tsRNA metadata

A tab seperated table of tsRNA metadata


Fields description:

  • tRF: Source tRNA and its cleavage site's position
  • tRNA: the source tRNA
  • type: the type of tsRNA molecules
  • seq: the sequence of tsRNA
  • tsRNAid: uniform names of the identified tsRNAs considering sequence and tRNA type (tsRNA+amino acid type+tsRNA type+unique code). For example, tsRNA-Ala-3-0055, with the sequence TCCCCGGCATCTCCACCA, was derived from position 58-75 in tRNA-Ala-CGC-1-1 and tRNA-Ala-CGC-2-1.
tsRinCancer

1. Differential expression result shown in tsRinCancer


Fields description:

  • tsRNAid: uniform names of the identified tsRNAs considering sequence and tRNA type (tsRNA+amino acid type+tsRNA type+unique code). For example, tsRNA-Ala-3-0055, with the sequence TCCCCGGCATCTCCACCA, was derived from position 58-75 in tRNA-Ala-CGC-1-1 and tRNA-Ala-CGC-2-1.
  • **_Tumor: RPM of the tsRNA in every tumor sample. ** is the abbreviation of TCGA cancer type.
  • **_Normal: RPM of the tsRNA in every normal sample. ** is the abbreviation of TCGA cancer type.
  • **_log2FC: log2( mean(tumor tissue expression)/mean(normal tissue expression) + 0.01). The average was calculated only in samples expressing tsRNA.


2. Zip file of the raw tsRNA expression value in each type of cancer


Fields description:

  • column: tsRNAid
  • row: TCGA barcodes
  • value: RPM


3. Zip file of the processed tsRNA expression value in each type of cancer


Fields description:

  • tsRNAid: uniform names of the identified tsRNAs considering sequence and tRNA type (tsRNA+amino acid type+tsRNA type+unique code). For example, tsRNA-Ala-3-0055, with the sequence TCCCCGGCATCTCCACCA, was derived from position 58-75 in tRNA-Ala-CGC-1-1 and tRNA-Ala-CGC-2-1.
  • expr: RPM of all samples
  • Tumor_expr: RPM of tumor sample
  • Normal_expr: RPM of normal sample
  • pVal: P-value of Kruskal-Wallis rank sum test.
  • TumorExpressedAvg: Average of tumor expression, calculated only in samples expressing tsRNA.
  • NormalExpressedAvg: Average of normal expression, calculated only in samples expressing tsRNA.
  • log2FC: log2( TumorExpressedAvg/NormalExpressedAvg )
tsRSurvival

1. Prognosis value of tsRNA.


Fields description:

  • colname: Diverse TCGA cancer types
  • rowname: Diverse tsRNAid
  • value: The p values calculated by log-rank test


2. Univariate Cox regresion model of tsRNA in pan-cancers


Fields description:

  • colname: Diverse TCGA cancer types
  • rowname: Diverse tsRNAid
  • value: The p values calculated by Univariate Cox regresion model
tsRNetwork

1. Competitive endogenous RNA network (miRNA-mRNA-tsRNA)


Fields description:

  • mRNA: ENSEMBL Transcript ID of mRNA
  • miRNA: miRNA that was predicted to target to mRNA
  • tsRNA: tsRNA that was predicted to target to tsRNA
  • SYMBOL: SYMBOL of mRNA
  • ENSEMBL: ENSEMBL GENE ID of mRNA


2. P-value of ceRNA pair


Fields description:

  • p: P-value calculated by hypergeometric test.
  • adj.p: Adjusted P-value by BH method
Applying tsRTools to TCGA

1. tsRFinder tool


Fields description:

  • tsRNA Type: the type of tsRNA molecules
  • Align Score: tsRFinder can use a scoring scheme to handle different types of mismatches / indels. Details in Tutorial page
  • tsRNA Length: the length of tsRNA molecules
  • Source tRNA: the source tRNA of tsRNA molecules
  • Fragment Position: the position of tsRNA molecules in their source tRNAs
  • RPM: the RPM value of tsRNA molecules
  • White list: we analysed 37 small-RNA seq data without RNA modifications from PANDORA research, and obtained the potential tsRNA molecules as White-list by tsRFinder, SPORTS, and MINTmap tools
  • Sequence: the sequence of tsRNA molecules


2. tsRTarget tool


Fields description:

  • tsRNAid: uniform names of the identified tsRNAs considering sequence and tRNA type (tsRNA+amino acid type+tsRNA type+unique code). For example, tsRNA-Ala-3-0055, with the sequence TCCCCGGCATCTCCACCA, was derived from position 58-75 in tRNA-Ala-CGC-1-1 and tRNA-Ala-CGC-2-1.
  • Target: the target gene name
  • TargetTrans: the ENST name of the target gene
  • MEF: the value of performance to evaluate the RNA-RNA interaction in canonical seed pattern
  • tsRNA-target Alignment:
  • Seed Mode: the partten of RNA-RNA interaction, canonical or non-canonical seed targeting.
  • tRNAall: the source tRNA of tsRNA molecules
  • tsRNAseq: the sequence of tsRNA molecules
  • tsRNAtype: the type of tsRNA molecules
  • genePos: