FAQs

What datasets are provided in iPVAS?
iPAVS provides curated human pathways diagrams and annotations. Along with curated data it integrates pathway information from several public databases. See the list of data sources considered for current version of iPAVS system here.

What organisms are considered in iPAVS?

iPAVS mainly supports Human. we are currently working to extend the pathway to other organism by homologous mapping.

Where can I find more details about the diagram notations used by IPAVS?
IPAVS diagrams were drawn using CellDesigner software which follows Systems Biology Graphical Notations (SBGN). For details see the section Diagram Notation

How to cite IPAVS website or content?

Manuscript citation:
Sreenivasaiah PK, Rani S, Cayetano J, Arul N, Kim DH. IPAVS: Integrated Pathway Resources, Analysis and Visualization System. Nucleic acids research. 2011:gkr1208v1-gkr.

When referring to the website, please site:
IPAVS: Integrated Pathway Resources, Analysis and Visualization System [http://ipavs.cidms.org]

When referring to a particular pathway, please site:
<Authors comma seperated>:<pathway title><data source><(organism)><[URL]

  • authors are optional
  • pathway title, data source and organism is mandatory
  • URL is mandatory can obtain it from the summary page of each pathway detail description tab.

e.g. Oxaprozin Drug Pathway curated by IPAVS
Pradeep Kumar Sreenivasaiah, Shilpa Rani:Oxaprozin Drug Pathway;IPAVS;(Homo Sapiens)
          [http://203.230.49.206/ipavs/pathwaysvg.do?DBID=Oxaprozin_Drug_Pathway]

          e.g. EGFR Pathway Map curated by Systems-biology.org
          EGFR Pathway Map;Systems-biology.org;(Homo Sapiens)           
          [http://203.230.49.206/ipavs/pathwaysvg.do?DBID=EGFR_signaling_for_RTKC]

Can we upload pathway diagrams and use them in analysis along with other pathways already present in the IPAVS?
At present we do not allow upload of pathways by users directly, as it involves intricate quality and consistency checks that has to be done manually. However we are currently working on the feature that will allow users to upload their pathway into separate folder which allows them to use their uploaded pathways in a combined analysis along with all the other pathways in iPAVS.

What is CellDesigner used for? Where do I get CellDesigner?
CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW). 
 CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver.and Copasi. By using CellDesigner, you can browse and modify existing SBML models with references to existing databases, simulate and view the dynamics through an intuitive graphical interface. Visit http://www.celldesigner.org/ for information about all the features supported by the tool. Contact: info @ celldesigner.org 
Reference: Kitano, H.et al. "Using process diagram for the graphical representation of biological networks", Nature Biotechnology 23(8), 961-966 (2005) 

I have a pathway and wish to make it available on iPAVS, what should I do?
We appreciate your contribution of any kind that could help us to improve iPAVS. If you have a pathway in SBML with layout information / CellDesigner files. You could email us the files and we will be happy to put them on iPAVS.  You should send us the CellDesigner/SBML Layout files along with the exported images from the CellDesigner / SBML rendering tool.

We are unable to automate the process of exporting image from the above formats directly because of current technical difficulties: 1) CellDesigner is a closed source code product owned by Systems Biology Institute in Tokyo. and 2) although all the modern browsers support SVG, their performance decreases drastically in terms of its navigation abilities and thus its easy usage, when we render large maps purely in svg elements. So for the above reasons and to optimize the quick navigation and exploration we use images embedded inside SVG. 

How do I export images form CellDesigner file?
Open your pathway in CellDesigner -> File -> export images -> choose your format ( Refer to CellDesigner user's guide for detailed information). iPAVS can use either JPG or PNG format.

What file formats are supported in data upload (microarray, proteomics, experimental data) for analysis?
Currently user data can be imputed as tab delimited or comma delimited (CSV) files or through pasting the data directly into into web-form. We will be supporting excel-2003(xls) and 2007(xlsx) soon.

What is the difference between my input molecules, Matched Identifier List (Matched Table) and Selected Identifier List (Selected Table) ?
User input molecules will be compared to the molecules in iPAVS. An unambiguous identifier will be assigned to all found molecules that are part of atleast one pathway in IPAVS. All of this identified molecules are listed in 'Matched' table.

The identifiers listed in 'Selected' table are from Matched Table that passed the use entered Filter criteria
(observation cutoff, organism etc) if set . All those identifiers that are in Matched Table but did not meet the filter criteria will be listed in 'Non-Selected' Table.

Why does some of the molecules in my uploaded list are missing/rejected in Matched and Selected tables?
My uploaded gene/protein list is not identified by iPAVS, I get zero hits.?
This could be because of one of the following reasons:
  • Improper Accession Type assigned to your list identifiers.
  • Identifier type used in the uploaded list is not supported by iPAVS
  • Identifier version may not be supported by iPAVS eg. Refseq/Genbank NM.234221.1 the number after period is version number. Remove the version number and try.
  • Identifier may not be part of any pathways that are included in iPAVS
  • Your set cutoff data filter criteria may be very stringent and those that passed the criteria may not be part of any pathways in iPAVS.
Can identifier column be assigned multiple identifiers?
No, You cannot assign a column more than one identifer at present. However there is a work-around. While assigning a identifer type choose a generic assignments. For example
instead of choosing ENSEMBL_PROTEIN (specific) you could choose ENSEMBL (genric)  which will then search ENSEMBL_(Protein, Gene, Transcript), similarly instead of choosing specific uniprot data set like uniprot_sp, uniprot_tremble you can choose uniprot_knowledgebase which will include all the datasets automatically, If you want to include data-sets across databases then use All_Gene_Identifiers, All_Protein_Identifiers or All_Identifiers. But Note as the search will include several datasets the processing time of your uploaded list may be more.

What if iPAVS is not supporting the identifier used in my uploaded list? OR iPAVS is not able to map your identifier list?
Its unlikely such a situation would occur as iPAVS integrates identifiers from several sources.
We would appreciate if you could inform us such an instance and send us the sample list via email. We will try to fix the problem as soon as possible. As a work around in such situation you could try using external idmapping services to convert identifiers in your list into to some standard commonly used identifiers like entrez, uniprot, ipi etc. Some of the external identifier services are: For Protein/Gene/RNA UNIPROT uniprot.org, ID CONVERTER http://idconverter.bioinfo.cnio.es/ and Small Molecule MBROLE http://csbg.cnb.csic.es/mbrole/conversion.jsp

Which microarrarys probe identifiers are supported by IPAVS?
Currently IPAVS does not support any microarrary technologies probe identifiers. We will provide support to Most common microarrary technologies are supported including Affymetrix, Illumina and Agilent.

Is metabolomic data be used in IPAVS?
Yes, all types of data that can be linked to identifiers (see the list) on the pathways are supported which includes metabolomic data ( KEGG compound, Pubchem, Chebi etc). With IPAVS you can perform over-representation (enrichment) analysis for set of compound of interest.

Is multiple testing correction performed on the calculated P-values?
There are multiple p-values reported by IPAVS analysis algorithms (Fisher's and PAGE (Parametric Analysis of Gene Set Enrichment) analysis algorithms). 
For Fisher's analysis, p-value are from Fisher exact test, users have option to use Bonferroni method for multiple test correction. 
For PAGE analysis Bonferroni multiple testing adjustments is applied by default.

What is a default compartment?
Default compartment is convention followed by CellDesigner models. The context of pathway decides what the default compartment would be. If the pathway was curated for a cell type then the default compartment represents cytosol. If the pathway model captures inter cellular  events then the default compartment would imply extracellular matrix / space. All the models in curated by IPAVS have explicit mention of the compartment vocabulary. In the context of imported CellDesigner pathways the 'default' terminology holds.

I enter a keyword "hydrogen peroxide" and applied filter to see results from only other-molecules page I see molecules like E14310, Paraxanthine etc. as my hits. How do I interpret the results. ?
IPAVS uses a powerful search engine ( Apache Lucene). The hits resulting from the searched keywords are ranked and displayed in descending order. If your search was
"hydrogen peroxide" and the top hits were E13310, Paraxanthine means that the Keyword you entered was found highly associated with the hits than others. The associations can be because of interaction or complex or descriptions associated with the resulting hits.



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