tRFtarget 2.0

Explore transfer RNA-derived Fragment targets

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Data Source

tRF Source

Organism Source Retrieve date tRF Inclusion Criteria
Homo sapiens tRFdb 2022-11-12
tsRNA study
tsRBase 2022-11-13 function / expression experimentally validated
tsRFun 2022-11-12 1) Expressed in > 30% of the TCGA samples; or 2) have experimentally validated targets
MINTbase v2.0 (04/04/2019) 2022-11-15 1) [#datasets RPM>100]≥10 and [#datasets RPM>100]/[#datasets expressed]≥0.05, or 2) have experimentally validated targets in tRFTar
tRFexplorer (2019-05) 2022-11-17 fragment type: 5' Leader and Minimum RPM value: 10
tatDB 2022-11-17 MFE≤-20, Read count≥25, Unique hybrids≥1, Motif checked and Intro Excised unchecked
OncotRF 2022-11-17 experimentally validated
Mus musculus tRFdb 2022-07-16
tsRBase 2022-08-21 function / expression experimentally validated
Caenorhabditis elegans tRFdb 2022-11-03
Danio rerio tRFdb 2022-11-01
Drosophila melanogaster tRFdb 2022-10-30
tsRBase 2022-10-30 function / expression experimentally validated
Rattus norvegicus tsRBase 2022-11-10 function / expression experimentally validated
Rhodobacter sphaeroides tRFdb 2022-11-06
Schizosaccharomyces pombe tRFdb 2022-11-09
Xenopus tropicalis tRFdb 2022-11-05

Target RNA Source

Reference Genome Version (protein-coding mRNA)

Organism Version Retrieve date
Homo sapiens GRCh38.p13 (GENCODE Release 42) 2022-11-12
Mus musculus GRCm39 (GENCODE Release M31) 2022-10-25
Caenorhabditis elegans WBcel235 (WormBase WS286) 2022-11-03
Danio rerio GRCz11 (Ensembl release 108) 2022-11-01
Drosophila melanogaster dmel_r6.32 (FlyBase FB2020_01) 2022-10-25
Rattus norvegicus mRatBN7.2 (Ensembl release 108) 2022-11-10
Rhodobacter sphaeroides ASM1640v1 (Ensembl Bacteria release 55) 2022-11-06
Schizosaccharomyces pombe ASM294v2 (PomBase update 2022-11-07) 2022-11-08
Xenopus tropicalis UCB_Xtro_10.0 (Ensembl release 108) 2022-11-05

rRNA & lncRNA

All rRNAs and lncRNAs are retrieved from RNA central v21.

Standardized tRF ID

Standardized tRF ID of one tRF sequence is determined by tDRnamer. When one tRF sequence can be matched to multiple standardized IDs, only the ID in "tDR Name" column is used, and all IDs in "Synonyms" column are discarded.

Target Prediction Method

All tRF-RNA interactions in tRFtarget are predicted using tRFtarget-pipeline v0.3.0.

Command options for calling tRFtarget-pipeline

--e_rnahybrid -15 --e_intarna -5 -b 5 -s 6

Add Experimental Evidences to Target Predictions

Gene-level Evidences

We add the manually curated gene-level experimental evidences to related binding sites predictions. For one tRF and one target gene in one gene-level evidence entry, we add this gene-level evidence to all predicted binding sites between all recorded tRFs with exactly the same sequence and all recorded transcripts of this specific target gene.

One-click Downstream Analysis

Users can effortlessly conduct downstream analysis with a single click after obtaining target genes for a specific tRF in one search (see figure below). The steps to select TOP genes for downstream analysis are:

  • All binding sites between one tRF and all target RNAs are ranked by an ascending order of free energy, and binding sites with the same free energy are further ranked by a descending order of maximum complementary length (MCL). When ranking consensus interactions, free energies derived from RNAhybrid are used.
  • Next top binding sites will be selected and mapped to corresponding genes. Then a list of gene Ensembl IDs/Symbols will be generated and copied to clipboard automatically. The default number of included top interactions is 2,000, and can be changed by users.
  • A new window will be opened in browser, and automatically redirected to corresponding website. Then the gene list can be pasted into the input box for donstream analysis.
  • Note:
    • All filterings on table showing retrieved binding sites will be discarded during binding sites ranking, that is, all retrieved binding sites will be included for ranking.
    • Interations with empty gene Ensembl IDs or Symbols are NOT included and counted, i.e. TOP 2,000 non-empty gene are identified by default.
Downstream Analysis Buttons