tsRFun

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.

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 )

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

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

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: