Welcome to KEGG based Collaborative Pathway Analysis and Visualization System for Comparative Biological Studies
 
KCPAVS is an integrated software platform having features required at different stages of biological research using pathway data. KCPAVS is highly interactive, user friendly, unified web server for: 1) browsing and searching KEGG metabolic -, signaling-, disease- pathways and global maps of ~25 organisms; 2) pathway analysis using general statistical methods like Fisher's test and Binomial proportions test and by specialized algorithms like like PAGE;  3) visualizing experimental data and analysis reports; 4) comparative pathway analysis;   5) collaboration and mind mapping on a pathway to exchange information and ideas;  and 6) accumulation of annotations from the biological research community and serving as a knowledge-base.


Organisms supported ( 25 species) :
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

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KCPAVS Features (click on the icons below for details or here for comparison charts)

 
Web based integrated software platform offering single point of access to information and tools
Get integrated data and tools for data management,  analysis and visualization all in one software accessible online.
Supports all the latest versions of Mac, Windows and Linux

Integrated data
KEGG global metabolic maps and KEGG pathways ( including metabolic, organismal, cellular processes and disease pathways).
Molecular annotations from Uniprot, Enzyme  data and Gene ontology.
Supports several identifiers for protein, gene and small molecules collated from from IPI, Uniprot, KEGG, PIR, Chebi and other databases.
 
User data management and comparison
Easily import experimental data.
Supports several identifiers for complete recognition and mapping of user data.
Manage experimental (sets of observations) data by creating logical groups.
Copy and move records across groups.
Use SET operation tools for finding Intersections, differences and union of two lists.

Powerful visualization
Overlay multidimensional experimental data on pathway diagrams
Customize overlay settings to suite your data
Visualize multiple data types simultaneously using shapes, fill color, symbols
Visualize multidimensional data using embedded charts and heat maps overlaid on pathway diagram

Analysis and reports
Implements several pathway analysis algorithm including Binomial proportion test, Fisher's exact test and Parametric Analysis of Gene-set Enrichment (PAGE).
Allows filter and customize pathway sets used in analysis in particular context
Compare analysis results in tabular, chart representations
Generate comprehensive customized publication quality reports in PDF, HTML and Excel formats 
 
Meticulously designed GUI
Designed after "all in one screen" concept. Get accesses to tools, contextual data and reports being in one screen
Easily browse pathways and its components
Enabled with simple and advanced search functionality. Search uses Apache Lucene technology allows Boolean, fuzzy, range and field searches
Search and filter capability is enabled for every grid displaying data
 
Downloads in standard and convenient formats
Dowload KEGG Pathways as SBML, BioPAX, SIF, XGMML, CSV and Tab-delimited (gene sets).
Allows individual pathway, batch and bulk download
Download pathways, gene list, annotations, analysis reports
Pathway diagram can be downloaded as interactive SVG, PDF and in other graphic formats like PNG and JPG.
The downloads can be complete pathway diagram or zoomed in region of the pathway.
Downloaded diagrams can also include overlays and annotations added by users.
 
Mind mapping and peer to peer collaboration capability
Use this tool as thinking aid(mind mapping tool).
Pick a symbols closely representing your concept from the library of readily available symbols while working with a pathway(s), thus assisting you in hypothesis generation or designing experiments.
Use tools and add custom annotation (text, shapes and symbols) for a pathway
Export the annotations as BioPAX; then email to your collaborators who could import that file which recreates the exact annotation that you made over the pathways.
Browser compatibility
Supports most of the widely used browsers like IE 9.0, IE 8.0, Firefox, Chrome, Safari, Opera.
Uses Scalable vector graphics (SVG) and Ajax for presentation of data, which has built in support by most of the modern browsers listed above                                                         
   KEGG XML (KGML) Converter
Supports conversion of KGML format to several standard and convenient formats.
Formats currently supported are SBML, CellDesigner, BioPax, SIF, XGMML, SVG and Txt.