Q1: How to Search

Q2: How to Browse

Q3: How to read search results

Q4: How to read detail page

Q5: How to visualize network

Q6: How to blast

Q7: How to submit data

A1: RNALocate provides an interface for convenient retrieval of all RNA subcellular localizations. Users can get each entry through 'Keyword Search' in 'Search' page. In 'Keyword Search', 5 datasets and relevant example have been provided, including 'RNA Symbol', 'RNA Category', 'Organism', 'Subcellular localization' and 'Other ID' (Entrez ID or miRBase ID). Firstly, Users should keep remember to choose an appropriate dataset for your keyword, otherwise, no result will be found. Secondly, fuzzy search is executable only when the associated option has been chosen.

A2: In 'Browse' page, RNALocate are accessible through three different approaches: 'By Localization', 'By Organism' and 'By RNA Category'.

1. For 'Browse By Localization', a treeview has been constructed to display the hierarchical relationship of RNA subcellular localization, according to the cell component annotations curated in Gene Ontology (GO). Users could browse the database by clicking the name on the left treeview or in the right cell graph. Note that the cell doesn't belong to any organism and only some well-known subcellular localizations with a specific structure have been shown in it.

2. For 'Browse By Organism', users could browse the database by clicking the logo of organism on the right phylogenetic tree or by clicking the name on the left treeview.

3. For 'Browse By RNA Category', there are 9 RNA categories in RNALocate: csRNA (chloroplast RNA), mRNA, miRNA, piRNA, rRNA, snRNA, snoRNA, lncRNA and tRNA. Users could get each entry associated with them by clicking the name on the left treeview or in the right graph.

Browse By Localization
Browse By Organism
Browse By RNA Category

A3: RNALocate provides brief details of search results as a table in the 'Search Result' page, including 'RNA Symbol', 'RNA Category', 'Organism, 'Tissue', 'Subcellular Localization' while more detailed descriptions such as PubMed ID and description of the reference are displayed in the 'Detail' page reached by selecting 'more'.

A4: Users will see the details associated with one search result entry in the 'Detail' page as following:

1. RLID: the unique ID owned in RNALocate. RLID format: RLID+ eight sequential number, eg. RLID00000112.

2. RNA Symbol: comes from literature and then be normalized according to NCBI, Ensemble and miRBase

3. RNA Category

4. Organism

5. Aliase: the aliase of RNA symbol

6. Sequence: comes from Refseq, Ensemble, miRBase

7. Homology: comes from HomoloGene and miRBase

8. Network: comes from RAID and StarBase

9. Subcellular Localization

10. Other Subcellular Localization: another subcellular localization entries associated with this RNA

Note: users could click the items with underline or button to get more information about this RNA.

A5: Details have been shown in the following figures:

A6: Blast could be done after parameters selection. Two databases have been provided for blast: miRNADB and othersDB (including mRNA, lncRNA, snoRNA ...). Please choose the appropriate database to blast for your submitted sequence. Details have been shown in the following figures:

A7: RNALocate invites users to upload novel RNA subcellular localization data. Details have been shown in the following figure: