KCPAVS features‎ > ‎

Integrated data

Data sources that are used by KCPAVS
  • KEGG Pathway/Maps from ~25 organism (list is provided below)
  • KEGG compound and glycan (webservice)
  • Uniprot knowledge base
  • Enzyme
  • Gene ontology
  • IPI
  • PIR
  • PubMed webservices
For Id-mapping data-sources used in KCPAVS see below.

Platforms, Organisms and Identifiers supported in KCPAVS

KCPAVS supports the upload and analysis of multiple organism (~18 organims listed below) plus the small molecule/chemical/drug identifiers. Mapping the identifiers/sequences between the organism is enential process ( usually done manually by researchers) needed for analyzing data sets from multiple animal models. This time-consuming task can be now avoided, biologist can focus their efforts in efficient biological interpretation of data while using KCPAVS.

KCPAVS supports analysis of molecular data for the following species through ortholog mapping of 
Uniprot accession or ids for protein, Entrez Gene IDs for genes, refseq identifiers for rna for the following orgnaisms:

    Species supported in KCPAVS

Taxon_gif
Figure from www.uniprot.org/taxonomy
    • Homo sapiens (human)    9606    hsa
    • Mus musculus (mouse)    10090    mmu
    • Rattus norvegicus (rat)    10116    rno
    • Canis familiaris (dog)    9615    cfa
    • Bos taurus (cow)    9913    bta
    • Danio rerio (zebrafish)    7955    dre
    • Gallus gallus (chicken)    9031    gga
    • Drosophila melanogaster (fruit fly)    7227    dme
    • Caenorhabditis elegans (nematode)    6239    cel
    • Arabidopsis thaliana (thale cress)    3702    ath
    • Oryza sativa japonica (Japanese rice)    39947    osa
    • Saccharomyces cerevisiae (budding yeast)    559292    sce
    • Yarrowia lipolytica    284591    yli
    • Schizosaccharomyces pombe (fission yeast)    284812    spo
    • Dictyostelium discoideum (cellular slime mold)    44689    ddi
    • Escherichia coli K-12 MG1655    511145    eco
    • Pseudomonas aeruginosa PA7    381754    pap
    • Pseudomonas putida KT2440    160488    ppu
    • Pseudomonas fluorescens Pf-5    220664    pfl
    • Staphylococcus aureus N315 (MRSA/VSSA)    158879    sau
    • Thermotoga maritima    243274    tma
    • Bacillus subtilis    1423    bsu
    • Bacillus anthracis Ames    1392    ban
    • Methanocaldococcus jannaschii    243232    mja
    • Methanothermobacter thermautotrophicus    187420    mth
    • Sulfolobus acidocaldarius    330779    sai

        Identifiers supported in KCPAVS

        The identifiers come from the following data sources were downlaoded and were then integrated together using our custom written loaders

        Data Sources that were used for collecting Identifiers
    • Uniprot idmapping files
    • PIR idmapping files
    • IPI idmapping files
    • Gene ontology annotation project
    • KEGG links (idmapping files)
    • ChEBI mapping file
    • Pubchem mapping file
    • KEGG compound and glycan (web service)
        KCPAVS supports the mapping of several standard identifiers such as 

        Sequence identifiers
    • Uniprot (Swissprot and Trembl)
    • Ensembl
    • Entrez (gene ids and symbol)
    • GenBank/EBL/DDBJ
    • Refseq(gene and protein)
    • Gene Symbol (Hugo, MGI, RGD and other organism)
    • IPI
    • GI (protein)
    • HGNC
    • MGI
    • RGD
    • Unigene

        Chemical identifiers
    • ChEBI
    • DRUGBANK
    • KEGG GLYCAN
    • KEGG Compound
    • KEGG gene
    • KEGG KO
    • Pubchem (substance and compound) 

        Experimental platfroms supported in KCPAVS

    • Gene Expression platform (mRNA, netx-gen sequencing (NGS), qPCR)
    • Proteomics
    • Metabolomics



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