ThaleMine 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 and it is manually curated; its contents are not indexed in our keyword search.
More data sets will be added in future releases, please contact us if there are any particular data you would like to see included.
Data Category | Data | Source | PubMed |
---|---|---|---|
Genome |
TAIR10 Genome assembly (5 chromosomes plus chloroplast and mitochondrial assemblies) | NCBI- Release TAIR10 (2018/04/06) | Arabidopsis Genome Initiative - PubMed: 11130711 |
Araport11 GFF3 data from TAIR | TAIR- Release Araport11 (2016/06/17) | Cheng et al., 2016 - PubMed: 27862469 | |
Proteins |
High-quality, manually annotated, non-redundant protein sequence database. | Swiss-Prot- Release 2024_06 | UniProt Consortium - PubMed: 17142230 |
Computationally analysed records, enriched with automatic annotation | TrEMBL- Release 2024_06 | ||
Protein family and domain assignments to proteins | InterPro- Release v103.0 | Mitchell et al., 2019 - PubMed: 30398656 | |
Homology |
Orthologue relationships based on the inferred speciation and gene duplication events in the phylogenetic tree. | Panther- Release 19.0 | Mi et al - PubMed: 23193289 |
Paralogue relationships based on the inferred speciation and gene duplication events in the phylogenetic tree. | Panther- Release 19.0 | Mi et al - PubMed: 23193289 | |
Phytozome Homologs generated with InParanoid | Phytozome- realtime | Goodstein et al - PubMed: 22110026 | |
Curation |
Manually curated TAIR functional descriptions | TAIR- Release 20230930 | Huala et al - PubMed: 11125061 |
Manually curated TAIR gene aliases | TAIR- Release 20230930 | Huala et al - PubMed: 11125061 | |
Gene Ontology |
GO annotations from Gene Ontology | Gene Ontology- Release 2024-11-03 | Berardini et al., 2004 - PubMed: 15173566 Gene Ontology Consortium - PubMed:10802651 |
Several electronic and manual GO annotation methods utilized by UniProt | UniProt- Release 2024_06 | UniProt Consortium - PubMed: 17142230 | |
Interactions |
Curated set of genetic and physical interactions for Arabidopsis thaliana | BioGRID- Release 4.4.239 | Chatr-Aryamontri et al., 2014 - PubMed: 25428363 |
Curated binary and complex protein-protein interactions for Arabidopsis thaliana | IntAct- Release 248 | Kerrien et al., 2012 - PubMed: 22121220 | |
Expression |
Electronic Fluorescent Pictograph (eFP) Visualization paints gene expression information from one of the AtGenExpress data sets or other compendia for a desired gene onto a diagrammatic representation of Arabidopsis thaliana plants. | BAR eFP Webservice- realtime | Winter et al., 2007 - PubMed: 17684564 Brady et al., 2009 - PubMed: 19401381 |
Co-Expression |
Co-regulated gene relationships deduced from microarray and RNA-seq data via ATTED-II web services | ATTED-II Co-expression- realtime | Obayashi et al., 2014 - PubMed: 24334350 |
Publications |
Curated associations between publications and genes from UniProt | UniProt- Release 2024_06 | UniProt Consortium - PubMed: 17142230 |
Publications from InterPro | InterPro- Release v103.0 | Mitchell et al., 2019 - PubMed: 30398656 | |
Publications from NCBI | NCBI- Downloaded 20241130 | Maglott et al., 2007 - PubMed: 17148475 | |
GeneRIF |
Concise phrase describing gene function and publication associated with NCBI Gene records | NCBI- Downloaded 20241130 | Maglott et al., 2007 - PubMed: 17148475 |