APA regulations of select genes in cancer

Citation

Xue Z, Warren RL, Gibb EA, MacMillan D, Wong J, Chiu R, et al. Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes. BMC Genomics. 2018;19:536

Introduction

In addition to the 77 cases (arc plots) reported in the manuscript and its supplemental materials, here, we present a total of 1593 arc plots (114 (genes) x 14 (cancer types) - 3) for all gene-cancer type pairs considered in this study in an interactive webpage. Hence, these plots represent a superset of what is presented in the manuscript. We note that for three pairs, (NKX2-1, COAD), (TERT, KICH), and (TERT, KIRP), no cleavage site was detected in the normal samples, so they have no corresponding arc plots; NA is shown instead.

Such an interactive format also enables the readers to inspect their genes of interest in more detail.

Instruction

To the left, the table layouts all 1596 gene-cancer type pairs with those that are identified to show tumor-specific APA regulations highlighted in blue (77 pairs).
To the right, by clicking any gene-cancer type pair in the left table, the corresponding arc plot will show up on the right. Arc plots of tumor-specific APA cases will be highlighted with blue borders.

#	Gene	Disease
1	ABL1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
2	AKT1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
3	AKT2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
4	ALK	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
5	AMER1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
6	APC	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
7	ATM	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
8	AXIN1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
9	BAP1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
10	BCL6	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
11	BRAF	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
12	BRCA1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
13	BRCA2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
14	CARD11	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
15	CCND1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
16	CCND2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
17	CCNE1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
18	CD47	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
19	CDH1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
20	CDKN2A	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
21	CDKN2C	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
22	CEBPA	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
23	CHURC1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
24	CREBBP	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
25	CTNNB1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
26	CYLD	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
27	DICER1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
28	DRAM1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
29	EGFR	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
30	EP300	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
31	ERBB2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
32	EZH2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
33	FAS	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
34	FBXW7	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
35	FGF2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
36	FGFR2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
37	FGFR3	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
38	FLT3	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
39	GATA3	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
40	GNA11	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
41	GNAQ	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
42	GNAS	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
43	HNF1A	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
44	HRAS	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
45	IDH1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
46	IGF2BP1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
47	JUN	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
48	KDM6A	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
49	KDR	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
50	KIT	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
51	KMT2A	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
52	KRAS	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
53	MAP2K1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
54	MAP2K2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
55	MAP2K4	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
56	MAX	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
57	MDM2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
58	MDM4	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
59	MEN1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
60	MET	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
61	MITF	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
62	MLH1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
63	MSH2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
64	MSH6	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
65	MYC	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
66	MYCL	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
67	MYCN	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
68	MYD88	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
69	NF1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
70	NF2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
71	NFE2L2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
72	NFE2L3	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
73	NFYA	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
74	NKX2-1	BLCA	BRCA	NA	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
75	NOTCH1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
76	NOTCH2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
77	NRAS	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
78	NSUN5	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
79	PAX5	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
80	PDGFRA	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
81	PIK3CA	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
82	PIK3R1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
83	PRKAR1A	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
84	PTCH1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
85	PTEN	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
86	RAB10	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
87	RB1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
88	REL	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
89	RET	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
90	RNF43	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
91	RTCA	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
92	SEC24A	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
93	SETD2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
94	SMAD4	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
95	SMARCA4	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
96	SMARCB1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
97	SMO	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
98	SOCS1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
99	SOX2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
100	STAT3	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
101	STK11	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
102	STK17A	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
103	SUFU	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
104	TERT	BLCA	BRCA	COAD	HNSC	NA	KIRC	NA	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
105	TET2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
106	TNFAIP3	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
107	TP53	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
108	TRAF7	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
109	TSC1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
110	TSC2	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
111	TSHR	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
112	TXNL4A	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
113	VHL	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC
114	WT1	BLCA	BRCA	COAD	HNSC	KICH	KIRC	KIRP	LIHC	LUAD	LUSC	PRAD	STAD	THCA	UCEC

Click on a gene-cancer type pair in the left table to see an arc plot

Legend: Inside each left-hand panel, each group of bars represents the frequency of a specific CS in normal (blue) and tumor (red) samples. Bar groups are ordered by corresponding CS genomic coordinates. The text box shows the number of normal (N) and tumor (T) samples that were used for frequency calculation. Vertical arrows indicate the positions of predicted CSs. Annotated and predicted CSs match well, but are not expected to overlap exactly. An arrow pointing upwards (downwards) represents an increase (decrease) in frequency from normal to tumor. Arrow height represents the difference (Δ). Bars and arrows of insignificant difference are colored gray. The X-axis represents the genomic coordinate offset by that of the first stop codon. The horizontal arrow indicates the gene strand.

When the 3' UTR length change is too complex to be resolved into a shortening or lengthening trend, the corresponding text box is left uncolored. NMD-related transcript elements are colored in cyan. An orange arrow indicates that a predicted CS with a significant frequency change is mapped to multiple stop codons, with its associated 3' UTR length being ambiguous.

Different from the figures in the main text, all predicted CSs are plotted without filtering by the low frequency (<5%) and insignificant change criteria. As a result, the number of CSs for the same gene in different cancer types may differ.

Besides, we also computed the distribution of expression in reads per kilobase of transcript per million sequenced reads (RPKMS).