mx-plore
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Database view
mx-plore is a database of miRNA-gene interactions retrieved from text mining NCBI PubMed abstracts and NCBI PubmedCentral full texts (oa_comm subset).
During text mining, interactions are classified as miRNA interacting with gene (MIR_GENE) or gene interacting with miRNA (GENE_MIR). The regulatory direction can either be negatively affecting the target (DOWN), positively affecting the target (UP) or undeterminable (NEU).
Even though the mx-plore text mining has a high F1-score (more than 0.9) in the Bagewadi et al. benchmark, this system is not fail proof.
Incorrect interactions can be retrieved from full texts. However, it is expected that the most prevalent interaction found in literature is a good proxy for correct interactions. Hence, the consensus column in the database view tells the user whether this is the most abundant interaction for this miRNA-gene pair (consensus = yes) or not (consensus = no).
By clicking on the details link in each entry the user is directed to a detailed view of the selected miRNA-gene interaction. Here the user can explore the underlying text-mining evidences, the context in which this miRNA is mentioned in as well as the history of publications on this miRNA-gene interaction.
Description of the table fields:
| Field |
Meaning |
| miRNA Family | miRNA name at pre-cursor level |
| Gene | Gene symbol of identified HGNC id |
| Interaction | Type of interaction between miRNA and gene |
| Organisms | Whether the gene identifier was found in the human (hsa) or mouse (mmu) gene synonym list. |
| Evidence Count | Number of documents identified for this interactions. This does not update upon filtering for context. |
| Consensus | Whether it is the most abundant interaction. |
| Details | Link to the details page with all text mining evidence. |
Entry details view
Interaction Details
The shown interaction details contain the same information as described in the table above for the database view.
Please note, that the organism is given in terms of whether a human or mouse gene synonym was matched.
Interaction Context
Article annotations are displayed in a word cloud. Annotations stem from textmining terms describing Gene Ontology terms, cell lines, diseases.
Words are displayed larger the more frequent a word (or term) is mentioned in all evidence articles. The size of each entry scales exponentially with the number of occurrences.
Note, this word cloud is only drawn if such annotations were retrieved for an article. The threshold for concepts to be shown is 1 if less than 100 distinct concepts were found, and 3 otherwise.
Interaction Binding Sites
Human gene structure and
TargetScan v8.0 miRNA binding site predictions (conserved sites of conserved miRNA families).
If no miRNA binding sites are shown, no
conserved sites of conserved miRNA families were predicted.
For interactions found with human (and mouse) gene synonyms, only the human gene structure and miRNA binding sites are displayed.
For interactions solely found with mouse gene synonyms, the corresponding mouse information from
TargetScan v8.0 mouse are displayed.
Interaction Evidences
Sentences in which evidence for the displayed miRNA-gene interaction and direction are found.
Both miRNA and gene are highlighted.
A link to the respective resource in
NCBI PubMed or
NCBI PubmedCentral is provided.
Interaction Timeline
Timeline plot of the timeline articles. The relation of the articles along the time axis is visible, and the articles are briefly described in terms of their main content.
The main content is determined by collecting the top 3 concepts from the celllines synonyms, biological processes and diseases.
The identified concepts are collected and processed per category (cell lines, biological processes and diseases).
For each identified concept the parent terms are retrieved from the underlying ontology.
Then, the concept is added to a counter with weight one. Each parent is added with weight 2.
Finally, the two top (highest weighted) elements from the counter are taken to describe the underlying concept in a publication.