A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

Table 1 Comparison of the highest fold change DEGs from E. coli (A) and C. elegans (B) observed in the different pipelines. Data includes only data with greater than 30 reads except for Partek which could not be adjusted

(A) Highest foldchange DEGs in E. coli
Gene Name	Fold change
Gene Name	CLC	Partek	DNAstar-E	DNAstar-D
gadA	-26.80	-25.97	-26	-1.7
gadB	-22.84	-23.54	-23	-2.5
asr	-17.23	-17.86	-17	-1.6
adiA	-16.58	-17.12	-17	-1.7
hdeB	-10.80	-9.934	-11	-2.5
adiC	-10.11	NS	-10	NS
(B) Highest foldchange DEGs in C. elegans
Gene name	Fold Change
Gene name	CLC	DNAstar-E	DNAstar-D
msp-19	NS	20.8	2.1
col-81	14.6	14.4	1.6
col-139	14.4	13.7	1.7
col-129	13.6	13.5	1.5
col-133	6.3	5.8	NS
fat-7	5.7	5.3	3.3
asm-3	4.9	5.0	3.0
K08D12.6	3.3	3.3	NS
rol-8	- 5.1	- 4.2	-1.6
col-17	- 4.5	- 4.1	NS
sqt-2	- 4.4	- 4.3	-1.6
cpt-4	- 4.4	- 4.4	- 2.1
F33D4.6	- 4.4	- 4.3	- 1.7

ISSN: 1471-2164