FAQs

What is KcPAVS?

KCPAVS is a highly interactive, user friendly, unified web interface for: 1) browsing and searching KEGG metabolic -, signaling-, disease- pathways and global maps of ~25 organisms; 2) analyzing and visualizing experimental data; 3) comparative pathway analysis;  4) reconstructing metabolic networks from user defined data; 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.
 

What are the data sources integrated into KcPAVS?

KCPAVS mainly provides access to curated pathways diagrams and annotations from KEGG. Along with the KEGG pathways it integrates annotations for genes, proteins, compounds, ontology from several public databases such as Uniprot, Expasy enzyme, EBI Gene Ontology Annotations, EBI IPI, PIR database, Gene Ontology, NCBI MESH and Pubmed. See the list of data sources considered for current version of KCPAVS system here.


What organisms are considered in KcPAVS?

KCPAVS currently supports 25 organism including: 

Eukaryotes -- Mammals
hsa Homo sapiens (human) 9606 
mmu Mus musculus (mouse) 10090
rno Rattus norvegicus (rat) 10116
cfa Canis familiaris (dog) 9615
bta Bos taurus (cow) 9913

Eukaryotes --Fishes
dre Danio rerio (zebrafish) 7955

Eukaryotes -- Insects
dme Drosophila melanogaster (fruit fly) 7227

Eukaryotes -- Worms
cel Caenorhabditis elegans (nematode) 6239
ath Arabidopsis thaliana (thale cress) 3702

Eukaryotes -- Plants
osa Oryza sativa japonica (Japanese rice) 4530
sce Saccharomyces cerevisiae (budding yeast) 4932

Prokaryotes -- Escherichia
eco Escherichia coli K-12 MG1655 511145

Prokaryotes -- Pseudomonas
pae Pseudomonas aeruginosa PAO1 990337
ppu Pseudomonas putida KT2440 160488
pfl Pseudomonas fluorescens Pf-5 220664

Prokaryotes -- Staphylococcus
sau Staphylococcus aureus N315 (MRSA/VSSA) 158879

Prokaryotes -- Thermotoga
tma Thermotoga maritima 2336

Prokaryotes -- Bacillus
bsu Bacillus subtilis 1423


What pathway types from KEGG are used in KcPAVS?

Pathways curated in organism context
SP = Signaling Pathways
MP = Metabolic Pathways
GRN = Gene Regulatory Pathways
IM = Integrated Maps
DP = Disease Pathways
OP = Organism Pathways
DRP = Drug Pathways

Generic Types
MAP = Global metabolic maps
KO = Orthology maps
EC = Enzyme maps
KO = KO Pathways
EC = EC enzyme pathways


Where can I find more details about the diagram notations used by KcPAVS?

KcPAVS uses KEGG Pathway data and follows its conventions. Please click here for details.

Color coding The pathway map without coloring is the original version that is manually drawn by in-house software named KegSketch. The other pathway maps with coloring are all computationally generated as follows.
  • Reference pathway: this is the original version; white boxes are hyperlinked to KO, ENZYME, and REACTION entries in metabolic pathways; they are hyperlinked to KO and GENES entries in non-metabolic pathways.
  • Reference pathway (KO): blue boxes are hyperlinked to KO entries that are selected from the original version.
  • Reference pathway (EC): blue boxes are hyperlinked to ENZYME entries that are selected from the original version.
  • Reference pathway (Reaction): blue boxes are hyperlinked to REACTION entries that are selected from the original version.
  • Organism-specific pathway: green boxes are hyperlinked to GENES entries by converting K numbers (KO identifiers) to gene identifiers in the reference pathway, indicating the presence of genes in the genome and also the completeness of the pathway. 

How to cite KCPAVS website or content?

when referring to the website, tools or services please site: 
KCPAVS: Kegg based Collaborative Pathway Analysis and Visualization System  [http://kcpavs.cidms.org]

When referring to a data, site:
primary databases from where data was obtained

Can we upload pathway diagrams and use them in analysis along with other pathways already present in the KcPAVS?

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 KCPAVS.


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 KCPAVS. An unambiguous identifier will be assigned to all found molecules that are part of atleast one pathway in KCPAVS. 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 KCPAVS, 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 KCPAVS
  • Identifier version may not be supported by KcPAVS 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 KcPAVS
  • Your set cutoff data filter criteria may be very stringent and those that passed the criteria may not be part of any pathways in KcPAVS.

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 KcPAVS is not supporting the identifier used in my uploaded list? OR KcPAVS is not able to map your identifier list?

Its unlikely such a situation would occur as KcPAVS 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 KcPAVS?

Currently KcPAVS 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 KcPAVS?

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 KcPAVS 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 KcPAVS 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.


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. ?

KcPAVS 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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