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 available here.

More information on cDNA clustering

For more information regarding our cDNA clustering process, please view the NemaGene clustering FAQ.

Publication Link

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.