A fuzzy method for RNA-Seq differential expression analysis in presence of multireads

BMC Bioinformatics

Table 7 Rankings of the genes for the simulated data

Ranking	Same-expression Possibility	Cuffdiff + TopHat (p-value)	DESeq2 + Centroids (p-value)	DESeq2 + RSEM (p-value)	edgeR + Centroids (p-value)	edgeR + RSEM (p-value)
1	IGF1R	false positive	HLA-DRA	PDE4DIP	IGF1R	PDE4DIP
2	POSTN	CD177	MUC5AC	WAC	PDE4DIP	POSTN
3	FADS2	CLCA1	FADS2	IGF1R	WAC	FADS2
4	MUC5AC	EEF1A1	HLA-DQB1	U2AF1	FADS2	IGF1R
5	WAC	false positive	WAC	HLA-DQB1	POSTN	IFI6
6	CLCA1	FADS2	IGF1R	FADS2	HLA-DQB1	WAC
7	IFI6	HLA-DQB1	POSTN	MUC5AC	U2AF1	U2AF1
8	S100A8	HLA-DRA	PDE4DIP	POSTN	CLCA1	MUC5AC
9	SCGB1A1	IFI6	S100A8	HLA-DRA	false positive	S100A8
10	CD177	IGF1R	CD177	EEF1A1	S100A8	NSUN5P1
11	PDE4DIP	false positive	EEF1A1	NSUN5P1	MUC5AC	false positive
12	HLA-DQB1	LYZ	CLCA1	false positive	HLA-DRA	false positive
13	LYZ	MUC5AC	IFI6	CD177	IFI6	HLA-DQB1
14	UBBP4	PDE4DIP	UBBP4	CLCA1	CD177	CD177
15	MTRNR2L12	POSTN	NSUN5P1	LYZ	EEF1A1	HLA-DRA
16	false positive	S100A8	LYZ	false positive	UBBP4	SCGB1A1
17	false positive	U2AF1	MTRNR2L12	false positive	SCGB1A1	CLCA1
18	HLA-DRA	WAC	SCGB1A1	IFI6	LYZ	false positive
19	false positive	false positive	U2AF1	BPG254F23.5	NSUN5P1	LYZ
20	false positive	false positive	false positive	UBBP4	MTRNR2L12	EEF1A1

In order to highlight the true positives, the other genes are hidden by a “false positive” label

ISSN: 1471-2105