Hi, all.
I am a newbie at bioinformatic analyses and coding. I recently came across an ontology database called "Zebrafish phenotype ontology (ZPO)" on the String platform. My supervisor wants me to create a list that states the ZP code, term and its associated genes so that we can use it for enrichment analyses using other packages such as clusterProfiler. I thought it should be readily available, but I could not find it. I then tried to create one myself.
I managed to create a customised list for enrichment of PATO ontologies downloaded from the ZFIN website. But the ZP terms are created by combining ZFA and PATO ontologies. I found a file describing which combination to which ZP on ZPO's GitHub. However, I am not sure how to link the genes with the specific ZP. This has overwhelmed my brain...
I'm thinking of three potential solutions but I can make none of them so far: (1) Locate a list with ZP terms and associated genes; (2) Perform the enrichment analyses on the String platform and transform the resulting enrichment table to an enrichment result object for clusterProfiler (there was a function called enrichDavid but not others). We want to do this because we want to apply the compare_cluster or merge_results functions on clusterProfiler for our data. (3) Create the list myself so that I can perform the enrichment analyses locally.
Hope someone would provide some hints or directions to achieve any of these. Thank you!
Some information mentioned above: Github of Zebrafish phenotype ontology https://github.com/obophenotype/zebrafish-phenotype-ontology
Zebrafish phenotype ontology analyses on String
