MiEEA integrated data sets Updated

If you make use of the here provided data sets for your publications, please cite our corresponding publication:

Kern, F. et al.

miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems

Precursor sets

Category Original source Annotations integrated in miEAA
Homo sapiens Mus musculus Rattus norvegicus Arabidopsis thaliana Bos taurus Caenorhabditis elegans Drosophila melanogaster Danio rerio Gallus gallus Sus scrofa
Families miRBase v22 miRBase_Family_precursor.gmt miRBase_Family_precursor.gmt miRBase_Family_precursor.gmt miRBase_Family_precursor.gmt miRBase_Family_precursor.gmt miRBase_Family_precursor.gmt miRBase_Family_precursor.gmt miRBase_Family_precursor.gmt miRBase_Family_precursor.gmt miRBase_Family_precursor.gmt
50 kb Clusters miRBase v22 miRBase_Cluster_precursor.gmt miRBase_Cluster_precursor.gmt miRBase_Cluster_precursor.gmt miRBase_Cluster_precursor.gmt miRBase_Cluster_precursor.gmt miRBase_Cluster_precursor.gmt miRBase_Cluster_precursor.gmt miRBase_Cluster_precursor.gmt miRBase_Cluster_precursor.gmt miRBase_Cluster_precursor.gmt
Chromosomal Locations miRBase v22 miRBase_Chromosomes_precursor.gmt miRBase_Chromosomes_precursor.gmt miRBase_Chromosomes_precursor.gmt miRBase_Chromosomes_precursor.gmt miRBase_Chromosomes_precursor.gmt miRBase_Chromosomes_precursor.gmt miRBase_Chromosomes_precursor.gmt miRBase_Chromosomes_precursor.gmt miRBase_Chromosomes_precursor.gmt miRBase_Chromosomes_precursor.gmt
Pubmed miRBase v22 miRBase_Pubmed_precursor.gmt miRBase_Pubmed_precursor.gmt miRBase_Pubmed_precursor.gmt miRBase_Pubmed_precursor.gmt miRBase_Pubmed_precursor.gmt miRBase_Pubmed_precursor.gmt miRBase_Pubmed_precursor.gmt miRBase_Pubmed_precursor.gmt miRBase_Pubmed_precursor.gmt miRBase_Pubmed_precursor.gmt
High confidence MirGeneDB 2.1 miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt - miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt
High confidence miRBase v22 miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt - miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt miRBase_High_confidence_precursor.gmt
Diseases HMDD3 HMDD_precursor.gmt - - - - - - - - -
Interactions NPInter 4.0 NPInter_precursor.gmt NPInter_precursor.gmt NPInter_precursor.gmt - - NPInter_precursor.gmt NPInter_precursor.gmt - - -
Transcription factors TransmiR 2.0 TransmiR_Transcription_factors_precursor.gmt TransmiR_Transcription_factors_precursor.gmt TransmiR_Transcription_factors_precursor.gmt - - TransmiR_Transcription_factors_precursor.gmt TransmiR_Transcription_factors_precursor.gmt - - -
Tissues with miRNA-TF interactions TransmiR 2.0 TransmiR_Tissues_precursor.gmt TransmiR_Tissues_precursor.gmt TransmiR_Tissues_precursor.gmt - - TransmiR_Tissues_precursor.gmt TransmiR_Tissues_precursor.gmt - - -
Diseases MNDR 2.0 MNDR_precursor.gmt MNDR_precursor.gmt MNDR_precursor.gmt - - - - - - -
Localization RNALocate RNALocate_precursor.gmt RNALocate_precursor.gmt RNALocate_precursor.gmt - - - RNALocate_precursor.gmt - - RNALocate_precursor.gmt
Function TAM 2.0 TAM_Function_precursor.gmt - - - - - - - - -
Tissues TAM 2.0 TAM_TissueSpecific_precursor.gmt - - - - - - - - -
Tissues Publication on precursor profiles in tissues:
doi:10.1101/430561 		- Published_expressed_tissue_precursor.gmt Published_specific_tissue_precursor.gmt - - - - - - - -

miRNA sets

Category Original source Annotations integrated in miEAA
Homo sapiens Mus musculus Rattus norvegicus Arabidopsis thaliana Bos taurus Caenorhabditis elegans Drosophila melanogaster Danio rerio Gallus gallus Sus scrofa
Diseases Own publications about blood borne miRNA profiles in different diseases:
PMID: 23895045
PMID: 21892151		 Published_Diseases_mature.gmt - - - - - - - - -
Age/Gender Own publication about age/gender dependent blood borne miRNA profiles
PMID: 24987111		 Published_Age_gender_mature.gmt - - - - - - - - -
Immune cells Own publication about miRNA profiles in different immune cells
PMID: 24928098		 Published_Immune_cells_mature.gmt - - - - - - - - -
Diseases miRWalk 2.0 miRWalk_Diseases_mature.gmt miRWalk_Diseases_mature.gmt miRWalk_Diseases_mature.gmt - - - - - - -
Organs miRWalk 2.0 miRWalk_Organs_mature.gmt miRWalk_Organs_mature.gmt miRWalk_Organs_mature.gmt - - - - - - -
Pathways miRWalk 2.0 miRWalk_Pathways_mature.gmt miRWalk_Pathways_mature.gmt miRWalk_Pathways_mature.gmt - - - - - - -
Gene Ontology miRWalk 2.0 miRWalk_GO_mature.gmt miRWalk_GO_mature.gmt miRWalk_GO_mature.gmt - - - - - - -
Target genes miRTarBase
Release 8.0: June 30, 2019		 miRTarBase_mature.gmt miRTarBase_mature.gmt miRTarBase_mature.gmt miRTarBase_mature.gmt miRTarBase_mature.gmt miRTarBase_mature.gmt miRTarBase_mature.gmt miRTarBase_mature.gmt miRTarBase_mature.gmt miRTarBase_mature.gmt
Seed families miRBase v22 miRBase_Seed_family_mature.gmt miRBase_Seed_family_mature.gmt miRBase_Seed_family_mature.gmt miRBase_Seed_family_mature.gmt miRBase_Seed_family_mature.gmt miRBase_Seed_family_mature.gmt miRBase_Seed_family_mature.gmt miRBase_Seed_family_mature.gmt miRBase_Seed_family_mature.gmt miRBase_Seed_family_mature.gmt
Chromosomal Locations miRBase v22 miRBase_Chromosomes_mature.gmt miRBase_Chromosomes_mature.gmt miRBase_Chromosomes_mature.gmt miRBase_Chromosomes_mature.gmt miRBase_Chromosomes_mature.gmt miRBase_Chromosomes_mature.gmt miRBase_Chromosomes_mature.gmt miRBase_Chromosomes_mature.gmt miRBase_Chromosomes_mature.gmt miRBase_Chromosomes_mature.gmt
High confidence miRBase v22 miRBase_High_confidence_mature.gmt miRBase_High_confidence_mature.gmt miRBase_High_confidence_mature.gmt - miRBase_High_confidence_mature.gmt miRBase_High_confidence_mature.gmt miRBase_High_confidence_mature.gmt miRBase_High_confidence_mature.gmt miRBase_High_confidence_mature.gmt miRBase_High_confidence_mature.gmt
High confidence MirGeneDB 2.1 MirGeneDB_High_confidence_precursor.gmt MirGeneDB_High_confidence_precursor.gmt MirGeneDB_High_confidence_precursor.gmt - MirGeneDB_High_confidence_precursor.gmt MirGeneDB_High_confidence_precursor.gmt MirGeneDB_High_confidence_precursor.gmt MirGeneDB_High_confidence_precursor.gmt MirGeneDB_High_confidence_precursor.gmt -
Node of origin (family) MirGeneDB 2.1 MirGeneDB_node_family_precursor.gmt MirGeneDB_node_family_precursor.gmt MirGeneDB_node_family_precursor.gmt - MirGeneDB_node_family_precursor.gmt MirGeneDB_node_family_precursor.gmt MirGeneDB_node_family_precursor.gmt MirGeneDB_node_family_precursor.gmt MirGeneDB_node_family_precursor.gmt -
Node of origin (locus) MirGeneDB 2.1 MirGeneDB_node_locus_precursor.gmt MirGeneDB_node_locus_precursor.gmt MirGeneDB_node_locus_precursor.gmt - MirGeneDB_node_locus_precursor.gmt MirGeneDB_node_locus_precursor.gmt MirGeneDB_node_locus_precursor.gmt MirGeneDB_node_locus_precursor.gmt MirGeneDB_node_locus_precursor.gmt -
Conserved miRNAs (at least 5 species) miRBase v22 miRBase_Conserved_miRNAs_5_organisms_mature.gmt miRBase_Conserved_miRNAs_5_organisms_mature.gmt miRBase_Conserved_miRNAs_5_organisms_mature.gmt miRBase_Conserved_miRNAs_5_organisms_mature.gmt miRBase_Conserved_miRNAs_5_organisms_mature.gmt miRBase_Conserved_miRNAs_5_organisms_mature.gmt miRBase_Conserved_miRNAs_5_organisms_mature.gmt miRBase_Conserved_miRNAs_5_organisms_mature.gmt miRBase_Conserved_miRNAs_5_organisms_mature.gmt miRBase_Conserved_miRNAs_5_organisms_mature.gmt
exRNA forms miRandola 2017 (v2) miRandola_mature.gmt miRandola_mature.gmt miRandola_mature.gmt - miRandola_mature.gmt - - miRandola_mature.gmt - -
Diseases MNDR 2.0 MNDR_mature.gmt MNDR_mature.gmt MNDR_mature.gmt - - - - - - MNDR_mature.gmt
Interactions NPInter 4.0 NPInter_mature.gmt NPInter_mature.gmt NPInter_mature.gmt NPInter_mature.gmt NPInter_mature.gmt NPInter_mature.gmt - NPInter_mature.gmt NPInter_mature.gmt NPInter_mature.gmt
Localization RNALocate RNALocate_mature.gmt RNALocate_mature.gmt RNALocate_mature.gmt - RNALocate_mature.gmt - - - - RNALocate_mature.gmt
Expressed in tissue TissueAtlas TissueAtlas_mature.gmt - - - - - - - - -
Tissue specific isomiRdb isomiRdb_Tissue_specific_mature.gmt - - - - - - - - -
Pathways KEGG KEGG_mature.gmt KEGG_mature.gmt KEGG_mature.gmt - - - - KEGG_mature.gmt KEGG_mature.gmt -
Annotations (Direct) Gene Ontology GO_Annotations_mature.gmt GO_Annotations_mature.gmt GO_Annotations_mature.gmt - GO_Annotations_mature.gmt - GO_Annotations_mature.gmt GO_Annotations_mature.gmt - GO_Annotations_mature.gmt
Annotations (Indirect over miRTarBase) Gene Ontology GO_Annotations_indirect_mature.gmt GO_Annotations_indirect_mature.gmt GO_Annotations_indirect_mature.gmt GO_Annotations_indirect_mature.gmt GO_Annotations_indirect_mature.gmt GO_Annotations_indirect_mature.gmt GO_Annotations_indirect_mature.gmt GO_Annotations_indirect_mature.gmt GO_Annotations_indirect_mature.gmt GO_Annotations_indirect_mature.gmt
Significant GO - Biological process annotations miRPathDB miRPathDB_GO_Biological_process_mature.gmt miRPathDB_GO_Biological_process_mature.gmt - - - - - - - -
Significant GO - Cellular component annotations miRPathDB miRPathDB_GO_Cellular_component_mature.gmt miRPathDB_GO_Cellular_component_mature.gmt - - - - - - - -
Significant GO - Molecular function annotations miRPathDB miRPathDB_GO_Molecular_function_mature.gmt miRPathDB_GO_Molecular_function_mature.gmt - - - - - - - -
Significant KEGG pathways miRPathDB miRPathDB_KEGG_mature.gmt miRPathDB_KEGG_mature.gmt - - - - - - - -
Significant Reactome pathways miRPathDB miRPathDB_Reactome_mature.gmt - - - - - - - - -
Significant WikiPathways pathways miRPathDB miRPathDB_WikiPathways_mature.gmt miRPathDB_WikiPathways_mature.gmt - - - - - - - -
Drugs SM2miR SM2miR_mature.gmt SM2miR_mature.gmt SM2miR_mature.gmt SM2miR_mature.gmt - SM2miR_mature.gmt - SM2miR_mature.gmt - -
Tissues Publication on miRNA profiles in tissues:
PMID: 25977763 		- - Published_expressed_tissue_mature.gmt Published_specific_tissue_mature.gmt - - - - - - -
Cell-types Human Cellular microRNAome (plus orthology conversion using MirGeneDB):
PMID: 36007182 		Cellular_miRNAome_Highly_expressed_mature.gmt Cellular_miRNAome_Highly_expressed_mature.gmt Cellular_miRNAome_Highly_expressed_mature.gmt - Cellular_miRNAome_Highly_expressed_mature.gmt - - - - -
Cell-types Publication on miRNA cell-type specificity:
PMID: 28829439 		Published_cell_specific_mature.gmt - - - - - - - - -
isomiRs miRNAs that generate specific isomiRs (isomiRdb):
PMID: 36243964 		isomiRdb_isomiRs_mature.gmt - - - - - - - - -