Downloads of short gene descriptions, gene expression, disease annotations, genetic and molecular interaction, and variant data for mouse available from theAlliance of Genome Resources.
| Sequence Data |
| 1. MGI Gene Model Coordinates (tab-delimited) | | MGI Marker Accession ID | Marker Type | Marker Symbol | Marker Name | Genome Build | Entrez Gene ID | NCBI Gene Chromosome | NCBI Gene Start | NCBI Gene End | NCBI Gene Strand | Ensembl Gene ID | Ensembl Gene Chromosome | Ensembl Gene Start | Ensembl Gene End | Ensembl Gene Strand |
| | MGI_Gene_Model_Coord.rpt (GRCm39) |
|
| 2. MGI Sequence Coordinates (in GFF format)(tab-delimited) | | Chromosome | Source of Feature | Marker Type | Start Coordinate | End Coordinate | Empty Column | Strand | Empty Column | ID=MGI ID;Name=marker symbol;Note=marker feature |
| | MGI_GTGUP.gff (GRCm39) |
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| 4. MGI Marker associations to Sequence (GenBank, RefSeq,Ensembl) information (tab-delimited) | | MGI Marker Accession ID | Marker Symbol | Status | Marker Type | Marker Name | cM Position | Chromosome | Genome Coordinate Start | Genome Coordinate End | Strand | GenBank Accession IDs
(pipe-delimited) | RefSeq Transcript ID
(if any) | Ensembl Transcript ID
(if any) | UniProt ID
(if any) | TrEMBL ID
(if any) | Ensembl protein ID
(if any) | RefSeq protein ID
(if any) | Unigene ID
(if any) |
| | MRK_Sequence.rpt |
|
| 5. MGI Marker associations to SWISS-PROT and TrEMBL protein IDs (tab-delimited) | | MGI Marker Accession ID | Marker Symbol | Status | Marker Name | cM Position | Chromosome | SWISS-PROT/TrEMBL Protein
Accession IDs
(space-delimited) |
| | MRK_SwissProt_TrEMBL.rpt |
|
| 6. MGI Marker associations to SWISS-PROT protein IDs (tab-delimited) | | MGI Marker Accession ID | Marker Symbol | Status | Marker Name | cM Position | Chromosome | SWISS-PROT Protein
Accession IDs
(space-delimited) |
| | MRK_SwissProt.rpt |
|
| 7. MGI Marker associations to Gene Trap IDs (tab-delimited) | | MGI Marker Accession ID | Marker Symbol | Status | Marker Name | cM Position | Chromosome | Mutant
Cell Line IDs
(space-delimited) |
| | MRK_GeneTrap.rpt |
|
8. MGI Marker associations to Entrez Gene (tab-delimited)| MGI Marker Accession ID | Marker Symbol | Status | Marker Name | cM Position | Chromosome | Type
| Secondary
Accession IDs
(|-delimited) | Entrez Gene ID | Synonyms
(|-delimited) | Feature Types (|-delimited) | Genome Coordinate Start | Genome Coordinate End | Strand | BioTypes
(|-delimited) |
| | MGI_EntrezGene.rpt | |
| 9. MGI Marker associations to Ensembl sequence information (tab-delimited) | | MGI Marker Accession ID | Marker Symbol | Marker Name | cM Position | Chromosome | Ensembl Accession ID | Ensembl Transcript ID
(space-delimited, if any) | Ensembl Protein ID
(space-delimited, if any) | Feature Types (|-delimited) | Genome Coordinate Start | Genome Coordinate End | Strand | BioTypes
(|-delimited) |
| | MRK_ENSEMBL.rpt |
|
| 10. MGI Marker associations to Ensembl or NCBI gene models where a gene vs. pseudogene discrepancy exists(tab-delimited) | | Marker Symbol | Provider Source | Gene ID | Biotype | MGI Representative Gene Model |
| | MGI_BioTypeConflict.rpt |
|
11. Primer Sequences| Marker Symbol | Marker Name | Primer Marker Name | MGI Marker Accession ID | MGI Primer Pair ID | Primer 1 Sequence | Primer 2 Sequence | Amplimer Size | Chromosome | Map Position |
| | PRB_PrimerSeq.rpt | |
| 12. InterPro Domains (tab-delimited) | | InterPro ID | Domain Marker Name | MGI Marker Accession ID | Marker Symbol |
| | MGI_InterProDomains.rpt |
|
| Vertebrate Homology |
| 1. Homology Classes - Includes: mouse, human, rat, zebrafish (tab-delimited) | | DB Class Key | Common Organism Name | NCBI Taxon ID | Symbol | EntrezGene ID | Mouse MGI ID | HGNC ID | OMIM gene ID | Genetic Location | Genome Coordinates (mouse or human Build) | Name | Synonyms (pipe-delimited) |
| | HOM_AllOrganism.rpt (sorted by DB Class Key) |
|
2. Human and Mouse Homology Classes with Sequence information (tab-delimited)| DB Class Key | Common Organism Name | NCBI Taxon ID | Symbol | EntrezGene ID | Mouse MGI ID | HGNC ID | OMIM gene ID | Genetic Location | Genome Coordinates (mouse or human Build) | Nucleotide RefSeq ID (comma-delimited) | Protein RefSeq ID (comma-delimited) | SWISS-PROT IDs
(comma-delimited) |
| | HOM_MouseHumanSequence.rpt (sorted by DB Class Key) | |
3. Mouse Genes with Alliance Homology and HGNC and CCDS IDs| MGI Marker Accession ID | Mouse Marker Symbol | Mouse Marker Name | NCBI Gene ID | NCBI Gene Chromosome | NCBI Gene start | NCBI Gene end | NCBI Gene strand | Ensembl Gene ID | Ensembl Gene chromosome | Ensembl Gene start | Ensembl Gene end | Ensembl Gene strand | CCDS IDs (comma delimited) | HGNC ID |
| | HGNC_AllianceHomology.rpt | |
4. Mouse/Human Orthology with Phenotype Annotations (tab-delimited)| Human Marker Symbol | Human Entrez Gene ID | Mouse Marker Symbol | MGI Marker Accession ID | High-level Mammalian Phenotype ID
(comma-delimited) |
| | HMD_HumanPhenotype.rpt | |
5. Mouse Protein Coding Genes having one-to-one Orthology with Human Genes| MGI Marker Accession ID | Mouse Gene Symbol | Mouse NCBI Gene ID | HGNC ID | Human Gene Symbol | Human NCBI Gene ID |
| | HOM_ProteinCoding.rpt | |
| Gene Expression |
| 1. MGI Genetic Markers with GXD Literature Content Records (tab-delimited) | | MGI Marker Accession ID | Mouse Marker Symbol | MGI Reference Accession ID (J:) (comma-delimited) |
| | MRK_GXD.rpt |
|
| 2. MGI Genetic Markers with GXD Assay Records (tab-delimited) | | MGI Marker Accession ID | Mouse Marker Symbol | MGI Assay Accession ID (comma-delimited) |
| | MRK_GXDAssay.rpt |
|
| 3. RNA-Seq assay results in GXD (tab-delimited file per experiment) | | MGI Gene ID | Ensembl ID | Gene Symbol | Gene Name | Experiment ID | Anatomical Structure | Theiler Stage | Age | Sex | Strain | Mutant Allele Pair(s) | Notes | Sample ID | Number of Biological Replicates | Bioreplicate Set Label | Detected | AVG TPM | QN TPM | AVG QN TPM |
| | RNA-Seq Report Download | | Comprehensive reports for each RNA-Seq Experiment in GXD with expression data loaded from the Expression Atlas at EMBL's European Bioinformatics Institute (EBI). Reports include GXD-curated sample metadata and GXD-computed TPM values per gene. | | | GXD imports selected sets of RNA-Seq data from EMBL-EBI's Expression Atlas for experiments that have been annotated to controlled biological source metadata by expert GXD curation. Leveraging curated source metadata, GXD processes the files further to effectively integrate RNA-Seq data with classical expression data in GXD. TPM processing includes several steps. First, we use TPM values in the files imported from the Expression Atlas to compute the average TPM value per gene per sample for technical replicates. Then, we group samples that have the same source information into biological replicate sets and quantile normalize (QN) the TPM values per gene across the samples in each biological replicate set. Finally, to minimize biological sample variation, we average these QN TPM values to arrive at a single TPM value per gene per set of bioreplicate samples. Average QN TPM values are used to assign TPM levels and expression detected/not detected status in the GXD interface. Average QN TPM values are also exported for visualization in Morpheus-derived heat maps of GXD expression results. |
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| 4. MGI Microarray Annotation Files (tab-delimited) | | Probeset ID | Sequence ID | MGI ID | Gene Symbol | Gene Name | Chromosome | Start Coordinate | End Coordinate | Strand |
| | Affy_1.0_ST_mgi.rpt (Affymetrix Mouse Gene 1.0 ST Array) | | Affy_430_2.0_mgi.rpt (Affymetrix GeneChip Mouse Genome 430 2.0 Array) | | Affy_U74_mgi.rpt (Affymetrix GeneChip Mouse Genome U74A-B-C_2) |
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| 6. Mammalian Phenotype (MP)-Mouse Developmental Anatomy (EMAPA) Mappings | | MP ID | MP Term | EMAPA ID | EMAPA Term |
| | MP_EMAPA.rpt |
|
| Alleles and Phenotypes |
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| 2. Mouse/Human Orthology with Phenotype Annotations (tab-delimited) | | Human Marker Symbol | Human Entrez Gene ID | Mouse Marker Symbol | MGI Marker Accession ID | High-level Mammalian Phenotype ID
(space-delimited) |
| | HMD_HumanPhenotype.rpt |
|
| 3. List of All Mouse Phenotypic Alleles (tab-delimited) | | MGI Allele Accession ID | Allele Symbol | Allele Name | Allele Type | Allele Attribute | PubMed ID for original reference | MGI Marker Accession ID | Marker Symbol | Marker RefSeq ID | Marker Ensembl ID | High-level Mammalian Phenotype ID (comma-delimited) | Synonyms (|-delimited) | Marker Name |
| | MGI_PhenotypicAllele.rpt |
|
| 4. List of All Mouse QTL Alleles (tab-delimited) | | MGI Allele Accession ID | Allele Symbol | Allele Name | Allele Type | PubMed ID for original reference | MGI Marker Accession ID | Marker Symbol | Marker RefSeq ID | Marker Ensembl ID | Marker Chromosome | Marker Start Coordinate | Marker End Coordinate | Genome Build | High-level Mammalian Phenotype ID (comma-delimited) |
| | MGI_QTLAllele.rpt |
|
| 5. All Genotypes and Mammalian Phenotype Annotations (tab-delimited) | | Allelic Composition | Allele Symbols (pipe-delimited) | Genetic Background | Mammalian Phenotype ID | PubMed IDs (pipe-delimited) | MGI Marker Accession IDs (pipe-delimited) |
| | MGI_PhenoGenoMP.rpt |
|
| 6. List of All KOMP Alleles (tab-delimited) | | Mutant Cell Line ID | Logical DB Name | MGI Allele Accession ID | Allele Symbol | Allele Name | MGI Marker Accession ID | Marker Symbol |
| | KOMP_Allele.rpt |
|
| 7. List of All EUCOMM Alleles (tab-delimited) | | Mutant Cell Line ID | Logical DB Name | MGI Allele Accession ID | Allele Symbol | Allele Name | MGI Marker Accession ID | Marker Symbol |
| | EUCOMM_Allele.rpt |
|
| 8. List of All NorCOMM Alleles (tab-delimited) | | Mutant Cell Line ID | Logical DB Name | MGI Allele Accession ID | Allele Symbol | Allele Name | MGI Marker Accession ID | Marker Symbol |
| | NorCOMM_Allele.rpt |
|
| 9. Genotypes and Mammalian Phenotype Annotations for Marker Type Genes excluding conditional mutations (tab-delimited) | | Allelic Composition | Allele Symbol(s) | Allele ID(s) | Genetic Background | Mammalian Phenotype ID | PubMed ID (pipe-delimited) | MGI Marker Accession ID (pipe-delimited) | MGI Genotype Accession ID (pipe-delimited) |
| | MGI_GenePheno.rpt |
|
| 10. Genotypes with both Phenotype and Disease Annotations for Marker Type Genes, excluding conditional mutations (tab-delimited) | | Allelic Composition | Allele Symbol(s) | Allele ID(s) | Genetic Background | Mammalian Phenotype ID | PubMed ID (pipe-delimited) | MGI Marker Accession ID (pipe-delimited) | DO ID (pipe-delimited) | MIM ID (pipe-delimited) |
| | MGI_Geno_DiseaseDO.rpt |
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| 11. Genotypes with both Phenotype and Negated Disease Annotations for Marker Type Genes, excluding conditional mutations (tab-delimited) | | Allelic Composition | Allele Symbol(s) | Allele ID(s) | Genetic Background | Mammalian Phenotype ID | PubMed ID (pipe-delimited) | MGI Marker Accession ID (pipe-delimited) | DO ID (pipe-delimited) | MIM ID (pipe-delimited) |
| | MGI_Geno_NotDiseaseDO.rpt |
|
| 12. Associations of Mouse Genes with DO Diseases | | DO Disease ID | DO Disease Name | OMIM ID (pipe delimited) | Common Organism Name | NCBI Taxon ID | Symbol | EntrezGene ID | Mouse MGI ID |
| | MGI_DO.rpt |
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| 13. IMSR/KOMP Counts | | Marker Symbol | MGI Marker Accession ID | Total number of IMSR Strains | Total number of Alleles |
| | MGI_IMSRKomp.rpt |
|
| 14.Genotypes with Sex-specific Phenotypes | | Genotype ID | Sex | MP ID | MP Term | Allelic Composition | Background Strain | Sex-specific Normal Y/N | Citation (MGI ID if no PubMed ID) |
| | MGI_Pheno_Sex.rpt |
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15. Mouse models of Human Disease by Human gene (tab-delimited)| Human gene symbol | Human gene name | HGNC id for human gene (pipe-delimited) | DO term name associated with human gene | DO term ID associated with human gene | Mouse genotype IDs associated with DO term (pipe-delimited) | Mouse gene | Mouse MGI ID | Facilities (pipe-delimited) | Repository ID (pipe-delimited) |
| | MGI_DiseaseGeneModel.rpt | |
16. Human Diseases and Mouse Models by Genotype (1:1 orthologs only) (tab-delimited)| DO term name associated with human gene | DO term ID associated with human gene | NOT model | Allele Pairs | Strain Background | Allele symbol | Allele MGI ID | Total number of allele references | Repository ID for allele (pipe-delimited) | Mouse genotype RR id (pipe-delimited) | Mouse gene symbol | Mouse gene ID | Repository ID for gene (pipe-delimited) |
| | MGI_DiseaseMouseModel.rpt | |