Table 2.

The overall features of existed homology resources

					Gene annotation types						Homologs view mode
Database	Homology inferring method	Homology relationship	#Organisms/ species	Homologs’ ID type	GO	Pathway	Protein/ domain ID	Trait	Variation	Expression	Single gene	By sequence	By comparing
COG	Graph-based	Pairwise, group	1309	NCBI Protein ID	×	√	√	×	×	×	√	×	×
InParanoid	Graph-based	Group	273	Uniprot ID	×	×	√	×	×	×	√	√	×
eggNOG	Graph-based	Group	5090	NCBI/Ensembl/ Uniprot Protein ID	√	√	√	×	×	×	√	√	×
OMA	Graph-based	Pairwise, group	2326	Self-definded Protein ID, Uniprot ID/ Ensembl ID/ NCBI ID	√	×	√	×	×	×	√	√	×
HomoloGene	Graph-based	Group	21	Gene symbol/NCBI Gene ID	×	×	√	√	√	√	√	√	×
Panther	Tree-based	Group	-	Ensembl/NCBI Gene ID,Protein ID	√	√	×	×	×	×	√	√	×
Hieranoid	Tree-based	Group	66	Uniprot ID	×	×	×	×	×	×	√	√	×
TreeFam	Tree-based	Pairwise, group	109	Ensembl Gene ID/Gene Name/ Uniprot ID	×	×	√	×	×	×	√	√	×
Ensembl Compara	Tree-based	Pairwise	-	Ensembl Gene ID	√	√	×	√	√	√	√	√	×
DIOPT	Integrated	Pairwise	10a	Ensembl/NCBI Gene ID	√	×	×	√	×	×	√	×	×
Alliance	Integrated	Pairwise	7a	Gene symbol	√	√	×	√	√	√	√	×	√

^a Mainly for model organisms.