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Data

HumanMine integrates data from a large number of sources into a single data warehouse. This page lists the data that are included in the current release. Many more data sets will be added in future releases, please contact us if there are any particular data you would like to see included.

The following data are loaded in HumanMine:


Data Category Organism Data Source Version

Genes

Human Human genome sequence and annotation NCBI GRCh38.p13; Annotation release 109.20200228
Human, Mouse, Rat Gene names and symbol HGNC, NCBI, MGI, RGD April 2020

Proteins

Human, Mouse Protein sequence and annotation UniProt Release 2020_02
Human, Mouse Protein domains InterPro 79.0; April 2020

Gene ontology

Human, Mouse Gene ontology annotations UniProt, MGI, GO Consortium April 2020

Pathways

Human, Mouse Gene-pathway annotations from Reactome Reactome April 2020, v72
Human, Mouse Gene-pathway annotations from Kegg KEGG May 2011

Expression

Human Protein localisation Human Protein Atlas (HPA) April 2020, v19.3
Human RNA-seq across human tissues Human Protein Atlas (HPA) April 2020, v19.3
Human Human gene expression atlas of 5372 samples representing 369 different cell and tissue types, disease states and cell lines ArrayExpress Atlas (experiment E-MTAB-62) June 2011
Human Expression data for 16 human tissue types ArrayExpress Atlas (experiment E-MTAB-513 Illumina body map) July 2014
Human RNA-seq data for human tissues and significant variant-gene associations GTex, Tissue specific gene expression and eQTLs Version 8; July 2019

Interactions

Human, Mouse Physical interaction data IntAct April 2020
Human, Mouse Genetic and physical interaction data BioGRID Version 3.5.185; April 2020

Disease and phenotypes

Human Gene-disease associations from Online Mendelian Inheritance in Man (OMIM) OMIM April 2020
Human Gene-Phenotype annotations HPO April 2020
Mouse Mouse alleles from MGI MGI April 2020
Human Clinically significant sequence variants ClinVar April 2020
Human Genome wide association studies GWAS catalog April 2020, V1.0

Orthologues

Human, Mouse, Rat, Drosophila, C. elegans, S.cerevisiae Orthologue and paralogue predictions between these organisms Panther April 2020, v15.0

Publications

Human, Mouse Gene to PubMed ID mappings NCBI PubMed April 2020