Table 1

Top 50 genes extracted from ANNs

RankaRelative expressionbGene symbolGene descriptionSAGEcClone ID no.
1+0−0+ ESR1 Estrogen receptor 1NS725321
2+2−0+ TFF3 Trefoil factor 3 (intestinal)NT298417
3+1−1+ GATA3 GATA-binding protein 3NS214068
4+0−2+ESTsNS132140
5+4−0 S100A8 S100 calcium-binding protein A8 (calgranulin A)NT562729
6+4−1 LCN2 Lipocalin 2 (oncogene 24p3)NS741497
7+3−2+ESTsNT155072
8+2−3 CDH3 Cadherin 3, type 1, P-cadherin (placental)NT773301
9+2−4+ P28 Dynein, axonemal, light intermediate polypeptideNT782688
10+3−4 PFKP Phosphofructokinase, plateletNS26184
11+5−2 LAD1 Ladinin 1NS121551
12+6−2 KCNN4 Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4NS756708
13+8−3+ SFRS5 Splicing factor, arginine/serine-rich 5NT143169
14+8−3+ IGFBP2 Insulin-like growth factor binding protein 2 (36kD)NS233721
15+7−4+ HSPC195 ESTsNS139354
16+6−5+ COX6C Cytochrome c oxidase subunit VIcNS838568
17+7−5 PFKP Phosphofructokinase, plateletNS950682
18+7−6+ FBP1 Fructose-1,6-bisphosphatase 1NS433253
19+7−6 EGFR Epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)NS324861
20+6−7+ CRIP1 Cysteine-rich protein 1 (intestinal)NS1323448
21+6−8+ STC2 Stanniocalcin 2+130057
22+5−8 SCYD1 Small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)NT140574
23+6−6 GALNT3 UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)NT148225
24+5−7 KRT7 Keratin 7NS843321
25+5−7 LMO4 LIM domain only 4NS162533
26+7−7+ TIMP3 Tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinflammatory)NS768370
27+6−6+ CCND1 Cyclin D1 (PRAD1: parathyroid adenomatosis 1)+841641
28+13−5 ATDC Ataxia-telangiectasia group D-associated proteinNT377275
29+12−6 ABP/ZF Alu-binding protein with zinc finger domainNT417424
30+14−5+ IGF2 Insulin-like growth factor 2 (somatomedin A)NT207274
31+13−5+ IGHG3 Immunoglobulin heavy constant γ 3 (Gm marker)NT855745
32+12−6+ PIB5PA Phosphatidylinositol (4,5) bisphosphate 5-phosphatase, ANT1359579
33+13−7+ ARHH Ras homolog gene family, member HNS302591
34+15−6 MSE55 Serum constituent proteinNS214982
35+14−7+ SLC9A3R1 Solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 1NS773286
36+13−8+ EIF3S4 Eukaryotic translation initiation factor 3, subunit 4 (δ, 44kD)NS857319
37+12−9 SOD3 Superoxide dismutase 3, extracellularNT795309
38+11−10 SLC7A5 Solute carrier family 7 (cationic amino acid transporter, y+ system), member 5755578
39+10−11 NDRG1 N-myc downstream regulatedNT842863
40+13−12 S100P S100 calcium-binding protein PNS135221
41+14−13+ THBS1 Thrombospondin 1NT810512
42+14−12 IMPA2 Inositol(myo)-1(or 4)-monophosphatase 2NS32299
43+13−13 CHI3L1 Chitinase 3-like 1 (cartilage glycoprotein-39)NT770212
44+13−14+ SERPINI1 Serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 1NT564621
45+14−12 HMGIY High-mobility group (nonhistone chromosomal) protein isoforms I and YNS782811
46+14−13+ APOD Apolipoprotein DNS838611
47+16−13+ PVALB ParvalbuminNT430318
48+16−14+ A2M α-2-macroglobulinNT878182
49+16−15+ SELENBP1 Selenium binding protein 1NS80338
50+27−10 FABP7 Fatty acid binding protein 7, brainNS345626
  • a The genes are ranked according to the sensitivity analysis (see “Materials and Methods”). The sensitivity is calculated averaged over all 600 ANN models. The errors for a rank are calculated from the SD of the sensitivities for the 600 ANN models.

  • b +, higher expression in ER+; −, higher expression in ER−. Defined as the sign of the ANN sensitivity.

  • c NT, no tag; NS, not significant; +, up-regulated by E2; −, down-regulated by E2.