OncotRF: an online resource for exploration of tRNA-derived fragments in human cancers

Figures & data

Figure 1. Schematic representation of data processing and flowchart of OncotRF construction.

Table 1. Summary of TCGA samples used in the study and 5ʹ-tRFs, 3ʹ-tRFs,3ʹU-tRFs and i-tRFs identified in the study.

Cancer Types	Sample size				Number of tRFs*				tRF Average Expression (RPM)
	miR-seq		RNA-seq		5ʹ-tRFs	3ʹ-tRFs	3ʹU-tRFs	i-tRFs	5ʹ-tRFs		3ʹ-tRFs		3ʹU-tRFs		i-tRFs
	Normal	Tumour	Normal	Tumour					Normal	Tumour	Normal	Tumour	Normal	Tumour	Normal	Tumour
ACC	0	80	0	0	501	235	102	1591	NA	11688	NA	4603	NA	1332	NA	18880
BLCA	19	418	17	301	461	237	76	1030	522	6833	497	2121	104	345	955	6017
BRCA	104	1102	113	1064	577	316	91	1363	3414	11402	2092	2750	316	504	4305	9828
CESC	3	308	3	261	557	281	97	1442	917	11639	606	2607	113	423	1327	11076
CHOL	8	36	0	0	377	185	71	843	12519	4324	2572	1206	500	342	6092	4159
CNTL	112	0	0	0	551	280	63	694	6265	NA	2610	NA	292	NA	2774	NA
COAD	1	446	41	453	628	393	119	1736	5832	7763	3899	4130	976	715	2206	11420
DLBC	0	47	0	0	580	357	112	1651	NA	12541	NA	2929	NA	606	NA	9320
ESCA	13	187	0	0	464	191	76	1121	2208	9521	1261	1539	322	327	1814	7075
GBM	0	5	0	166	338	250	92	1144	3589	NA	2721	NA	553	NA	5930	NA
HNSC	44	525	42	482	626	403	104	1732	6674	13675	8379	4117	757	460	11119	12588
KICH	25	65	0	0	432	280	79	1153	4896	9312	1567	4476	412	1130	5560	7468
KIRC	71	544	72	526	519	319	84	1199	8251	8798	2851	2913	641	429	9783	6928
KIRP	34	292	32	222	418	257	76	882	6766	5099	2423	2913	624	875	9019	6454
LAML	0	191	0	173	755	577	220	3298	NA	14229	NA	12815	NA	2670	NA	27673
LGG	0	530	0	453	460	269	92	1124	NA	9055	NA	2002	NA	320	NA	5917
LIHC	50	375	48	297	482	289	86	1166	14143	8717	5934	3649	759	666	15178	8268
LUAD	46	521	55	488	469	330	69	1017	1916	5742	2466	2970	268	401	2338	4942
LUSC	45	478	45	428	614	362	94	1611	3391	10699	2019	3246	216	442	3453	10265
MESO	0	87	0	0	439	174	76	916	NA	12810	NA	907	NA	274	NA	4642
OV	0	499	0	265	375	402	99	1082	NA	10152	NA	8407	NA	493	NA	7507
PAAD	4	179	3	142	288	143	40	466	2822	2456	1087	687	271	173	1827	1732
PCPG	3	184	0	0	248	139	61	680	13334	3859	3484	955	553	284	18051	3699
PRAD	52	499	52	379	366	212	49	988	2041	6482	1675	1985	96	175	3081	6984
READ	0	160	9	154	664	395	116	1863	NA	8979	NA	3621	NA	732	NA	12740
SARC	0	263	0	0	308	151	55	654	NA	4043	NA	678	NA	158	NA	2649
SKCM	2	450	1	433	749	701	138	2547	5171	22597	4188	13301	534	1009	6392	20000
STAD	45	446	35	415	467	241	70	997	2545	4935	1115	1526	234	315	1877	5089
TGCT	0	156	0	0	539	247	114	1373	NA	18264	NA	2040	NA	599	NA	9003
THCA	79	540	58	508	547	338	96	1435	17057	10478	6791	4977	594	1032	11702	12670
THYM	2	123	0	0	389	192	78	912	5375	7991	1642	1262	288	392	3795	5316
UCEC	33	545	23	517	605	330	89	1632	4508	18719	2236	3115	336	576	5058	13612
UCS	0	55	0	0	559	172	81	1342	NA	24084	NA	1194	NA	355	NA	9374
UVM	0	80	0	0	511	478	109	1391	NA	8595	NA	7941	NA	1024	NA	11367
Total	795	10416	649	8127	992	799	271	4933

*number of tRFs identified in the study after the filtering. NA, not available.

ACC, Adrenocortical carcinoma; BLCA, Bladder Urothelial Carcinoma; BRCA, Breast Invasive Carcinoma; CESC, Cervical Squamous Cell Carcinoma; CHOL, Cholangiocarcinoma; CNTL, Controls; COAD, Colon Adenocarcinoma; DLBC, Lymphoid Neoplasm Diffuse Large B-cell Lymphoma; ESCA, Oesophageal carcinoma; GBM, Glioblastoma multiforme; HNSC, Head and Neck Squamous Cell Carcinoma; KICH, Kidney Chromophobe; KIRC, Kidney Renal Clear Cell Carcinoma; KIRP, Kidney Renal Papillary Cell Carcinoma; LAML, Acute Myeloid Leukaemia; LGG, Lower Grade Glioma; LIHC, Liver Hepatocellular Carcinoma; LUAD, Lung Adenocarcinoma; LUSC, Lung Squamous Cell Carcinoma; MESO, Mesothelioma; OV, Ovarian Serous Cystadenocarcinoma; PAAD, Pancreatic adenocarcinoma; PCPG, Pheochromocytoma and Paraganglioma; READ, Rectum adenocarcinoma; SARC, Sarcoma; SKCM, Skin Cutaneous Melanoma; STAD, Stomach Adenocarcinoma; TGCT, Testicular Germ Cell Tumours; THCA, Thyroid Carcinoma; THYM, Thymoma; UCEC, Uterine Corpus Endometrial Carcinoma; UCS, Uterine Carcinosarcoma; UVM, Uveal Melanoma.

Figure 2. Search functions of OncotRF. (A) Search result of 3ʹ-M-tRNA-Gly-GCC-2-6_L22. (B) 3ʹ-M-tRNA-Gly-GCC-2-6_L22 expression in cancers. (C) Validation result of 3ʹ-M-tRNA-Gly-GCC-2-6_L22. (D) 3ʹ-M-tRNA-Gly-GCC-2-6_L22 alignment with tRNA-Gly-GCC-2-1, its position on the secondary structure of tRNA-Gly-GCC-2-1, and possible modifications of tRNA-Gly-GCC-2-1 from MODIFICS database.

Figure 3. Cancer functions. (A) Differentially expressed 3ʹU-tRFs in BLCA. (B) Differentially expressed mRNAs in BLCA. (C) Correlation analysis of tRFs and mRNAs in BLCA. tRF-mRNA pairs with their absolute correlation coefficients > 0.4 (i.e., |r|>0.4) were presented. (D) Network analysis of differentially expressed tRFs and mRNAs in BLCA. tRF-mRNA pairs with |r|>0.4 in Figure 3 C were subjected to network analysis. (E) Functional enrichment analysis of genes that are co-expressed with 3ʹ- U-tRFs (|r|>0.4). (F) Survival analysis of differentially expressed 3ʹU-tRFs in BLCA.

Figure 4. Custom functions. (A) Clinical criteria and other parameters for custom functions. (B) tRF differences between two customized groups as defined in (A).

Figure 5. Kaplan-Meier plotter. (A) Choosing plot parameters for the overall survival analysis of 3ʹ-M-tRNA-Gly-GCC-2-6_L22 in ACC. (B) Survival curves of 3ʹ-M-tRNA-Gly-GCC-2-6_L22 in ACC.