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Table 4 Selected candidate genes for validation using qPCR. The progression-associated genes were identified after analysis of the fresh frozen investigation and are significantly differentially expressed between DCIS and IBC of the same tumours. Six of them are also differentially expressed between DCIS and IBC of the investigated FFPE tumours. The differential expressions of COL10A1 of SULF1 are almost significant. Differential expression of PLEKHC1 could not be verified

From: Progression-specific genes identified in microdissected formalin-fixed and paraffin-embedded tissue containing matched ductal carcinoma in situ and invasive ductal breast cancers

  

Fresh frozen investigation

FFPE investigation

Gene

RefSeq_ID

logFC

p-value

fold change

t-test p-value

COL10A1

NM_000493.3

5.11

4.34E-05

1.86

0.06

MMP11

NM_005940.3

5.09

4.92E-06

2.31

0.0042

COL11A1

NM_001854.2

3.64

4.75E-05

1.96

0.0006

THBS2

NM_003247.2

3.50

4.34E-05

1.02

0.0479

CSPG2

NM_004385.2

3.23

0.00126

2.74

0.0033

GREM1

NM_013372.5

3.02

7.36E-05

1.85

0.0033

SULF1

NM_015170.1

2.15

0.000101

1.40

0.0553

PLEKHC1

NM_006832.1

1.84

0.000101

0.33

0.5244

KRT14

NM_000526.3

−4.00

0.00433

−1.74

0.0015