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Table 3 ENCODE RNA-seq chimeric junctions sent to RT-PCR validation

From: ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data

Chimeric junction identifier

Gene A

Gene B

SK-N-SH_RA:4

AG04450:4

MCF-7:4

H1-hESC:7

GM12878:9

A549:4

HUVEC:11

NHEK:13

HepG2:11

BJ:2

NHLF:4

HSMM:4

K562:16

HeLa-S3:11

HMEC:2

chr19_34957919

UBA2

WTIP

7.3:0.5

3:0.3

3.5:0.8

2.3:0.7

3.1:1.6

12.5:0.8

4.2:1.5

2.2:0.2

2.5:0.2

3:0

2.3:1.3

4:5.3

7.1:1.2

6.6:1.7

6:2.5

_+:chr19_

34981281_+

chr11_85685751_-:chr11_85469157_-

PICALM

SYTL2

0:0

4.5:0

5.3:90.8

0:0

1.2:0.2

0.8:0

0.7:0

0.9:0

0.2:0.1

1.5:0

0:0

1.8:0.3

2.3:0.1

0.3:0

0:0

chr17_72200329_

RPL38

TTYH2

2.8:0

0.3:0

0.5:0

0.3:0.4

4.3:5.7

0.5:0

0.9:0.7

0.5:0

0.6:1.4

0.5:0

0.3:0

0.3:0.5

0.3:0.7

0.1:0

0:0

+:chr17_72218624_+

chr16_19603196_+

C16orf62

IQCK

0:0

0:0

33.8:65.8

0:0

0:0

0:0

0:0

0:0

0:0

0:0

0:0

0:0

0:0

0:0

0:0

:chr16_19867809_+

  1. This table lists the 4 chimeric junctions derived from the 106 ENCODE RNA-seq experiment, that we selected for RT-PCR validation (the successful ones are the three first ones). For each junction, its identifier (junction coordinates in ChimPipe format), the name of its 5’ and 3’ genes, and its expression in terms of number of staggered split-reads and discordant paired-end reads in each of the 15 ENCODE cell lines (separated by :), are provided. Since each cell line is associated to several RNA-seq experiments (number indicated in the header after the : sign), we provide the average number of staggered split-reads and the average number of discordant paired end reads across all experiments of a cell line