About PathwAX

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

• How To

  1) SELECT: SPECIES

  

  2) SUBMIT: GENE LIST
  The query searches for exact matches of symbols or identifiers and supports a variety of different identifier types including Ensembl, gene symbol IDs, NCBI/EntrezGene IDs, FlyBase IDs, WormBase IDs, PomBase IDs, ZFIN IDs or TairLocusAccession. For a search with multiple genes the identifiers should be separated by spaces or commas. Select which pathway database you want to use to run your analysis (KEGG or Reactome). 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: OVERVIEW
  The result overview will give you an overview of significant related pathways. You can filter them by class or top hits. Moreover, you can also select the significant pathways that are only enriched, depleted or that they have an overlap with the gene list you submitted. 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 entry of the pathway database you selected in the previous step (KEGG or Reactome). A red name indicates depletion whereas a blue one indicates enrichment. Furthermore you can choose which multiple testing correction you want to perform, Bonferroni, Benjamini-Hochberg or none, as well as the cut off. The corrected p-value 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. If you click on a pathway you are interested in it will redirect you to RESULT: DETAILS.

  

  4) RESULT: DETAILS
  The result details will give you a crosstalk viewer to get detailed insights of specific pathway-query relations. The genes are represented as nodes and their sizes depend on their degree. Gene label are by default Uniprot IDs but you can change them, depending on the species, to Ensembl IDs, gene symbol IDs, NCBI/EntrezGene IDs, FlyBase IDs, WormBase IDs, PomBase IDs, ZFIN IDs, TairLocusAccession, node degree or none. The color indicates if a node belongs to the pathway set (orange) or query set (green), or if it is a shared node (purple) present in both sets. Moving the mouse to the gene of interest will give you all its connections, hiding all unconnected nodes. The network can be zoom-in or zoom-out with the mouse wheel.
  It will display the main statistical facts of the analysis in the Analysis panel. Additional information can be displayed by expanding the panel More.
  You can select the graph style you want to display, force field or gridview. If the graph contains more than 1000 links it will only be displayed in gridview. Gridview will display the query nodes first, followed by shared and pathway nodes. The order of the nodes within the group depends on their link degree. The graph can be saved in csv format.
  

  Force field viewer display:

  

  Grid viewer display:

  

• Networks

  Species	Genes	Links	Pathways KEGG v94.1	Pathways Reactome v72	Unique pathway genes in KEGG v94.1	Unique pathway genes in Reactome v72
  Homo sapiens	12 051	1 222 749	327	289	7 679	7 894
  Mus musculus	12 105	1 309 394	323	210	8 185	6 485
  Rattus norvegicus	11 979	1 534 726	323	210	8 162	6 531
  Canis familiaris	10 189	665 143	323	181	6 660	5 935
  Gallus gallus	6 327	284 502	164	151	3 301	3 099
  Danio rerio	8 723	757 523	163	190	5 860	5 017
  Drosophila melanogaster	6 420	444 885	132	189	2 944	2 862
  Caenorhabditis elegans	6 828	674 507	130	220	2 489	3 128
  Saccharomyces cerevisiae S288c	4 901	495 380	109	68	2 027	1 063
  Arabidopsis thaliana	12 035	1 465 923	131	117	5 186	3 156
  Plasmodium falciparum	1 191	36 806	80	49	1 024	457
  Schizosaccharomyces pombe	2 441	73 698	106	125	1 462	1 164
  Oryza sativa	5 620	845 755	130	117	4 656	2 166
  Bos taurus	11 988	1 167 678	323	57	6 863	2 910
  Ciona intestinalis	3 783	314 715	121	−	1 588	−
  Escherichia coli	2 860	49 736	107	−	1 520	−
  Bacillus subtilis	2 680	12 573	104	−	1 231	−

• Error Messages

  
  

  • Message: "Gene Identifier Problem"
    Caused by using unsupported gene IDs. PathwAX II supports Ensembl id, Gene Symbol, NCBI id, Uniprot id, FlyBase id, WormBase id, PomBase id, ZFIN id and TairLocusAccession.
  
  
  • 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 the pathway database.

  
  

• Contact

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

  E-Mail: miguel.castresana@scilifelab.se

  
  
  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