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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 109.20201120; November 2020
Human, Mouse, Rat Gene names and symbol HGNC, NCBI, MGI, RGD December 2020

Proteins

Human, Mouse Protein sequence and annotation UniProt Release 2020_06
Human, Mouse Protein domains InterPro 83.0; December 2020

Gene ontology

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

Pathways

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

Expression

Human Protein localisation Human Protein Atlas (HPA) November 2020, v20.0
Human RNA-seq across human tissues Human Protein Atlas (HPA) November 2020, v20.0
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 December 2020; v4.2.16
Human, Mouse Genetic and physical interaction data BioGRID Version 4.2.192; December 2020

Disease and phenotypes

Human Gene-disease associations from Online Mendelian Inheritance in Man (OMIM) OMIM December 2020
Human Gene-Phenotype annotations HPO December 2020
Mouse Mouse alleles from MGI MGI December 2020; v6.16
Human Clinically significant sequence variants ClinVar December 2020
Human Genome wide association studies GWAS catalog December 2020, V1.0

Orthologues

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

Publications

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