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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 109.20190905
Human, Mouse, Rat Gene names and symbol HGNC, NCBI, MGI, RGD October 2019

Proteins

Human, Mouse Protein sequence and annotation UniProt Release 2019_08
Human, Mouse Protein domains InterPro 76.0; September 2019

Gene ontology

Human, Mouse Gene ontology annotations UniProt, MGI, GO Consortium October 2019

Pathways

Human, Mouse Gene-pathway annotations from Reactome Reactome September 2019, v70
Human, Mouse Gene-pathway annotations from Kegg KEGG May 2011

Expression

Human Protein localisation Human Protein Atlas (HPA) September 2019, v19
Human RNA-seq across human tissues Human Protein Atlas (HPA) September 2019, v19
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 Version 227; October 2019
Human, Mouse Genetic and physical interaction data BioGRID Version 3.5.177; October 2019

Disease and phenotypes

Human Gene-disease associations from Online Mendelian Inheritance in Man (OMIM) OMIM April 2019
Human Gene-Phenotype annotations HPO August 2019
Mouse Mouse alleles from MGI MGI October 2019
Human Clinically significant sequence variants ClinVar October 2019
Human Genome wide association studies GWAS catalog October 2019, V1.0

Orthologues

Human, Mouse, Rat, Drosophila, C. elegans, S.cerevisiae Orthologue and paralogue predictions between these organisms Panther March 2019, v14.1

Publications

Human, Mouse Gene to PubMed ID mappings NCBI PubMed October 2019