In the following sections detailed information regarding the DIANA-LncBase interface are provided.

1.1 Single or multiple miRNA and/or lncRNA names or ids

Users can browse the results by querying with a single miRNA or gene identifier as well as multiple combinations of the previous terms separated by spaces. For the user’s convenience, searching can be performed using a miRNA name in miRBase v18+ nomenclature (e.g. hsa-miR-103a-3p, hsa-miR-320a etc), a MIMAT id, an lncRNA name (e.g. HOTAIR, NEAT1, MALAT1 etc) or an external database gene id. Supported gene ids specifically include Ensembl ids (e.g. ENSG00000259758), gene identifiers used by Cabili et al (e.g. XLOC008672) and NONCODE v3 database ids (e.g. n343070).

1.2 Specialized genomic location search

The Predicted Module specifically offers the option to query the database using a genomic location. The provided results correspond to all the predicted lncRNA-miRNA interactions having at least one MRE within the examined location. Note that for this query to properly function, users need to use a specific format describing the chromosome followed by a colon and the genomic coordinates separated by a dash.

1.3 Personalized search space

DIANA-LncBase provides a personalized search space. Users are able to create their own account by completing a simple registration form. After login in the server a history for every query made is stored in the database automatically while users can additionally bookmark important search results. Upon clicking the relevant buttons in the search space users can access their bookmarks and history and navigate through past search results.

2.1 Filtering the results

An additional option is the filtering of computationally predicted target results on lncRNAs. The user can filter the results using an arbitrary microT threshold, fine-tuning prediction sensitivity and precision levels. The default threshold value is 0.8 which provides adequate sensitivity and precision for most analyses. The results can be additionally refined by an lncRNA tissue specificity filter.

2.2 Interactions

Each entry presents general information, regarding the lncRNAs and miRNAs participating in each interaction, along with the predicted score, and an indication of whether each interaction has also been experimentally verified. A green (predicted & validated) or grey (predicted) colored indicator is utilized to this end. Upon clicking the indicator, direct access to the corresponding section in the experimental module is provided. By expanding each entry, the user can access several informative sections. Note that the queried results can be downloaded by clicking the appropriate button in the result space.

2.3 Genes

The Gene details section supports links and general information regarding the lncRNAs, such as tissue expression.

2.4 microRNAs

The section miRNA details provides a hyperlink to the relevant miRBase entry, shows the corresponding miRBase id, miRNA sequence and also presents a tag cloud with Medical Subject Headings (MeSH) terms derived from MedLine publications.

2.5 MREs

Each miRNA-lncRNA interaction has also one expandable entry with general information per predicted MRE, such as the binding type, MRE location on the transcript, the prediction score and the number of species that the MRE was found to be conserved. Upon expanding the MRE entry, the user can access additional information regarding the position of the MRE on the chromosome, the species that the MRE is conserved and a graphical representation of the binding area. An additional feature of the Predicted Module is the ability to visualize the interactions in the UCSC genome browser. Upon clicking the relevant button, a graphical representation appears containing all the MREs, of the selected lncRNA, whose interaction score is above 0.8. This threshold has been deliberately chosen in order to produce a graphic that is not crowded and can be efficiently interpreted by the user.

3.1 Filtering the results

The Experimental Module hosts an enhanced filtering system, able to reduce results based on species, experimental method, publication year and predicted interaction score.

3.2 Interactions

Query results initially display general information about the interactions, participating lncRNAs/miRNAs and the methods used for validating each interaction. In cases where a specific interaction has also been predicted by DIANA-microT-CDS, DIANA-LncBase provides the relevant score, along with an active link to the corresponding entry in the target prediction module. All results can be further expanded to reveal a wealth of useful information.

3.3 Genes

The section Gene details supports general gene-related information, as well as links to the external database originally indexing this specific lncRNA.

3.4 microRNAs

The section miRNA details provides a hyperlink to the relevant miRBase entry, shows the corresponding miRBase id, miRNA sequence and also presents a tag cloud with Medical Subject Headings (MeSH) terms derived from MedLine publications. If no related diseases have been found then a proper indication text appears in the place of the tag cloud.

3.5 Publications

The section Publications provides specific data for each supporting publication, such as regulation type (up-regulated or down-regulated), targeting (direct or indirect) and tissue / cell type information.