This example shows the multiple sample/state integration with Pathview KEGG view.
This example shows the multiple sample/state integration with Pathview Graphviz view.
This example shows the ID mapping capability of Pathview.
This example covers an integration pathway analysis workflow based on Pathview.
Gene Data accepts data matrices in tab- or comma-delimited format (txt or csv). Data matrix has genes as rows and samples as columns. First column should be gene IDs, first row sample IDs. The data may also be a single-column of gene IDs (example). Here gene ID is a generic concept, including multiple types of transcript or protein IDs, for example ENTREZ Gene, Symbol, RefSeq, GenBank Accession Number, UNIPROT, Enzyme Accession Number, etc. Users can specify this information through the Gene ID Type option below. uniquely mappable to KEGG gene IDs. KEGG ortholog IDs are also treated as gene IDs as to handle metagenomic data.
Both the absolute or original expression levels and the relative expression levels (log2 fold changes, t-statistics) can be visualized on pathways. However, the latter are more frequently used. If you supply data as original expression levels, but you want to visualize the relative expression levels (or differences) between two states. You need to specify a few extra options(NOT needed if you just want to visualize the input data as it is):
If you intend to do a full pathway analysis plus data visualization (or integration), you need to set Pathway Selection below to Auto. Gene Data and/or Compound Data will also be taken as the input data for pathway analysis. Frequently, you also need to the extra options: Control/reference, Case/sample, and Compare in the dialogue box. However, these options are NOT needed if your data is already relative expression levels or differential scores (log ratios or fold changes). Example 4 covers the full pathway analysis.
Please cite our paper if you use this website. This will help the Pathview project in return.
Please also cite GAGE paper if you are doing pathway analysis besides visualization, i.e. Pathway Selection set to Auto on the New Analysis page.
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