About PathwAX

PathwAX, Pathway Analysis with crosstalk, is a webservice for pathway annotation based on crosstalk derived through FunCoup, a framework for genome wide functional association networks. A pathway is statistically enriched/depleted if the crosstalk, which is the number of links between the pathway and your gene set, is more/less than one would observe in a random network.

This enables the possibility to see the gene sets in a bigger context allowing for more evidence to compute enriched pathway terms.

Ogris C., Helleday T., Sonnhammer E.L.L.. PathwAX: a web server for network crosstalk based pathway annotation. Nucleic Acids Res. 2016;44:W105−W109.

Ogris, C., Guala, D., Helleday, T. and Sonnhammer, E.L., 2017. A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation. Nucleic acids research, 45(2), pp.e8-e8.

  • How To

    1) Select Species:

    2) Enter a gene set of you choice:
    The query searches for exact matches of symbols or identifiers and supports a variety of different identifier types including ENSEMBL gene, protein, and transcript IDs, NCBI gene IDs, RefSeq IDs and UniProt IDs. For a search with multiple genes the identifiers should be separated by spaces or commas.
    The search and computation may take some 1-5 min depending on the query gene set.

    This part is computationaly heavy and depends on your browser. Best performance can be achieved using Chrome

    3) Result explorer:
    The result explorer will give you an overview of significant related pathways. You can filter them by class or top hits.
    The pathway class table provides a hint of which classes are most common in the results. A second table will visualize all hits. The pathway names are linked to the kegg entry. A red name indicates depletion whereas a blue one indicates enrichment. Furthermore we correct the p-values via Benjamini Hochberg procedure to account for multiple testing, the derived FDR will show up in column 3. The last column illustrates each query gene as a box and its connectivity. Dark boxes indicate the gene to be a hub with multiple connections to a pathway. In addition, if the gene is present in the pathway it will be colored in purple.

  • Networks

    Species Genes Links Pathways Unique pathway genes
    Homo sapiens 11 882 1 002 371 289 6 482
    Mus musculus 12 903 1 495 536 286 7 299
    Rattus norvegicus 12 025 1 668 050 271 6 458
    Canis familiaris 9 292 667 556 244 4 712
    Gallus gallus 6 211 299 485 135 3 210
    Danio rerio 8 480 769 808 148 4 502
    Ciona intestinalis 3 282 212 110 87 1 263
    Drosophila melanogaster 5 762 385 691 124 2 395
    Caenorhabditis elegans 6 014 686 340 124 2 014
    Saccharomyces cerevisiae S288c 3 991 179 499 101 1 784
    Arabidopsis thaliana 9 306 1 433 523 121 4 239

  • Error Messages

    • Message: "Gene Identifier Problem"
      Caused by using unsupported gene IDs. PathwAX supports ENSEMBL gene, protein, and transcript IDs, NCBI gene IDs, RefSeq IDs and UniProt IDs.

    • Message: "Too many query genes"
      Caused by submitting a too large quene query. Query size is limited to 400 genes.

    • Message: "No links found""
      Caused if the network search did not return any links at all.

    • Message: "No pathways found""
      Caused if pathwAX did not find any connections between the query and kegg pathways.

  • Contact

    Please do not hesitate to contact us for feedback, questions, and suggestions.

    If you want to report any problems or errors, please consider including the following information:
    - the browser you are using
    - the query
    - a screenshot showing the problem

    Sonnhammer Group
    Science for Life Laboratory
    KISP (Karolinska Institutet Science Park)
    Tomtebodavägen 23A
    17165 Solna, Sweden