Selected by1 | Gene symbol | FC2 qPCR | P value3 | FC2 microarray | FC2 RNA-Seq |
---|
BOTH
|
ALDH3A1
|
0.5
|
0.046
|
0.4
|
0.3
|
BOTH | TGM2 | 1.6 | 0.762 | 0.4 | 0.3 |
BOTH
|
IL8
|
3.2
|
0.002
|
3.7
|
3.4
|
BOTH
|
IL1R1
|
2.6
|
0.033
|
4.5
|
3.9
|
Array | IRF7 | 0.5 | 0.068 | 2.0 | 1.4 |
Array
|
TAF11
|
1.8
|
0.045
|
1.7
|
1.5
|
Array | PLCL1 | 1.2 | 0.469 | 0.7 | 0.8 |
Array | LIPE | 1.5 | 0.565 | 0.6 | 0.5 |
SEQ
|
GGT1
|
6.1
|
0.043
|
1.0
|
2.6
|
SEQ | GGT7 | 4.8 | 0.077 | 1.7 | 2.9 |
SEQ
|
MAPK10
|
7.1
|
0.013
|
2.1
|
3.3
|
SEQ
|
RPSA
|
0.5
|
0.009
|
1.7
|
0.4
|
SEQ | EFNB1 | 2.0 | 0.605 | 0.8 | 0.4 |
SEQ | SPARC4 | INF | <<0.001 | 0.8 | INF |
- The predicted polarity of the fold change for each DEG is listed along with the qRT-PCR calculated fold change (2-ΔΔCt). The P-values were calculated based on applying the T-test to ΔCt values of the control cells in comparison with the ΔCt values of the 5 μM 5-Aza treated cells (see Methods).
- 1Genes confirmed by RT-PCR as DEGs are marked in bold style (SEQ: Illumina RNA-Seq platform; Array: Affymetrix microarray platform)
- 2FC (fold change) is calculated as the group average of 5µM (5-aza-deoxycytidine)/Control, the normalized expression intensity value is used for microarray data while FPKM values from Cufflinks program are used for RNA-Seq data.
- 3P value is calculated using unpaired t-test on qPCR data; Genes that are significantly different between two groups are highlighted in bold style.
- 4The SPARC gene (not part of the 13 genes list) was specially added into the qPCR experiment for validation. On both qPCR and RNA-Seq platforms, its expression values in control group are all found to be zeros (below detection cutoff) whereas there are moderate expressions in 5µM group, therefore we consider the fold change as infinite positive denoted by INF with infinite minimal p values.