Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes

BMC Bioinformatics

Table 1 Data cleaning increases the number of genes with functional annotation

Cleaning method	#genes after cleaning	#DEGs total*	#DEGs with
Cleaning method	#genes after cleaning	#DEGs total*	Any annotated function	Regulation of biological process	Transcription regulation	Molecular function regulator
RNAdeNoise	25,356	2439	2144	338	92	40
Raw data	37,336	2392	2086	326	87	38
HTSFilter	22,907	2348	2056	319	83	38
counts > 3	26,089	2309	2025	320	84	38
counts > 5	25,215	2287	2005	318	85	36
counts > 10	23,973	2128	1898	310	85	38
FPKM > 0.3	23,237	1930	1770	304	87	34
½samples > 3	24,173	2363	2063	360	84	38

Differentially translated genes were identified using EdgeR and annotated using DAVID classification system. Presented are the three most populated categories related to regulation. Results using DESeq2 are similar and can be found in (Additional file 1: Table S3)

ISSN: 1471-2105