tRFtarget 2.0

Search ways of tRFtarget

The typical data retrieving of tRFtarget includes 4 ways:

• Search by tRF ID (also support Standardized tRF ID) to see the information of all potential transcripts which can interact with this specific tRF.
  • Only top 50,000 binding sites with lower free energy and larger maximum complementary length will be provided in one search.
  • When retrieving consensus binding sites of one tRF, 25,000 top RNAhybrid predictions and 25,000 top IntaRNA predictions will be provided.
• Search by target RNA Ensembl ID or name to see the information of all potential tRFs which can interact with this specific RNA.
• Search by gene Ensembl ID or symbol to see the information of all potential tRFs which can interact with any transcripts transcribed by this specific gene.
• Advanced Search to see the information of all binding sites between the specific tRF and target RNA or gene.

Users can also browse the information of all tRFs, target RNAs and genes covered in tRFtarget.

For tRFs, target RNAs and genes not covered by tRFtarget, users can obtain the binding site information via our online service.

Linking to tRFtarget

Linking to binding sites in tRFtarget

Please use the following format to link to page showing binding sites in tabular form:

• Binding sites for Homo sapiens tRF tRFdb-1001:
  • http://trftarget.net/show_target?trf_id=tRFdb-1001&organism=Homo sapiens
• Binding sites for Homo sapiens transcript ARF5-201 (ENST00000000233):
  • http://trftarget.net/show_target?rna_name=ARF5-201&organism=Homo sapiens
  • http://trftarget.net/show_target?rna_id=ENST00000000233&organism=Homo sapiens
• Binding sites for Homo sapiens gene ARF5 (ENSG00000004059):
  • http://trftarget.net/show_target?gene_name=ARF5&organism=Homo sapiens
  • http://trftarget.net/show_target?gene_id=ENSG00000004059&organism=Homo sapiens
• Binding sites between Homo sapiens tRF tRF-db1001 and transcript ARF5-201 (ENST00000000233):
  • http://trftarget.net/show_target?trf_id=tRFdb-1001&rna_name=ARF5-201&organism=Homo sapiens
  • http://trftarget.net/show_target?trf_id=tRFdb-1001&rna_id=ENST00000000233&organism=Homo sapiens
• Binding sites between Homo sapiens tRF tRFdb-1001 and gene ARF5 (ENSG00000004059):
  • http://trftarget.net/show_target?trf_id=tRFdb-1001&gene_name=ARF5&organism=Homo sapiens
  • http://trftarget.net/show_target?trf_id=tRFdb-1001&gene_id=ENSG00000004059&organism=Homo sapiens

Linking to experimental evidences in tRFtarget

Linking to gene-level experimental evidences

Please use the following format to link to page showing gene-level experimental evidences in tabular form:

• Gene-level evidences for Homo sapiens tRF tRFdb-3009a:
  • http://trftarget.net/gene_evidence?trf_id=tRFdb-3009a&organism=Homo sapiens
• Gene-level evidences for Homo sapiens gene FER (ENSG00000151422):
  • http://trftarget.net/gene_evidence?gene_name=FER&organism=Homo sapiens
  • http://trftarget.net/gene_evidence?gene_id=ENSG00000151422&organism=Homo sapiens
• Gene-level evidences between Homo sapiens tRF tRFdb-3009a and gene FER (ENSG00000151422):
  • http://trftarget.net/gene_evidence?trf_id=tRFdb-3009a&gene_name=FER&organism=Homo sapiens
  • http://trftarget.net/gene_evidence?trf_id=tRFdb-3009a&gene_id=ENSG00000151422&organism=Homo sapiens