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Table 3 Assignment rules for differentially expressed contigs

From: DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

  Conditions
Event class DU P value Number of junctions Maps gene Maps antisense gene Clipped 3’ Is mapped SNV Exonic Intronic Number of hits Contig length Other rules Contigs Loci
Splicing   >0 T    T F    1    1879 1280
Splicing DU <0.01 >0 T    T F    1    391 345
PolyA      ≥5 T     1   1 105 95
PolyA DU <0.01   T   ≥5 T     1   1 9 8
lincRNA    F F   T     1 >200   1061 329
asRNA    F T   T     1 >200   479 180
SNV DU <0.01   T F   T T T   1   2 929 680
Intron    T F 0 T    T 1   3 49897 6689
Intron DU <0.01   T F 0 T    T 1   3 10688 3128
Repeats       T     ≥5 >50 4 1136 612
Unmapped       F      >50   112  
  1. Each class of event is defined by a set of rules applied to annotated contigs. Other rules refers to the following: (1) contig ends with AAAAA, (2) mean counts >20 in at least one condition and mapped region <10 kb, (3) mapped region <10 kb, and (4) the mapped gene is not differentially expressed. Contigs indicates the number of contigs of each class found in the epithelial–mesenchymal transition experiment. Loci is the number of loci implicated by these contigs (see “Methods”)
  2. asRNA antisense RNA, DU differential usage, F false, lincRNA long intergenic non-coding RNA, PolyA polyadenylated, SNV single-nucleotide variation, T true