Help
Search Options
We have implemented two search menus - ‘Search: piRNA/Gene Name’ and ‘Search: piRNA sequence’ for querying tarpiD and obtain results. ‘Search: piRNA/Gene Name’ is the default search option.

Search by piRNA/Gene Name:
  1. The user will first select ‘Species’ from the drop-down menu.
  2. Then, user will ‘Select Query Type’ from the drop-down menu. Upon selecting query type, user will be asked to select and search by any of these three modes below to obtain piRNA:gene interactions and associated information:
    1. piRNA(s): User can select to search either for a single piRNA or multiple piRNAs that should be separated with comma without any space in between. While typing piRNA name (Genbank, e.g., piR-xxxx, where xxxx represent numbers) in the search box, it’ll show piRNA names populated from the database to enable user to select the piRNA of interest. If user wishes to search multiple piRNAs, piRNA names won’t show up and s/he needs to type the piRNA name with comma in between to enable searching multiple piRNAs for their targets. For ease of understanding on querying options, “Examples” have also been given on the Search page. User can select query type and then click on the respective example(s) to get familiar with the database.
    2. Gene(s): User can also select to search for a single gene or multiple genes that are separated with comma without any space in between. While typing gene name (i.e., NCBI gene symbol, e.g., RRM2) in the search box, it’ll show gene names populated from the database to enable user to select query gene of interest. If user wishes to search multiple genes, gene symbols won’t show up and s/he needs to type the gene symbols manually with comma in between to enable searching for piRNAs that are targeting these genes.
    3. Both piRNA and Gene: In this search mode, it’ll allow users to search for interaction(s) between a specific pair of piRNA and gene. This option won’t allow to search for multiple piRNAs and multiple genes.
  3. The users also need to select ‘Validation Type’ as direct, indirect or both (refer to “Legends on Methods” for more details). Then, click on ‘Submit’ to obtain the results.


Search by piRNA sequence:
User will first select ‘Species’ from the drop-down menu, type or paste the piRNA sequence in the piRNA sequence query box, and then select ‘Validation Type’ before clicking on ‘Submit’ to obtain the results.

Results (Display)
Upon exercising any of the above search options, the results will be displayed showing information related to piRNA:gene interactions reported in various species, organ/tissues/cells, disease/healthy, methods, mode of regulations, etc. Up-arrow (↑) and Down-arrow (↓) provided adjacent to piRNA/gene names represent their up-regulated and down-regulated expression, respectively. This main results page has also a hyperlink to ‘More info …..’, which will show additional information related to the piRNAs, and targets as a new page upon clicking over it.

In addition, there are hyperlinks to individual piRNA, and gene that are shown on the Results page. Hyperlink to individual piRNA will enable user to obtain additional information on specific piRNA as a separate page if the user clicks on it, whereas hyperlink to gene will redirect the user to the Genbank database to obtain additional information on target gene.
Results (Download)
The ‘Download’ option provided below the results table enables the users to download the main results table including the more info results as a text file, which can be opened in excel to see the results in tabular format.


Legends on Methods