Analysing a S. mansoni gene list

To analyse a list of Schistosoma mansoni genes with a particular expression pattern, to see if they have some unusual features, here are some things you can try:

1. STITCH (protein-protein interactions)  http://stitch.embl.de/
If there is no S. mansoni in the STITCH database, one could try C. elegans orthologs, and/or human orthologs (see 2 below). You could try with ortholog_one2one orthologs, and separately with ortholog_one2many orthologs; one-to-one orthologs might be a cleaner set, but adding one-to-many orthologs may give you a much larger sample, so allow you to pick up more.
2. To get C. elegans (or human) orthologs
  - go to wormbase parasite https://parasite.wormbase.org/index.html
  - click on biomart at top
  - click species, tick genome, choose S. mansoni
  - click on 'Gene', then in the 'id list' box, paste in your S. mansoni Smp id list
  - This gives it your list of S. mansoni genes
  - To tell it you want eg. C. elegans orthologs, click on 'output attributes' on the left (blue link)
  - Click on 'orthologs', then under C. elegans orthologs choose for example gene id, gene name, protein stable id, % id, homology type
   Note: STITCH might want gene id (WBGene) or the protein id (e.g. AC5.3)
  - click on 'Count' at top of page to get id of number of results, then 'Results' at top of page to get Results. Save as tab separated file

3. Another thing to try is tissue/phenotype/GO enrichment using the C. elegans wormbase page, and your C. elegans orthologs: https://wormbase.org/tools/enrichment/tea/tea.cgi
  Could try with ortholog_one2one orthologs, and separately with ortholog_one2many.

4. Can try GO enrichment for S. mansoni (or your C.elegans/human orthologs) using TopGO (an R package).
  First you need your S. mansoni GO terms for S. mansoni genes from WormBase parasite Biomart :
  - go to wormbase parasite https://parasite.wormbase.org/index.html
  - click on biomart at top
  - click species, tick genome, choose S. mansoni
  - To tell it you want GO terms, click on 'output attributes' on the left (blue link)
  - Select 'Gene ontology' and tick all the boxes beside it
  - Click on "results' at top of the page
  - Then run TopGO. See  my notes here on TopGO: http://avrilomics.blogspot.com/2015/07/using-topgo-to-test-for-go-term.html

Note: 4-Feb-2019:
Another thing to try could be https://biit.cs.ut.ee/gprofiler/gost for GO enrichment, can take WormBase ParaSite gene lists.

Note: 3-July-2019:
Other things to try:
- find Drosophila melanogaster orthologs, paste into the FlyMine website
- find Drosophila melanogaster orthologs, and test for enrichment of phenotypes downloaded from FlyBase
- try the GSEA Gene Set Enrichment software