A unified gene catalog for the laboratory mouse reference genome

Abstract

We report here a semi-automated process by which mouse genome feature predictions and curated annotations (i.e., genes, pseudogenes, functional RNAs, etc.) from Ensembl, NCBI and Vertebrate Genome Annotation database (Vega) are reconciled with the genome features in the Mouse Genome Informatics (MGI) database (http://www.informatics.jax.org) into a comprehensive and non-redundant catalog. Our gene unification method employs an algorithm (fjoin—feature join) for efficient detection of genome coordinate overlaps among features represented in two annotation data sets. Following the analysis with fjoin, genome features are binned into six possible categories (1:1, 1:0, 0:1, 1:n, n:1, n:m) based on coordinate overlaps. These categories are subsequently prioritized for assessment of annotation equivalencies and differences. The version of the unified catalog reported here contains more than 59,000 entries, including 22,599 protein-coding coding genes, 12,455 pseudogenes, and 24,007 other feature types (e.g., microRNAs, lincRNAs, etc.). More than 23,000 of the entries in the MGI gene catalog have equivalent gene models in the annotation files obtained from NCBI, Vega, and Ensembl. 12,719 of the features are unique to NCBI relative to Ensembl/Vega; 11,957 are unique to Ensembl/Vega relative to NCBI, and 3095 are unique to MGI. More than 4000 genome features fall into categories that require manual inspection to resolve structural differences in the gene models from different annotation sources. Using the MGI unified gene catalog, researchers can easily generate a comprehensive report of mouse genome features from a single source and compare the details of gene and transcript structure using MGI’s mouse genome browser.

Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development

“…We also compared the mDLCS gene list to all mouse genes currently annotated to the Gene Ontology term “lung development” ( GO:0030324 ) and to genes annotated with the Mammalian Phenotype ontology term “respiratory system phenotype” ( MP:0005388 ). We downloaded these annotations from the MGI database (v6.01; 12/22/15) based on MGI’s unified gene catalog (genome assembly GRCm38) ( Zhu et al, 2015 ). The resulting list included 209 genes annotated to the GO term of lung development ( GO:0030324 ) and its child terms and 1,076 genes annotated to the MP term “respiratory system phenotype” ( MP:0005388 ) and its child terms; 134 genes shared both “lung development” and “respiratory system phenotype” annotations.…”

Emerging Putative Associations between Non-Coding RNAs and Protein-Coding Genes in Neuropathic Pain: Added Value from Reusing Microarray Data

“…Undoubtedly, ENSEMBL 3 represents a main source of genome annotation and interpretation currently available. As prediction remains the most important factor determining genome annotation, the way the available evidence is consolidated and curated differentiates ENSEMBL say, from other annotation systems [see an interesting reading on biotype conflicts, Zhu et al ( 68 )]. This is one of the current limitations in the analyses we have proposed here, as the lack of harmonization between annotations of different DB resources makes part of the evidences disagree or contradict each other.…”

Peer Review #1 of "Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development (v0.1)"

“…We also compared the mDLCS gene list to all mouse genes currently annotated to the Gene Ontology term "lung development" (GO:0030324) and to genes annotated with the Mammalian Phenotype ontology term "respiratory system phenotype" (MP:0005388). We downloaded these annotations from the MGI database (v6.01; 12/22/15) based on MGI's unified gene catalog (genome assembly GRCm38) (Zhu et al 2015). The resulting list included 209 genes annotated to the GO term of lung development (GO:0030324) and its child terms and 1076 genes annotated to the MP term "respiratory system phenotype" (MP:0005388) and its child terms; 134 genes shared both "lung development" and "respiratory system phenotype" annotations.…”