I'm trying iPath 2.0, but I found some inconsistencies. It is supposed to use the KEEG database and my organisms is contained in this database, and I'm using a set of orthologous groups that have been retrieved by using the same database, but in some cases it is not able to find some of the orthologous groups introduced in the input file.
Can anyone recommend any other alternative tool?
Thank you very much in advance.
If you just have a pathway name and want to visualize it, maybe REACTOME could be a choice. BTW, I think the definition of pathways are different among databases, so it totally depends on which software you usd to find your interested pathways, and to visualize them directly from their source databases.
iPath is only based on a limited subset of the full KEGG set of pathways and thus only includes an overview. So try using the full KEGG system at http://www.genome.jp/kegg/
KEGG, REACTOME, METACORE, Ingenuity's ontology, etc... are all somewhat different too. These are all curated ontologies, and thus each curation team makes its own decisions about what does or does not constitute an ontology or pathway. REACTOME, in my experience, has the least inclusive genetic identifiers of all, in part as it is relatively young and they are trying to be very careful about the validity of the data they do include (in other words, you are more likely to find few or no matching gene/elements in REACTOME than any of the others). The public GO ontology is the largest database available, but that in some ways also makes it the least informative - almost any gene list will find many enriched categories in GO, and many of those are such large inclusive categories that they are not very informative.
So if you have a list of gene or gene products, you may need to explore multiple ontologies to really explore what the data may or may not be telling you.
P.S. there may well also be Bacterial specific curated ontologies that would be best suited to your data, but I just don't know of them as they are outside of my areas of knowledge.
If you just want to visualize, try tPaintomics
http://www.paintomics.org/cgi-bin/main2.cgi
In fact, what I'm intended to do is to visualized the comparative metabolic pathways for several species. I have the draft genome of a set of gram-negative bacteria belonging to two genera. From the draft genomes, the bioinformatic of the department constructed a orthologos list based on KEGG database. So, my aim is just typing the a defined set of orthology groups, visualize the metabolic pathways in with those proteins (orthologs) are involved… In order to compare two species, I want to visualize at the same time the shared and specific pathways for each bacterial specie.
iPath was working very well, but it seems that it doesn't contain all the information from KEGG.
I tried to do the same using KEGG Atlas and had no success… Really, have no idea how this tool may be used :-S.
I will try some of the alternative tools you propose.
Thank you very much.
If you are familiar with R you may try http://bioconductor.org/packages/release/bioc/html/pathview.html
I am not familiar with bacterias, but it seems you have two protein list for two species, and want to visualize their common/differences from a pathway level?
you will find a lot of pathway tools and databases to find pathways with your input protein/gene list, as discussed above. and the visualization part is highly related to which pathway databases you used. in current case, you want to use KEGG pathways, therefore its much better to directly use KEGG to visualizing your interested pathways. If you use ipath tools, you can only get pathway information this tool included.
What I don't understand is what is the tool included in KEGG database? KEEG Atlas?? I've been trying a lot and only succeed in introducing the pathways in which one protein (one ortholog number , Knnnnn) at a time. No multiple searches are allowed, so I can't see the whole picture of my protein lists.
The idea is obtaining something like the picture I attach: in red common pathways present in both species, and in green and blue the specific ones, found only in one of the two species.
You can drop an entire list of elements in the KEGG Mapper search box, or upload a text file of identifiers - http://www.kegg.jp/kegg/tool/map_pathway1.html
I'm not sure of the syntax, but they have examples.
Thank you Michael! It works real well to visualize a list of KEGG indetifiers… :-)
unfortunately afraid I'm is not possible to see two list at the same time, with different colors, but at least I can combine this tool to retrieve the missing data in iPath.
Great information, thank you again.
P.D. I'm still looking for the perfect tool… :-)
The KEGG Mapper within the MG-RAST platform (http://metagenomics.anl.gov/) offers what you are looking for, but unfortunately this pipeline is only for metagenomes. The RAST platform (http://rast.nmpdr.org/) for single genomes offers at least a table view for comparison of genomes (but unfortunately no visualization). These platforms also do all necessary processing steps on your raw data and may be used as an additional tool.
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