tRFtarget 2.0

Typical usage of tRFtarget

Search ways of tRFtarget

The typical data retrieving of tRFtarget includes 3 ways:

• Search by tRF ID to see the information of all potential transcripts which can interact with this specific tRF. tRF ID can be chosen from the drop-down selection box.
  • Only top 5,000 interactions with lower free energy and longer maximum complementary length will be provided, as one tRF can have up to 500 thousands interactions.
  • When retrieving consensus interactions with one tRF, 2,500 top RNAhybrid predictions and 2,500 top IntaRNA predictions will be provided.
• Search by transcript Ensembl ID or name to see the information of all potential tRFs which can interact with this specific transcript.
• Search by gene Ensembl ID or approved symbol to see the information of all potential tRFs which can interact with any transcripts transcribed by this specific gene.

Additional filters

For each data retrieving way of tRFtarget, an additional filter of free energy and maximum complementary length can be used to filter out less likely interactions with higher free energy and shorter maximum complementary length.

• Default free energy threshold:
  • RNAhybrid predictions: -25 kcal/mol
  • IntaRNA predictions: -10 kcal/mol
  • Consensus predictions: -10 kcal/mol
• Default maximum complementary length threshold:
  • RNAhybrid predictions: 8 bases
  • IntaRNA predictions: 8 bases
  • Consensus predictions: 8 bases

Display tabular search result

The retrieved data from tRFtarget will be formatted into a tabular form for display, and the result table supports following operations:

• Press the column name will sort all rows of the table in the ascending order by this column. Press that column name again will change the sorting to the descending order.
• Search user inputted text in all columns in the table, and show only matched rows.
• Download the current results into a CSV file. If sorting or text searching operations are performed, only the sorted or matched results will be save into the CSV file.

Perform downstream analysis

We provide several buttons to perform downstream analysis conveniently.

• All interactions between one tRF and all target transcripts are ranked by an ascending order of free energy, and interactions with the same free energy are further ranked by a descending order of maximum complementary length.
• When ranking consensus interactions, free energies derived from IntaRNA are used.
• Top interactions will be selected, and corresponding genes are found. Then a list of gene Ensembl IDs/Symbols will be generated and copied to clipboard automatically. The default number of included top interactions is 2000, and can be changed by users.
• A new window will be opened, and automatically redirected to corresponding website. Then the gene list can be pasted into the input box for donstream analysis.
• The filtering will be discarded during ranking interactions, that is, all retrieved entries will be included for ranking.

Definition of maximum complementary length

tRFtarget will report the maximum complementary length (MCL) feature of a specific binding site on a transcript. The MCL is defined as the length of the longest successively complementary sequences. For example, the figure below shows a binding interaction between tRF tRF-5013b and transcript ARF-201 predicted by RNAhybrid. The interaction has 3 distinct parts of complementary sequences as covered by green lines. The lengths of complementary sequences of the 3 parts are 6, 5, and 7, respectively. Therefore, the MCL of this interaction is 7 bases.

Definition of duplicated entries in IntaRNA predictions

IntaRNA tool will return similar binding interactions between the same tRF and transcript, and among these similar entries only the one with the lowest free energy will be kept. For example, all the 5 binding interactions between tRF tRF-3001a and transcript DCTPP1-201 predicted by IntaRNA are shown in the below figure. The 5 interactions have the similar interaction structure, and are almost in the identical location on the transcript. So only the toppest one entry with the lowest free energy (-20.36 kcal/mol) is kept and stored in tRFtarget database, while the other 4 entries will be defined as duplicated entries and discarded.

Definition of consensus entries in RNAhybrid and IntaRNA predictions

1 RNAhybrid prediction and 1 IntaRNA predction will be defined as consensus if them have a similar interaction structure. The interaction need to be on the identical location on the transcrpt, allowing a 2 bases offset on the beginning and/or ending of the interaction sequence. For example, the RNAhybrid prediction and IntaRNA predction of tRF-1001 and trandcript ARF1-213 are defined as consensus (see figure below). The beginning site of both predictions are identical, while the ending site has a offset of 1 base (RNAhybrid prediction ends on the 1683rd base while IntaRNA predction ends on the 1682nd base).