Gene-centric prediction
If you want to know if your query gene is for a pathway, development of a organ, or a disease, you can use such information about network neighbors for the query gene.

This prediction option prioritizes five categories of functional terms:
i) Zebrafish Gene Ontology Biological Process (GOBP) terms
ii) Zebrafish Anatomical (ZFA) terms
iii) Human disease (OMIM) terms
iv) Human GOBP terms
v) Human Phenotype Ontology (HPO) terms.

For each category, DanioNet finds significantly enriched terms among network neighbors of the query gene.
Pathway-centric prediction
If you want to identify new genes for a pathway or phenotype, you may prioritize genes by network association to the known genes for it. Here we can use two alternative algorithms, direct neighborhood (direct neighbor sum) and network diffusion (Gaussian smoothing).

For this prediction option, we need a “guide genes”, which represent known genes for a pathway or phenotype from either zebrafish or human. DanioNet reports the list of candidate genes related to a certain pathway or phenotype.
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