Features


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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

 

Features

Example of Databases and online analysis tools supporting the feature

Data & Standards

Pathway types curated

 

IPAVS

OtherDBs

Signaling

YES

Reactome, PID, KEGG, Panther

Metabolic

YES

Reactome, KEGG, Panther

Gene regulatory network

YES

KEGG, Panther

Disease

YES

Reactome, KEG

Various Cell types

YES

SBI

Tissue and Organ

YES

 

Drug action

YES

Pharmakgb, KEGG

Perturbed conditions

YES

 

Integrates curated information with data integrated form other external databases

Uniprot, GO, Enzyme, IPI, PIR

 

Provides links to external databases

Yes

Most of them do

Categorical selection of pathways while analysis

YES

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

 

 

IPAVS

Others DBs

Molecules

Sometimes

 

Interactions

YES

PID, Reactome,SBI

Pathway

YES

KEGG, Reactome,Panther

Map/Network

YES

SBI

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

YES

 

Allows download of component lists

YES

 

Allows download of pathways

YES

 

Allows download of pathways with visual cues

YES

 

Allows bulk export of pathways

YES

 

Import of data in SBML and BioPAX formats

YES

 

Uses an open access freely available tool for content curation

CellDesigner

Reactome

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)

YES

 

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

IPAVS

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

IPAVS

Filter data with cutoff values of expression data, chemical concentrations

IPAVS,

Handles duplicate entries depending on the data types

IPAVS,

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

IPAVS,

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

IPAVS,

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

IPAVS

Ability to move data between groups

IPAVS

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

IPAVS,

Data compar-son

 

Draw venn diagram

IPAVS

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

IPAVS,

Multiple analysis methods

PAGE, Fishers Exact and Binomial Proportion

IPAVS, ConscensusPathDB (16)

Analysis

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

IPAVS

Compare two different analysis results

IPAVS

Visualize analysis results as charts

IPAVS

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

Visualization

Overlay data on nodes as shape and bio-concept symbols

IPAVS

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

IPAVS, GenMAPP (11)

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

IPAVS

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

IPAVS, GenMAPP (11)

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

IPAVS

Change layout schemes of pathways visualized

Cytoscape(11), GenMapp(11),

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

IPAVS, SMPD

User Interface Design

All in one Screen Design

 

Customizable layouts and change perspectives

 

IPAVS

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 )

Other

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

IPAVS

SVG for visualization

IPAVS

Apache Lucene for search

IPAVS, Pathwaycommons

XML standards for data integration and exchange

IPAVs

 

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.


References

  • 1.       Berger, S. I., J. M. Posner, et al. (2007). "Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases." BMC bioinformatics 8: 372.
  • 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.
  • 5.       Herve, A. (2007). Bonferroni and Sidak corrections for multiple comparisons. In N.J Salkind. Thousand Oaks, California, Encyclopedia of Measurement and Statistics: 103-107.
  • 6.       Osier, M. V., H. Zhao, et al. (2004). "Handling multiple testing while interpreting microarrays with the Gene Ontology Database." BMC bioinformatics 5: 124.
  • 7.       Farrell, S.R., Ross, J.L. and Howlett, S.E. (2010) Sex differences in mechanisms of cardiac excitation-contraction coupling in rat ventricular myocytes. American journal of physiology. Heart and circulatory physiology, 299, H36-45.
  • 8.       Dennis, G., Jr., Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C. and Lempicki, R.A. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome biology, 4, P3.
  • 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.
  • 12.   Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res, 39, D691-697.
  • 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.
  • 16.   Kamburov, A., Wierling, C., Lehrach, H. and Herwig, R. (2009) ConsensusPathDB--a database for integrating human functional interaction networks. Nucleic Acids Res, 37, D623-628.
  • 17.   Pico, A.R., Kelder, T., van Iersel, M.P., Hanspers, K., Conklin, B.R. and Evelo, C. (2008) WikiPathways: pathway editing for the people. PLoS biology, 6, e184.



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