FAQ of Contents

Frequently Asked Questions.

What is a dataset in piRBase?
How can I browse the piRNA data contained in a dataset?
How can I browse the piRNA data of a distinct organism?
How is piRNA quality score computed?
What is the detailed information of a distinct piRNA provided by piRBase?
How can I browse a piRNA's location in genome browser?
What is gene/repeat derived piRNA?
What is a piRNA target mRNA?
How can I browse the H3K9me3 data?
What is the meaning of the different colors in DNA methylation track?
What kind of information can we get from genome browser?
How can I download piRBase data?

Question:
What is a dataset in piRBase?

Response:
We regarded piRNA sequences from a distinct library as one dataset in piRBase. Such as a sample in GEO data series (eg.GSM113695), or a supplementary file from literature. We recorded a few basic information of every distinct dataset: organism and tissue of the sample, the method to obtain the sequences, amount of the data, accession of the dataset in other databases, and the literature reported this dataset.

Question:
How can I browse the piRNA data contained in a dataset?

Response:
To browse detailed information of piRNA data contained in a dataset, please open the webpage of 'Browse Datasets', and click on the 'id' or 'uniq seq' column of a distinct dataset.

Question:
How can I browse the piRNA data of a distinct organism?

Response:
To browse piRNA data of a distinct organism in piRBase, please open the webpage of 'Browse piRNAs' and select a an organism.

Question:
How is piRNA quality score computed?

Response:
The quality score is generated for each piRNA sequence according to the "reliability" of the method by which the piRNAs is obtained (small RNA sequencing: 1 point, protein IP or chromatography: 2 points, protein CLIP: 3 points) and the number of papers reporting this piRNA (1 point for each paper).

Question:
What is the detailed information of a distinct piRNA provided by piRBase?

Response:
For every distinct piRNA sequence, we recorded its detailed information including: aliases (piRNA alias provided by NCBI or RNAdb), accession (piRNA accession in NCBI), organism, sequence, length, dataset (the datasets reporting this piRNA), PubMed (PubMed id of corresponding literature), method (small RNA sequencing, protein IP, protein CLIP or Chromatography), piRNA location and annotation (annotation of the piRNA location according to RefSeq Gene and RepeatMasker).

Question:
How can I browse a piRNA's location in genome browser?

Response:
To browse a piRNA in genome browser, please open the detailed information page of the piRNA via 'Browse piRNAs' or 'Search piRNAs', such as: http://www.regulatoryrna.org/database/piRNA/pirna.php?name=piR-hsa-1, and click the link 'Location 1' in the 'Location' column.

Question:
What is gene/repeat derived piRNA?

Response:
We mapped piRNAs to the corresponding genome with bowtie allowing 1 mismatch. piRNAs mapped to the genome region of RefSeq gene or repeat element annotated by RepeatMasker are referred to as gene/repeat derived piRNAs.

Question:
What is a piRNA target mRNA?

Response:
It has been reported that piRNAs are able to instruct mRNA elimination, we referred to these mRNA as piRNA target. To know more about piRNAs' regulation of mRNA, please read "Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis".

Question:
How can I browse the H3K9me3 data?

Response:
Please open the "H3K9me3" webpage, and enter a genome position to view H3K9me3 data of a specific region.

Question:
What is the meaning of the different colors in DNA methylation track?

Response:
The display conventions of DNA methylation track are setted according to HAIB Methyl RRBS track Settings from ENCODE. Methylation status is represented with an 11-color gradient using the following convention:

Question:
What kind of information can we get from genome browser?

Response:
Genome browser is an interface to browse the combined data of piRBase. For example, DNA methylation data, H3K9me3 data, piRNA targets, piRNA location and its relative location with refseq genes and repeating elements. Table browser can be used to retrieve the data associated with a track.

Question:
How can I download piRBase data?

Response:
Please open "Download" interface and click on the links to get the corresponding data you need. Also, there are download buttons in browse and search pages.