Skip to main content

Table 2 Top ten samples across the 21,504 analyzed in this paper in order of descending junction inclusion ratio D, as defined in the table

From: Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive

Rank

Sample (i.e., run)

Project

Description of sample

Junction

Junction

Total junction

D=(B-A)/C

    

coverage A for ALK

coverage B for ALK

coverage C

 
    

exons 1–19

exons 20–29

across ALK

 

1

SRR545713

SRP007461

NHEM.f_M2: normal human

0

139

139

1

   

melanocyte

    

1

SRR396804

SRP010166

Non-small cell lung

0

172

172

1

   

adenocarcinoma

    

1

SRR620100

SRP017262

Leukemia

0

108

108

1

4

SRR1289650

SRP042031

Macrophage

1

85

86

0.976

5

SRR1289651

SRP042031

Macrophage cultured

1

77

78

0.974

   

with fibroblast

    

6

SRR545716

SRP007461

NHEM_M2: normal human

2

94

96

0.958

   

melanocyte

    

7

SRR628586

SRP017413

Uveal melanoma

12

111

123

0.805

8

DRR016705

DRP001919

H2228, an EML4-ALK-expressing

38

285

333

0.765

   

lung adenocarcinoma cell line

    

9

SRR545714

SRP007461

NHEM.f_M2: normal human

14

63

77

0.636

   

melanocyte

    

10

ERR532612

ERP006077

Prostate tumor

16

53

69

0.536

  1. D essentially measures the difference in expression between junctions across ALK exons 1–19 and junctions across ALK exons 20–29. Values of D close to 1 may point toward expression of ALK ATI, a novel transcript variant of ALK recently identified in [29] across several cancers but not normal cells. Several cancer samples appear, but interestingly, normal cell samples also appear, including melanocytes and macrophages