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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