Costello2008

CREATED: 200810200328 Title: Limitations of pseudo genes in identifying gene loss ** Motivation

• loss of mgh16 associated with cranial enlargement (less is more)
• Identifying human-specific gene loss ** all methods rely on finding pseudo genes ** assumption: gene loss always results in pseudo gene ** Finding gene loss using gene families
• gene family: groups of orthologs and paralogs
• obtain genes from Ensembl -> obtain families using TribeMCL
• inferring gene loss/gain ** 231 human specific gene loss in 207 families ** under counting? (equal number of gene gain and loss) ** Ensembl included pseudo genes as real genes
• verifying gene loss ** blast chimp homolog against human using GeneWise to check gene model ** pseudo gene based methods miss many genes but fewer false positives ** gene family based methods identify deleted genes but have false positives