@Guangchuang Yu I see that you are yourself the author of clusterProfiler , yes? if so, can you give me a demo on the use of your package or direct me to the place that I can use it for worm pathway analysis ? should i orthologue the gene names or not needed it works on gene name or symbol ?
the right way in analysing Tml
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clusterProfiler supports GO & KEGG and ReactomePA supports Reactome pathway analyses. Over-representation test and gene set enrichment analysis for worm are all supported.
GOSemSim supports measuring GO term and gene semantic similarity for many species and worm is also supported.
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If you are looking for pathway annotation or enrichment tool based on your gene list, GeneSCF will work. It supports organisms from this list.
Example for Bombyx mori (domestic silkworm), bmor,
./geneSCF -m=update -i=INPUTgene.list -t=gid -db=KEGG -o=/ExistingOUTPUTfolder/ -org=bmor --plot=yes --background=#TotalGenesFromAnnotation
't=gid' for Gene IDs and 't=sym' for Gene Symbols.
Sample supported ids for bmor,
**GeneIDs** **GeneSymbols**
100856801 EAAT-1
100856802 EAAT-2
733034 St1
733035 mRpS12
Good luck :)
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Define "best". Because of all them are that within their own parameters. You are probably looking for one that helps you get published :-) If you have not tried these two (appear to have worm support).
Reactome
WebGestalt
Were you able to get your gene names resolved?
@genomax2 I don't care about publication. It seems very interesting that annotation etc of genomics of worm model are poorly studied . at least I cannot find a great solution ! Reactome is useless (I have tried few data sets) the analysis is not logical.
Then IPA may be your best bet. Have you asked tech support there about what we had discussed in the last thread?
@genomax2 Not yet, but i checked and I found in core analysis the main focus is on Human, mouse and rat. out of 8000 genes only 100 genes were mapped in a try which is coming from Uniprot and I checked them one by one. so I am sure that IPA is not supporting it
IPA support confirmed (paraphrasing from their reponse) that the information in IPA Knowledge Base is limited to human/mouse/rat studies. If you use ID's from a different organism then IPA is able to recognize which genes/proteins they are associated with (for the species they support).
Results generated in IPA are limited to literature/sources specific for human/mouse/rat and should be interpreted in that context.
@genomax2 that is right, however, even if you do homologue (e.g. you get the genes from worm equivalent to that of human) still it is hell lot of work and without success ! I tried it at least for one case was like this
As I interpret it, IPA is already doing that for you (which is why only 50% of your genes were recognized, I suppose). You could export just the mapped genes from IPA to get the human equivalents.
@genomax2 yes , you are right and yes it is possible but having only very very few which are not those that I would like, does not get me to anywhere ! actually now i am more and more convinced that I need to work in this domain because of the need. probably everybody focuses on human models