Table 2.
Most frequent differentially expressed genes between normal breast epithelium and ductal carcinoma in situ (DCIS)
| Tag | Gene | Description | Locus link | Fold change | P value |
| DCIS overexpressed genes | |||||
| GTATTTAACT | PKD1-like | Polycystic kidney disease 1-like | 79932 | 13.7 | 0.0100 |
| CGGACTCACT | STARD10 | START domain containing 10 | 10809 | 11.2 | 0.0086 |
| GTGTTGGGGG | EPS8L2 | EPS8-like 2 | 64787 | 9.6 | 0.0099 |
| TTTCTGGAGG | KIAA0545 | KIAA0545 protein | 23094 | 8.6 | 0.0100 |
| GATAAATTAA | FLJ14153 | Hypothetical protein | 64747 | 8.5 | 0.0055 |
| GAGAAATATC | NP220 | Nuclear protein | 27332 | 8.0 | 0.0088 |
| CCCTCTTTGG | LOC118487 | mRNA similar to RIKEN cDNA 1110001019 | 118487 | 7.4 | 0.0037 |
| CTGGGACTGA | LSM4 | U6 small nuclear RNA associated (S. cerevisiae) | 25804 | 6.4 | 0.0055 |
| CTGGGCCAGC | VAMP5 | Vesicle-associated membrane protein 5 | 10791 | 6.4 | 0.0068 |
| GCCCTTTCTC | MRC2 | Mannose receptor, C type 2 | 9902 | 5.8 | 0.0015 |
| TCTTGATTTA | A2M | Alpha-2-macroglobulin | 2 | 5.8 | 0.0083 |
| TAGTTTGTGG | MSH2 | MutS homolog 2, colon cancer | 4436 | 5.6 | 0.0091 |
| TCAGTGAACT | HPS4 | Hermansky–Pudlak syndrome 4 | 89781 | 5.6 | 0.0100 |
| GTTTATTCTT | FOXA1 | Forkhead box A1 | 3169 | 5.3 | 0.0044 |
| GCCGCTGCCA | PPP1R13B | Protein phosphatase 1 | 23368 | 4.3 | 0.0054 |
| TAAAGTGTCT | PIGS | Phosphatidylinositol glycan, class S | 94005 | 3.9 | 0.0100 |
| DCIS underexpressed genes | |||||
| GGGACGAGTG | TM4SF1 | Transmembrane 4 superfamily member 1 | 4071 | -442.6 | 0.0083 |
| TAACAGCCAG | NFKBIA | Nuclear factor kappa light polypeptide gene | 4792 | -158.6 | 2.4 × 10-6 |
| CAACTAATTC | CLU | Clusterin | 1191 | -63.9 | 0.0036 |
| GCCTTAACAA | PBEF | Pre-B-cell colony-enhancing factor | 10135 | -44.3 | 0.0020 |
| GGGTTTTTAT | NSEP1 | Nuclease sensitive element binding protein 1 | 4904 | -36.2 | 0.0001 |
| GACACGAACA | RASD1 | RAS, dexamethasone-induce 1 | 51655 | -31.4 | 0.0095 |
| AAGATTGGTG | CD9 | CD9 antigen (p24) | 928 | -29.6 | 0.0003 |
| ACCAAATTAA | TNFRSF10B | Tumor necrosis factor receptor superfamily | 8795 | -29.4 | 0.0003 |
| CTGGGCCTGA | LITAF | Lipopolysaccharide-induced tumor necrosis factor | 9516 | -28.9 | 0.0076 |
| CTGCCATAAC | SBDS | Shwachman–Bodian–Diamond syndrome | 51119 | -24.2 | 0.0005 |
| CACAGGCAAA | BZW1 | Basic leucine zipper and W2 domains 1 | 9689 | -22.1 | 0.0056 |
| GTTCCCTGGC | FAU | Finkel–Biskis–Reilly murine sarcoma virus | 2197 | -22.1 | 0.0028 |
| GTCTGCACCT | DKFZp547C1 | Hypothetical protein | 254851 | -21.9 | 0.0087 |
| TACGTTGCAG | GC20 | Translocation factor sui1 homolog | 10289 | -21.8 | 0.0079 |
| TGTAAAGATT | CCNL1 | Cyclin L1 | 57018 | -21.2 | 0.0008 |
| TGTTAAGTTC | CRY1 | Cryptochrome 1 (photolyase-like) | 1407 | -18.7 | 0.0091 |
| GAAATAAAGT | FLJ21657 | Hypothetical protein | 64417 | -18.5 | 0.0032 |
| ATGGGCTTGA | SQRDL | Sulfide quinone reductase-like (yeast) | 58472 | -17.3 | 0.0061 |
| TCAAGAAATT | PSME3 | Proteasome activator subunit 3 | 10197 | -15.7 | 0.0028 |
| CCGTGGTCGT | FBL | Fibrillarin | 2091 | -15.3 | 0.0100 |
| TGGAACAGGA | TGIF | Transforming growth factor beta-induced factor (TALE family homeobox) | 7050 | -12.2 | 0.0030 |
| AATGCTGGCA | DNAJB6 | DnaJ homolog, subfamily B, member 6 | 10049 | -11.7 | 0.0065 |
| AATGAGCAAC | GBP2 | Guanylate binding protein 2, interferon-inducible | 2634 | -11.1 | 0.0082 |
| GACCTATCTC | KIAA0992 | Paladin | 23022 | -10.9 | 0.0092 |
| AACTCTTGAA | EIF3S3 | Eukaryotic translation initiation factor 3 | 8667 | -10.6 | 0.0082 |
| GGGATTTTGT | PMAIP1 | Phorbol-12-myristate-13-acetate-induced protein 1 | 5366 | -10.6 | 0.0091 |
| AAAGCAAAAA | PTPN4 | Protein tyrosine phosphatase, non-receptor type 4 | 5775 | -10.4 | 0.0040 |
| ACTGACTATC | NEU1 | Sialidase 1 (lysosomal sialidase) | 4758 | -10.3 | 0.0095 |
| TTCCAGTTCA | PDE4B | Phosphodiesterase 4B, camp-specific | 5142 | -9.9 | 0.0087 |
| GAATGATTTC | ORF1-FL49 | Putative nuclear protein | 84418 | -9.5 | 0.0070 |
| GACTCGCTCC | HSJ001348 | cDNA for differentially expressed CO16 gene | 54742 | -9.5 | 0.0072 |
| TGGTTACAAA | NDEL1 | Nude nuclear distribution gene E homolog like 1 | 81565 | -8.9 | 0.0100 |
| AGTATGAGGA | TNFAIP3 | Tumor necrosis factor, alpha-induced protein 3 | 7128 | -8.1 | 0.0083 |
| CAGTTTAAAA | CRSP6 | Cofactor required for Sp1 transcriptional activation | 9440 | -7.7 | 0.0100 |