In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy

BMC Bioinformatics

Table 4 Top 20 peptide-HLA targets prioritized by the number of associated off-targets

	Tumor	Peptide	Gene	IC₅₀	RPKM.tumor	Sim.5
1	DLBC	HLSPIDCEV	NLRP4	42.48	6.57	0
2	LAML	LTSMWSPAV	UMODL1	279.13	6.47	1
3	DLBC	HLDHPHPAV	NLRP4	147.43	6.57	2
4	SKCM	SLSVMSSNV	MAGEC2	265.87	19.91	3
5	DLBC	MMAWSDNKI	NLRP4	90.11	6.57	3
6	LIHC	TQIGIEWNL	COX7B2	229.74	19.13	4
7	DLBC	CLFEMQDPA	NLRP4	37.51	6.57	5
8	LAML	YLSHPSCNV	UMODL1	16.04	6.47	5
9	LIHC	GIEWNLSPV	COX7B2	361.90	19.13	7
10	LUSC	GLGCSPASI	MAGEA11	471.75	10.52	7
11	LGG	RQAFEFPQI	RPE65	456.69	6.60	7
12	GBM	RQAFEFPQI	RPE65	456.69	6.30	7
13	DLBC	GMWTDTFEF	NLRP4	172.47	6.57	10
14	SKCM	YLNWQDTAV	TRIM51	10.30	7.35	11
15	LUSC	VLWGPITQI	MAGEA11	24.07	10.52	15
16	DLBC	TLDHTGVVV	NLRP4	497.98	6.57	15
17	LGG	TMGVWLHIA	RPE65	314.41	6.60	16
18	GBM	TMGVWLHIA	RPE65	314.41	6.30	16
19	SKCM	KVWVQGHYL	MAGEC2	407.64	19.91	18
20	LAML	KINCNNFRL	UMODL1	304.37	6.47	18

The table lists the peptides which in complex with HLA-A*02:01 form the targets, the cancer types which specifically express the targets, the genes from which the peptide were derived, the predicted binding affinities (IC₅₀ in nanomolars) of the target complexes, the 75% expression (in RPKM) of genes in the tumor samples, and the number of potential off-targets at DoS ≥ 5 (Sim.5) and DoS ≥ 6 (Sim.6). See Additional file 1 for the description of TCGA tumor types

ISSN: 1471-2105