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MGI Data and Statistical Reports

 MGI Data and Statistical Reports

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Table of Contents
Additional Reports
Mouse Genetic Markers
Sequence Data
Vertebrate Homology
Gene Ontology Data
Strains and Polymorphisms
Gene Expression
Alleles and Phenotypes
Recombinase (cre) Specificity
References
Clone Collections
DNA Mapping Panels
   Each entry contains the following information:

Summary description of data
Description of data in Field 1Description of data in Field 2etc.
        filename on FTP server (link) (additional details)
Additional Reports

These files, along with some additional reports, are also available from this Index.


Mouse Genetic Markers
1. List of Mouse Genetic Markers (sorted alphabetically by marker symbol, tab-delimited)
MGI Marker Accession IDChromosomecM PositionGenome Coordinate StartGenome Coordinate EndGenome StrandMarker SymbolStatusMarker NameMarker TypeFeature Types (|-delimted)Marker Synonyms (|-delimited)
        MRK_List1.rpt (including withdrawn marker symbols)
        MRK_List2.rpt (excluding withdrawn marker symbols)
2. MGI Marker Coordinates (tab-delimited)
MGI Marker Accession ID Marker Type Feature Type Marker Symbol Marker Name Chromosome Start Coordinate End Coordinate Strand Genome Build Provider Provider Display
        MGI_MRK_Coord.rpt (GRCm38)

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 VEGA Gene ID VEGA Gene Chromosome VEGA Gene Start VEGA Gene End VEGA Gene Strand
        MGI_Gene_Model_Coord.rpt (GRCm38)
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 (GRCm38)
3. MGI Sequence Coordinates (in GFF3 format)(tab-delimited)
Specification file: MGI_GFF_Spec.docx
        MGI.gff3.gz
4. MGI Marker associations to Sequence (GenBank, RefSeq,VEGA, 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)
VEGA Transcript ID
(if any)
Ensembl Transcript ID
(if any)
UniProt ID
(if any)
TrEMBL ID
(if any)
VEGA protein 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 IDMarker SymbolStatusMarker NamecM PositionChromosome 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 IDMarker SymbolStatusMarker NamecM PositionChromosome SWISS-PROT Protein
Accession IDs
(space-delimited)
        MRK_SwissProt.rpt
7. MGI Marker associations to Gene Trap IDs (tab-delimited)
MGI Marker Accession IDMarker SymbolStatusMarker NamecM PositionChromosome Mutant
Cell Line IDs
(space-delimited)
        MRK_GeneTrap.rpt
8. MGI Marker associations to Entrez Gene (tab-delimited)
MGI Marker Accession IDMarker SymbolStatusMarker NamecM PositionChromosome Type
Gene
DNA Segment
Other Genome Feature
Complex/Cluster/Region
microRNA
Secondary
Accession IDs
(|-delimited)
Entrez Gene IDSynonyms
(|-delimited)
Feature Types (|-delimited)Genome Coordinate StartGenome Coordinate EndStrandBioTypes
(|-delimited)
        MGI_EntrezGene.rpt
9. MGI Marker associations to VEGA sequence information (tab-delimited)
MGI Marker Accession IDMarker SymbolMarker NamecM PositionChromosome VEGA Accession IDVEGA Transcript ID
(space-delimited, if any)
VEGA Protein ID
(space-delimited, if any)
Feature Types (|-delimited)Genome Coordinate StartGenome Coordinate EndStrandBioTypes
(|-delimited)
        MRK_VEGA.rpt
10. MGI Marker associations to Ensembl sequence information (tab-delimited)
MGI Marker Accession IDMarker SymbolMarker NamecM PositionChromosome Ensembl Accession IDEnsembl Transcript ID
(space-delimited, if any)
Ensembl Protein ID
(space-delimited, if any)
Feature Types (|-delimited)Genome Coordinate StartGenome Coordinate EndStrandBioTypes
(|-delimited)
        MRK_ENSEMBL.rpt
11. MGI Marker associations to VEGA, Ensembl or NCBI gene models where a gene vs. pseudogene discrepancy exists(tab-delimited)
Marker SymbolProvider SourceGene IDBiotypeMGI Representative Gene Model
        MGI_BioTypeConflict.rpt
12. Primer Sequences
Marker SymbolMarker NamePrimer Marker NameMGI Marker Accession IDMGI Primer Pair IDPrimer 1 SequencePrimer 2 SequenceAmplimer SizeChromosomeMap Position
        PRB_PrimerSeq.rpt
13. InterPro Domains (tab-delimited)
InterPro IDDomain Marker NameMGI Marker Accession IDMarker Symbol
        MGI_InterProDomains.rpt

Vertebrate Homology
1. Homology Classes - Includes: mouse, human, chimpanzee, rhesus macaque, dog, cattle, rat, chicken, western clawed frog, zebrafish (tab-delimited)
HomoloGene ID Common Organism Name NCBI Taxon ID Symbol EntrezGene ID Mouse MGI ID HGNC ID OMIM gene ID Genetic Location Genome Coordinates: Build NameSynonyms (pipe-delimited)
        HOM_AllOrganism.rpt (sorted by HomoloGene ID)
2. Human and Mouse Homology Classes with Sequence information (tab-delimited)
HomoloGene ID Common Organism Name NCBI Taxon ID Symbol EntrezGene ID Mouse MGI ID HGNC ID OMIM gene ID Genetic Location Genome Coordinates: Build Nucleotide RefSeq ID (comma-delimited) Protein RefSeq ID (comma-delimited) SWISS-PROT IDs
(comma-delimited)
        HOM_MouseHumanSequence.rpt (sorted by HomoloGene ID)
3. Mouse Genes with HomoloGene, HGNC and CCDS IDs
MGI Marker Accession IDMouse Marker SymbolMouse Marker NameNCBI Gene IDNCBI Gene ChromosomeNCBI Gene startNCBI Gene endNCBI Gene strandEnsembl Gene IDEnsembl Gene chromosomeEnsembl Gene startEnsembl Gene endEnsembl Gene strandVEGA Gene IDVEGA Gene chromosomeVEGA Gene startVEGA Gene endVEGA Gene strandCCDS IDs (comma delimited)HGNC IDHomoloGene ID
        HGNC_homologene.rpt
4. Mouse/Human Orthology with Phenotype Annotations (tab-delimited)
Human Marker SymbolHuman Entrez Gene IDHomoloGene IDMouse Marker SymbolMGI Marker Accession IDHigh-level Mammalian Phenotype ID
(space-delimited)
        HMD_HumanPhenotype.rpt

Gene Ontology Data
1. Gene Ontology (GO) Annotations of Mouse Markers (tab-delimited) Notice: as of 21-Aug-2009, MGI will be providing this daily gene_association.mgi file in GAF 2.0 format. This file has two additional columns, 16 and 17, explained in detail here.

A GAF 2.0 file can be easily converted to GAF 1 by the removal of the last two columns. Additionally, a GAF 1 version of this file which is updated weekly is available here.
Database
Designation
MGI Marker Accession IDMouse Marker SymbolNOT
Designation
GO
Term ID
MGI
Reference Accession ID
GO
Evidence Code
Inferred From Ontology
P=Biological Process
F=Molecular Function
C=Cellular Component
Mouse Marker NameMouse Marker Synonyms
(if any)
Mouse Marker Type
gene
transcript
protein
TaxonModification DateAssigned ByAnnotation ExtensionGene Product
        gene_association.mgi.gz
2. Marker/SWISS-PROT Associations for Markers with GO Annotations (tab-delimited)
MGI Marker Accession IDSWISS-PROT ID (;-delimited)
        gp2protein.mgi
3. GO terms and GO IDs for all three ontologies (Biological Process, Cellular Component, Molecular Function) (tab-delimited)
OntologyGO IDGO Term
        go_terms.mgi (only those terms annotated to MGI markers are included)

Strains and Polymorphisms
1. Official Strain Nomenclature (tab-delimited)
MGI Strain IDStrain NameStrain Type
        MGI_Strain.rpt
        (sorted alphabetically by strain name)
2. Unreviewed Nonstandard Mouse Strain and Stock Nomenclature (tab-delimited)
MGI Strain IDStrain NameStrain Type
        MGI_Nonstandard_Strain.rpt
        (sorted alphabetically by strain name)
3. List of ES Cell Line Names and Strains of Origin (tab-delimited)
ES Cell Line NameStrain Name
        ES_CellLine.rpt

Gene Expression
1. MGI Genetic Markers with GXD Literature Content Records (tab-delimited)
MGI Marker Accession IDMouse Marker SymbolMGI Reference Accession ID (J:) (comma-delimited)
        MRK_GXD.rpt
2. MGI Genetic Markers with GXD Assay Records (tab-delimited)
MGI Marker Accession IDMouse Marker SymbolMGI Assay Accession ID (comma-delimited)
        MRK_GXDAssay.rpt
3. Mouse Anatomy in OBO Format
        adult_mouse_anatomy.obo
4. Mouse-Human Anatomy Mappings
        ma2ncit.obo
5. MGI Microarray Annotation Files (tab-delimited)
Probeset IDSequence IDMGI IDGene SymbolGene NameChromosomeStart CoordinateEnd CoordinateStrand
        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)

Alleles and Phenotypes
1. Mammalian Phenotype Vocabulary in OBO v1.2, tab-delimited and OWL Formats
        MPheno_OBO.ontology
        VOC_MammalianPhenotype.rpt
        mp.owl
2. Mouse/Human Orthology with Phenotype Annotations (tab-delimited)
Human Marker SymbolHuman Entrez Gene IDHomoloGene IDHGNC Association?Mouse Marker SymbolMGI Marker Accession IDHigh-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)
        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 CompositionAllele Symbol(s)Genetic BackgroundMammalian Phenotype IDPubMed IDMGI Marker Accession ID (comma-delimited)
        MGI_PhenoGenoMP.rpt
6. List of All KOMP Alleles (tab-delimited)
Mutant Cell Line IDLogical DB NameMGI Allele Accession IDAllele SymbolAllele NameMGI Marker Accession IDMarker Symbol
        KOMP_Allele.rpt
7. List of All EUCOMM Alleles (tab-delimited)
Mutant Cell Line IDLogical DB NameMGI Allele Accession IDAllele SymbolAllele NameMGI Marker Accession IDMarker Symbol
        EUCOMM_Allele.rpt
8. List of All NorCOMM Alleles (tab-delimited)
Mutant Cell Line IDLogical DB NameMGI Allele Accession IDAllele SymbolAllele NameMGI Marker Accession IDMarker Symbol
        NorCOMM_Allele.rpt
9. Genotypes and Mammalian Phenotype Annotations for Marker Type Genes excluding conditional mutations (tab-delimited)
Allelic CompositionAllele Symbol(s)Allele ID(s)Genetic BackgroundMammalian Phenotype IDPubMed 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 CompositionAllele Symbol(s)Allele ID(s)Genetic BackgroundMammalian Phenotype IDPubMed ID (pipe-delimited)MGI Marker Accession ID (pipe-delimited)DO ID (pipe-delimited)
        MGI_Geno_DiseaseDO.rpt
11. Genotypes with both Phenotype and Negated Disease Annotations for Marker Type Genes, excluding conditional mutations (tab-delimited)
Allelic CompositionAllele Symbol(s)Allele ID(s)Genetic BackgroundMammalian Phenotype IDPubMed ID (pipe-delimited)MGI Marker Accession ID (pipe-delimited)DO ID (pipe-delimited)
        MGI_Geno_NotDiseaseDO.rpt
12. Associations of Mouse Genes with DO Diseases
DO Disease IDDO Disease NameHomoloGene IDCommon Organism NameNCBI Taxon IDSymbolEntrezGene IDMouse MGI ID
        MGI_DO.rpt
13. IMSR/KOMP Counts
Marker SymbolMGI Marker Accession IDTotal number of IMSR StrainsTotal number of Alleles
        MGI_IMSRKomp.rpt

Recombinase (cre) Specificity
1. Recombinase (cre) Specificity
DriverAllele SymbolNameDetected inAbsent inIMSR StrainAllele ID
        MGI_Recombinase_Full.html
        MGI_Recombinase_Full.rpt (Tab-delimited version)

References
1. Association of MGI Markers and PubMed IDs (tab-delimited)
MGI Marker Accession IDMarker SymbolMarker NameMarker Synonyms
(|-delimited)
PubMed IDs
(|-delimited)
        MRK_Reference.rpt
2. Association of MGI Reference Accession IDs and PubMed IDs (tab-delimited)
MGI Reference Accession IDPubMed IDAlternative MGI Reference Accession ID (J:)
        BIB_PubMed.rpt

Clone Collections
1. All Clones (tab-delimited)
MGI Clone IDClone NameMGI Marker IDMarker SymbolClone Set
        MGI_CloneSet.rpt

DNA Mapping Panels
1. Copeland-Jenkins - (C57BL/6J x M.spretus)F1 x C57BL/6J
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 205 animals (1 column per animal)J Number
        MGI_Copeland-Jenkins_Panel.rpt (tab-delimited)
2. EUCIB (BSB) - (C57BL/6J x SPR or SEG/Pas)F1 x C57BL6J
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 482 animals (1 column per animal)J Number
        MGI_EUCIB_BSB_Panel.rpt (tab-delimited)
3. EUCIB (BSS) - (C57BL/6J x SPR or SEG/Pas)F1 x SPR or SEG/Pas
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 501 animals (1 column per animal)J Number
        MGI_EUCIB_BSS_Panel.rpt (tab-delimited)
4. JAX (BSB) - (C57BL/6J x M.spretus)F1 x C57BL/6J
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 94 animals (1 column per animal)J Number
        MGI_JAX_BSB_Panel.rpt (tab-delimited)
5. JAX (BSS) - (C57BL/6JEi x SPRET/Ei)F1 x SPRET/EiJ
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 94 animals (1 column per animal)J Number
        MGI_JAX_BSS_Panel.rpt (tab-delimited)
6. JAX Mouse Mutant Resource BCB - (C57BL/6J x CAST/Ei)F1 x C57BL/6J
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 144 animals (1 column per animal)J Number
        MGI_JAX_Mouse_Mutant_Resource_BCB_Panel.rpt (tab-delimited)
7. JAX Mouse Mutant Resource BSS - (C57BL/6J x SPRET/Ei)F1 x SPRET/EiJ
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 139 animals (1 column per animal)J Number
        MGI_JAX_Mouse_Mutant_Resource_BSS_Panel.rpt (tab-delimited)
8. Kozak FvC58 - (NFS/N x M.spretus)F1 x C58/J
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 93 animals (1 column per animal)J Number
        MGI_Kozak_FvC58_Panel.rpt (tab-delimited)
9. Kozak FvSpr - (NFS/N x M.spretus)F1 x M.spretus
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 24 animals (1 column per animal)J Number
        MGI_Kozak_FvSpr_Panel.rpt (tab-delimited)
10. Kozak Skive - (NFS/N or C58/J x M.m.musculus)F1 x M.m.musculus
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 94 animals (1 column per animal)J Number
        MGI_Kozak_Skive_Panel.rpt (tab-delimited)
11. MIT - (C57BL/6J-Lep<ob> x CAST)F1 x (C57BL/6J-Lep<ob> x CAST)F1
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 46 animals (1 column per animal)J Number
        MGI_MIT_Panel.rpt (tab-delimited)
12. Reeves (Chr 16) - Sex averaged intersubspecific mapping panel
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 707 animals (1 column per animal)J Number
        MGI_Reeves_Chr_16_Panel.rpt (tab-delimited)
13. Seldin - (C3H/HeJ-Fasl<gld> x M.spretus)F1 x C3H/HeJ-Fasl<gld>/J
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 849 animals (1 column per animal)J Number
        MGI_Seldin_Panel.rpt (tab-delimited)
14. UCLA (BSB) - (C57BL/6J x M.spretus)F1 x C57BL/6J
ChromosomeMGI Marker Accession IDMarker SymbolAllele data for 67 animals (1 column per animal)J Number
        MGI_UCLA_BSB_Panel.rpt (tab-delimited)