What is PANDA-mini?
PANDA-mini (Priority ANalysis using DAta-mining) is a gene ranking system based on functional similarity to the queried gene(s).
The ranking method of PANDA-mini
PANDA-mini provides each gene with a score of functional similarity based on seven key features: 1) paralog gene analysis, 2) InterPro, 3) EC number, 4) KEGG pathway, 5) GO molecular function, 6) GO biological process, and 7) GO cellular localization. These are obtained from H-InvDB. When a gene shares the functional annotations with the queried gene(s), it is assigned a score of 1. The rank of a gene is based on the sum of the annotation scores for each of the seven key features described above (Maximum = 7).
Why have we developed PANDA-mini?
We have constructed a gene ranking system for prediction of novel disease candidate genes of multifactorial diseases, called the PANDA (Priority ANalysis for Disease Association) system. It is necessary for PANDA to select known disease genes as a training set. Our collaborators, who are disease researchers, want to be able to select the training set by themselves at any time. Since we use a complicated scoring scheme for PANDA analysis, it takes more than 1 week for the calculation. Therefore, we have constructed PANDA-mini as a simple version of PANDA.
How to use this system?