How to use this resource
NemaPath provides information about the presence, absence and composition of enzymatic pathways in given organisms based on actual transcript data and allows for the comparison of any two organisms represented in the database. It also provides higher-order comparisons across clades and hosts. This is useful in many ways, from identifying potential drug targets to helping understand the differences between species utilizing different survival strategies. Browsing the clade- or host- specific NemaPath comparisons can offer insight into taxa defining differences, while the ability to directly compare any two species in the database provides a direct visualization of enzymatic differences between the two.
A Note on KEGG (Kyoto Encyclopedia of
Genes and Genomes)
KEGG is a suite of databases and associated software, integrating
our current knowledge on molecular interaction networks in biological
processes (PATHWAY database), the information about the universe
of genes and proteins (GENES/SSDB/KO databases), and the information
about the universe of chemical compounds and reactions (COMPOUND/REACTION
databases). For more information see: KEGG: Kyoto Encyclopedia of Genes and Genomes
A Note about how we make KEGG associations
KEGG Orthology (KO) numbers are assigned to nematode cDNA contigs/isotigs by primary sequence similarity. The KO numbers are then lit up in every pathway in which they are represented. We do not provide exhaustive curation, therefore proper interpretation requires the users' cognizance of the various pathways.
Sequences used for KEGG associations
To eliminate data redundancy, cDNAs are clustered by identity into contigs/isotigs
and further organized into clusters/isogroups. cDNAs within a contig/isotig derive from
nearly identical transcripts whereas contigs/isotigs within a cluster or isogroup may
represent splice isoforms of a gene or transcripts from multigene families
with extremely high sequence identity (Mitreva et al, 2004).
The KEGG associations are done on the contig level. For summarizing the
associations on cluster level use the contig-cluster membership files
More information on cDNA clustering
For more information regarding our cDNA clustering process, please view the NemaGene clustering FAQ.
NemaPath: online exploration of KEGG-based metabolic pathways for nematodes,Todd Wylie, John Martin, Sahar Abubucker, Yong Yin, David Messina, Zhengyuan Wang, James P McCarter, and Makedonka Mitreva, BMC Genomics 2008; 9: 525.