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Comparison of iPAVS with other databases

For detailed comparison of features between iPAVS and some of the useful, open access pathway databases and web based tools (such as Reactome, Nature NCI-PID, KEGG, Pathwaycommons, ConsensusPathDB, Panther, Payao, CellPublisher) 

Key Features



Example of Databases and online analysis tools supporting the feature

Data & Standards

Pathway types curated






Reactome, PID, KEGG, Panther



Reactome, KEGG, Panther

Gene regulatory network


KEGG, Panther



Reactome, KEG

Various Cell types



Tissue and Organ



Drug action


Pharmakgb, KEGG

Perturbed conditions



Integrates curated information with data integrated form other external databases

Uniprot, GO, Enzyme, IPI, PIR


Provides links to external databases


Most of them do

Categorical selection of pathways while analysis


Some commercial products

Cell subcellular compartment information registered with pathway model and displayed

IPAVS, Panther, Reactome,KEGG

Summary of pathway





Curation of pathway information at level of




Others DBs






PID, Reactome,SBI



KEGG, Reactome,Panther




Allows download of pathways in SBML, BioPAX, Cytoscape standard format



Allows download of component lists



Allows download of pathways



Allows download of pathways with visual cues



Allows bulk export of pathways



Import of data in SBML and BioPAX formats



Uses an open access freely available tool for content curation



Support import of pathway from other tools ( as long as co-ordinate information avaialble and is in SBML format + generate a graphic output in SVG, JPG or PNG)



Data Manipulation, Comparison, Search and  Browsing

Simple search

IPAVS,Reactome (12), PID (13), KEGG (14), PathwayCommons (15),Panther (10),DAVID (8)

Advance search supports
allows wild card * and ?

Logical operators ( AND, NOT, NOR)

Fuzzy search ( ~ place holder for unknown letters )

Field search

Range search

IPAVS, PathwayCommons

Batch search

IPAVS,Reactome (12), PID (13), DAVID (8)

Pathway Browser integrated with find


Tree like access to hierarchical pathway information

Reactome (12), IPAVS

Data upload Wizard

IPAVS,Reactome (12), PID (13), KEGG (14), PathwayCommons (15),Panther (10),DAVID (8), ConcsensusPathDB (16)

Upload-form or use web interface file-valut to submit data


Data upload Wizard

Data compar-ison

Multiple files upload and use it in analysis


Filter data with cutoff values of expression data, chemical concentrations


Handles duplicate entries depending on the data types


Withdraw all the list molecules that did not find a match in IPAVS  or did not meet the cutoff criteria


Override cutoff criteria for few molecules that you feel have biological relevance in analysis


Allows assign logical grouping of data ( by row manipulation (group genes) and column manipulation (group observations)


Ability to move data between groups


Compare data in groups using SET operation ( intersection, differences)


Data compar-son


Draw venn diagram


Compare data based on different columns in the groups ( user uploaded accession or IPAVS assigned molecule name)


Multiple analysis methods

PAGE, Fishers Exact and Binomial Proportion

IPAVS, ConscensusPathDB (16)


Multiple test correction (Benjamin correction)

IPAVS, Reactome (12), PID (13),  DAVID (8), Panther (10), ConsensusPathDB (16)

Contextual Data Analysis ( ability to focus analysis on set of pathways that closely relevant to biological questions researchers are trying to answer)

Filters available: database, Pathway types, Organism, common biological processes, biological roles


Compare two different analysis results


Visualize analysis results as charts


Overlay analysis results on the pathway

IPAVS, Reactome (12), PID (13), Panther (10), ConsensusPathDB (16)

View details for analysis records

IPAVS, ConsensusPathDB (16)

Overlay data on nodes using color

IPAVS, Reactome (12), PID (13), Panther (10), wiki pathways


Overlay data on nodes as shape and bio-concept symbols


Manipulate and customize molecule visual properties ( shape, size and color, symbol , etc)

IPAVS, GenMapp (11)

Overlay isomers as multi boxes

IPAVS, wiki pathways

Uses SBGN for visual representation

IPAVS, GenMapp (11), wikipathways,Panther  (10) ,Reactome (12)

Attach annotation on to the components of pathway

IPAVS, GenMAPP (11), Wikipathways

Layout information when visualizing the pathway

IPAVS, Panther (10), Wiki pathway, Reactome (12)

Overlay data one condition/time point at a time using color and charts and heat maps for multiple time points / conditions


Muti-linked views for the data ( overlay on pathwyas, charts, heatmaps)


Overlay two or types of data-points ( e.g. pvalue and foldchange) together on single pathway  component simultaneously


Multi-pathway visualization simultaneously ( multi time point or conditions as tiled view one condition/time point on one pathway)


Change layout schemes of pathways visualized

Cytoscape(11), GenMapp(11),

Protein structure, Chemical structure, Genome position can be displayed on pathway diagram


User Interface Design

All in one Screen Design


Customizable layouts and change perspectives



Opted for tool bars with icons instead of cascading menu system

Tools are localized to regions where it will make sense. We do not mix analysis tools with that of tools that will help navigate map. Provide easy access and avoids confusion

Customize data columns ( hide and show columns )


Facilitate sharing across community

IPAVS, Panther (10)


Ability to accept updates to pathway diagrams or annotations



Software Design, Architect. and Implement.

Modular, scalable, MVC architecture

Visualization module is independent of analysis module and pathway information module but they all interact in an integrated fashion

Based on Ajax

RServe for statistical computation


SVG for visualization


Apache Lucene for search

IPAVS, Pathwaycommons

XML standards for data integration and exchange



Webserver Glassfish (can be configured for load balancing and supports SOAP implementation)



Uses J2EE, Ajax, XML, MySQL,SVG with EMCA


Supporting Hardware

The entire systems is physically deployed on a node of IBM Blade cluster having 2 Quad core processor (3.0Gz each) and 16GB RAM.   Data is hosted on a separate Mysql database server (community server v5.5) running on windows XP 64 bit OS and physically deployed on identical node, as above, of IBM Blade Cluster. Rserve run on 64bit Redhat Linux Enterprise 6. Hardware will be scaled according to load.


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  • 2.       Kim, S. Y. and D. J. Volsky (2005). "PAGE: parametric analysis of gene set enrichment." BMC bioinformatics 6: 144.
  • 3.       Beissbarth, T. and T. P. Speed (2004). "GOstat: find statistically overrepresented Gene Ontologies within a group of genes." Bioinformatics 20(9): 1464-1465.
  • 4.       Luo, W., M. S. Friedman, et al. (2009). "GAGE: generally applicable gene set enrichment for pathway analysis." BMC bioinformatics 10: 161.
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  • 9.       Matsuoka, Y., Ghosh, S., Kikuchi, N. and Kitano, H. (2010) Payao: a community platform for SBML pathway model curation. Bioinformatics, 26, 1381-1383.
  • 10.   Mi, H., Dong, Q., Muruganujan, A., Gaudet, P., Lewis, S. and Thomas, P.D. (2010) PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res, 38, D204-210.
  • 11.   Salomonis, N., Hanspers, K., Zambon, A.C., Vranizan, K., Lawlor, S.C., Dahlquist, K.D., Doniger, S.W., Stuart, J., Conklin, B.R. and Pico, A.R. (2007) GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics, 8, 217.
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  • 13.   Schaefer, C.F., Anthony, K., Krupa, S., Buchoff, J., Day, M., Hannay, T. and Buetow, K.H. (2009) PID: the Pathway Interaction Database. Nucleic Acids Res, 37, D674-679.
  • 14.   Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. and Hirakawa, M. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res, 38, D355-360.
  • 15.   Cerami, E.G., Gross, B.E., Demir, E., Rodchenkov, I., Babur, O., Anwar, N., Schultz, N., Bader, G.D. and Sander, C. (2011) Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res, 39, D685-690.
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