Extensive stage-regulation of translation revealed by ribosome profiling of Trypanosoma brucei

BMC Genomics

Table 1 Mechanisms of gene regulation

slBF:PCF	Stage^a	DESeq	Both DESeq and edgeR^b	%
no change	-	5212	5749	68.5%
TE only	PCF	62	59	0.7%
both	PCF	872	746	8.9%
mRNA only	PCF	654	485	5.8%
TE only	slBF	130	126	1.5%
both	slBF	1023	870	10.3%
mRNA only	slBF	445	363	4.3%
cBF:PCF	Stage	DESeq	Both DESeq and edgeR	%
no change	-	6528	6671	79.5%
TE only	PCF	16	15	0.2%
both	PCF	607	538	6.4%
mRNA only	PCF	212	185	2.2%
TE only	cBF	124	124	1.5%
both	cBF	737	714	8.5%
mRNA only	cBF	174	151	1.8%

^astage with higher protein production.
^bconcordance of edgeR analysis indicating 2-fold up-regulation for ribosome footprint read counts (FDR <0.01) and DESeq GLM model. Those that were not concordant were binned into the “no change” group in this column.

ISSN: 1471-2164