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Table 3 Confirmation of DEGs selected using both RNA-Seq and microarray data, RNA-Seq only and microarray only by qRT-PCR.

From: Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

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

  1. 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).
  2. 1Genes confirmed by RT-PCR as DEGs are marked in bold style (SEQ: Illumina RNA-Seq platform; Array: Affymetrix microarray platform)
  3. 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.
  4. 3P value is calculated using unpaired t-test on qPCR data; Genes that are significantly different between two groups are highlighted in bold style.
  5. 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.