (R00*****. ***** is the number part of KEGG REACTION ID)
KEGG ORTHOLOGY 17479 (R10*****. ***** is the number part of KEGG ORTHOLOGY ID)
Others
1366 (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) 9176 on the maps, 28959 in the database (KEGG hsa)
Mus musculus (mouse) 9925 on the maps, 25398 in the database (KEGG mmu)
Rattus norvegicus (rat) 9929 on the maps, 23615 in the database (KEGG rno)
Caenorhabditis elegans (nematode) 3437 on the maps, 44504 in the database (KEGG cel)
Drosophila melanogaster (fruit fly) 3843 on the maps, 15395 in the database (KEGG dme)
Plants
Arabidopsis thaliana (thale cress) 6057 on the maps, 27464 in the database (KEGG ath)
Oryza sativa (Japanese rice) 5065 on the maps, 28524 in the database (KEGG osa)
Populus trichocarpa (black cottonwood, poplar) 6673 on the maps, 40529 in the database (KEGG pop)
Ricinus communis (castor bean) 4564 on the maps, 31412 in the database (KEGG rcu)
Sorghum bicolor (sorghum) 4936 on the maps, 33079 in the database (KEGG sbi)
Vitis vinifera (wine grape) 5130 on the maps, 22747 in the database (KEGG vvi)
Vitis vinifera (wine grape), draft genome (CRIBI) 5440 on the maps, 29927 in the database (KEGG T10027)
Zea mays (maize) 4760 on the maps, 22638 in the database (KEGG zma)
Physcomitrella patens subsp. patens 4618 on the maps, 35996 in the database (KEGG ppp)
Chlamydomonas reinhardtii (KEGG cre) 2306 on the maps, 14473 in the database (KEGG ppp)
Bacteria
Escherichia coli K-12 MG1655 2180 on the maps, 4497 in the database (KEGG eco)
Saccharomyces cerevisiae (budding yeast) 2597 on the maps, 6330 in the database (KEGG sce)
Correlation Data (gene-to-gene)
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
Vitis vinifera (wine grape), draft genome CRIBI Gene code (V1 new) CRIBI Gene code (V1 new) / VIT_00s0120g00010
KEGG vvi T10027 Draft dVvi
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
Chlamydomonas reinhardtii KEGG Entry ID KEGG Entry ID / CHLREDRAFT_183515
NCBI Entrez Gene ID / 5715011
KEGG cre * Cre
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.