Table 1.
List of putative ER target genes
| Accession number | Symbol | Gene name | Number of time points* | Gene ontology |
| (a) Putative ER target genes that are upregulated (59 out of 89) | ||||
| AL049265 | mRNA; cDNA DKFZp564F053 | 14 | Biological_process unknown [0000004] | |
| NM_003246 | THBS1 | thrombospondin 1 | 13 | Cell adhesion [0007155] |
| NM_016339 | Link-GEFII | Link guanine nucleotide exchange factor II | 13 | Neurogenesis [0007399] |
| U79299 | OLFM1 | Olfactomedin 1 | 13 | Signal transduction [0007165] |
| AK026062 | DNAJC1 | DnaJ (Hsp40) homolog, subfamily C, member 1 | 12 | Protein folding [0006457] |
| M62403 | IGFBP4 † | Insulin-like growth factor binding protein 4 | 12 | Signal transduction [0007165] |
| NM_001089 | ABCA3† | ATP-binding cassette, sub-family A (ABC1), member 3 | 12 | ATP-binding cassette (ABC) transporter [0004009] |
| NM_003714 | STC2 | Stanniocalcin 2 | 12 | Cell-cell signaling [0007267] |
| AF075060 | Hypothetical protein DKFZp761P0423 | 11 | Biological_process unknown [0000004] | |
| AF271070 | SLC38A1 | Solute carrier family 38, member 1 | 11 | Amino acid transport [0006865] |
| AK024639 | Hypothetical protein FLJ20986 | 11 | Cation transport [0006812] | |
| AL080199 | mRNA; cDNA DKFZp434E082 | 11 | Biological_process unknown [0000004] | |
| NM_014365 | H11 | Protein kinase H11 | 11 | Translational regulation, initiation [0006446] |
| AF245389 | GREB1 †‡ | GREB1 protein | 10 | High-affinity zinc ion transport [0006830] |
| NM_002894 | RBBP8 † | Retinoblastoma binding protein 8 | 10 | DNA repair [0006281] |
| NM_005067 | SIAH2 | Seven in absentia homolog 2 (Drosophila) | 10 | Ubiquitin-dependent protein degradation [0006511] |
| U16752 | CXCL12 † | Chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1) | 10 | Immune response [0006955] |
| AF086500 | FZD8 | Frizzled homolog 8 (Drosophila) | 9 | Biological_process unknown [0000004] |
| AF176012 | JDP1 | J domain containing protein 1 | 9 | Physiological processes [0007582] |
| AF182416 | NIF3L1 | NIF3 NGG1 interacting factor 3-like 1 (S. pombe) | 9 | DNA methylation [0006306] |
| AK023772 | Hypothetical protein FLJ13710 | 9 | Developmental processes [0007275] | |
| AK024361 | Hypothetical protein FLJ14299 | 9 | Transcription regulation [0006355] | |
| AK025812 | cDNA: FLJ22159 fis, clone HRC00251, mRNA sequence | 9 | Biological_process unknown [0000004] | |
| NM_001037 | SCN1B | Sodium channel, voltage-gated, type I, beta polypeptide | 9 | Sodium transport [0006814] |
| NM_003287 | TPD52L1 | Tumor protein D52-like 1 | 9 | Signal transducer [0004871] |
| NM_003646 | DGKZ | Diacylglycerol kinase, zeta 104 kDa | 9 | Signal transduction [0007165] |
| NM_014333 | IGSF4 | Immunoglobulin superfamily, member 4 | 9 | Virulence [0009406] |
| NM_016300 | ARPP-21 | Cyclic AMP-regulated phosphoprotein, 21 kD | 9 | Biological_process unknown [0000004] |
| AF200341 | HPYR1 | Helicobacter pylori responsive 1 | 8 | Biological_process unknown [0000004] |
| AK023199 | cDNA FLJ13137 fis, clone NT2RP3003150, mRNA sequence | 8 | Biological_process unknown [0000004] | |
| AK025571 | Hypothetical protein FLJ21918 | 8 | RNA processing [0006396] | |
| D00265 | CYCS | Cytochrome c, somatic | 8 | Electron transport [0006118] |
| NM_000926 | PGR † | Progesterone receptor | 8 | Signal transduction [0007165] |
| NM_001634 | AMD1 | S-adenosylmethionine decarboxylase 1 | 8 | Polyamine biosynthesis [0006596] |
| NM_002184 | IL6ST‡ | Interleukin 6 signal transducer (gp130, oncostatin M receptor) | 8 | Signal transduction [0007165] |
| NM_003489 | NRIP1 † | Nuclear receptor interacting protein 1 | 8 | Transcription regulation [0006355] |
| NM_004878 | PTGES | Prostaglandin E synthase | 8 | Prostaglandin metabolism [0006693] |
| NM_012111 | C14orf3 | Chromosome 14 open reading frame 3 | 8 | Protein folding [0006457] |
| NM_015878 | OAZIN | Ornithine decarboxylase antizyme inhibitor | 8 | Polyamine biosynthesis [0006596] |
| AK023680 | PPP1R15B | Protein phosphatase 1, regulatory (inhibitor) subunit 15B | 7 | Biological_process unknown [0000004] |
| NM_001909 | CTSD † | Cathepsin D (lysosomal aspartyl protease) | 7 | Proteolysis and peptidolysis [0006508] |
| NM_003774 | GALNT4 | UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 | 7 | Biological_process unknown [0000004] |
| NM_014810 | CAP350 | Centrosome-associated protein 350 | 7 | Non-selective vesicle transport [0006899] |
| NM_016391 | HSPC111 | Hypothetical protein HSPC111 | 7 | Leading strand elongation [0006272] |
| AK021773 | cDNA FLJ11711 fis, clone HEMBA1005152, mRNA sequence | 6 | Biological_process unknown [0000004] | |
| AK025766 | BRI3BP | BRI3 binding protein | 6 | Biological_process unknown [0000004] |
| L23401 | Human repeat region mRNA | 6 | Biological_process unknown [0000004] | |
| NM_000427 | LOR | Loricrin | 6 | Cell shape and cell size control [0007148] |
| NM_001932 | MPP3 | Membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3) | 6 | Signal transduction [0007165] |
| NM_002227 | JAK1 | Janus kinase 1 (a protein tyrosine kinase) | 6 | Protein phosphorylation [0006468] |
| NM_006392 | NOL5A | Nucleolar protein 5A (56 kDa with KKE/D repeat) | 6 | Transcription [0006350] |
| NM_006796 | AFG3L2 | AFG3 ATPase family gene 3-like 2 (yeast) | 6 | Biological_process unknown [0000004] |
| NM_013324 | CISH | Cytokine inducible SH2-containing protein | 6 | JAK-STAT cascade [0007259] |
| NM_016233 | PADI3 | Peptidyl arginine deiminase, type III | 6 | Protein modification [0006464] |
| NM_020120 | UGCGL1 | UDP-glucose ceramide glucosyltransferase-like 1 | 6 | Protein modification [0006464] |
| AB037842 | KIAA1421‡ | KIAA1421 protein | 5 | RNA dependent DNA replication [0006278] |
| NM_001116 | ADCY9 | Adenylate cyclase 9 | 5 | Signal transduction [0007165] |
| NM_014121 | PRO0233 protein | 5 | Double-strand break repair [0006303] | |
| NM_018053 | Hypothetical protein FLJ10307 | 5 | Cell death [0008219] | |
| (b) Putative ER target genes that are downregulated (30 out of 89) | ||||
| NM_012342 | NMA † | Putative transmembrane protein | 13 | Melanin biosynthesis from tyrosine [0006583] |
| AF039944 | NDRG1 | N-myc downstream regulated gene 1 | 11 | Biological_process unknown [0000004] |
| AL049471 | mRNA; cDNA DKFZp586N012 | 11 | Biological_process unknown [0000004] | |
| AK024964 | NFIA | Nuclear factor I/A | 9 | DNA replication [0006260] |
| M16006 | SERPINE1 | Serine (or cysteine) proteinase inhibitor, clade E, member 1 | 9 | Acute-phase response [0006953] |
| NM_004438 | EPHA4 | EphA4 | 9 | Signal transduction [0007165] |
| NM_006449 | CDC42EP3 | CDC42 effector protein (Rho GTPase binding) 3 | 9 | Signal transduction [0007165] |
| AK026298 | NMES1 | Normal mucosa of esophagus specific 1 | 8 | Biological_process unknown [0000004] |
| D16875 | Human HepG2 3' region cDNA, clone hmd1f06, mRNA sequence | 8 | Biological_process unknown [0000004] | |
| NM_002237 | KCNG1 | Potassium voltage-gated channel, subfamily G, member 1 | 8 | Potassium transport [0006813] |
| NM_003032 | SIAT1 | Sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase) | 8 | Protein modification [0006464] |
| NM_006605 | RFPL2 | Ret finger protein-like 2 | 8 | Protein binding [0005515] |
| AK025922 | Hypothetical protein FLJ22269 | 7 | Developmental processes [0007275] | |
| NM_000504 | F10 | Coagulation factor X | 7 | Proteolysis and peptidolysis [0006508] |
| NM_001139 | ALOX12B | Arachidonate 12-lipoxygenase, 12R type | 7 | Epidermal differentiation [0008544] |
| NM_004354 | CCNG2 | Cyclin G2 | 7 | Cell cycle checkpoint [0000075] |
| NM_006137 | CD7 | CD7 antigen (p41) | 7 | Humoral defense mechanism [0006959] |
| NM_007273 | REA‡ | Repressor of estrogen receptor activity | 7 | Negative control of cell proliferation [0008285] |
| NM_014583 | LMCD1 | LIM and cysteine-rich domains 1 | 7 | Transcription factor [0003700] |
| NM_017572 | MKNK2 | MAP kinase-interacting serine/threonine kinase 2 | 7 | Protein phosphorylation [0006468] |
| D49356 | Human mRNA (S100C-related gene) | 6 | Cell cycle [0007049] | |
| NM_001878 | CRABP2 | Cellular retinoic acid binding protein 2 | 6 | Signal transduction [0007165] |
| NM_004388 | CTBS | Chitobiase, di-N-acetyl- | 6 | Carbohydrate metabolism [0005975] |
| NM_006622 | SNK | serum-inducible kinase | 6 | Protein phosphorylation [0006468] |
| AK022072 | cDNA FLJ12010 fis, clone HEMBB1001635, mRNA sequence | 5 | Biological_process unknown [0000004] | |
| AL137529 | Hypothetical protein FLJ23751 | 5 | Lipid metabolism [0006629] | |
| NM_000430 | PAFAH1B1 | Platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45 kDa | 5 | Signal transduction [0007165] |
| NM_013332 | HIG2 | Hypoxia-inducible protein 2 | 5 | Biological_process unknown [0000004] |
| NM_014770 | CENTG1 | Centaurin, gamma 1 | 5 | Cell growth and/or maintenance [0008151] |
| NM_001719 | BMP7 † | Bone morphogenetic protein 7 (osteogenic protein 1) | 4 | Cell growth and/or maintenance [0008151] |
*Number of time points that met the 1.2-fold change in the same direction selection criteria. †Genes in bold have previously been shown to be direct targets in other ER+ breast tumor cell lines (ZR75-1 and/or MCF-7). ‡CHX treatments alone had agonistic effects on these genes; therefore their CHX sensitivity in the presence of E2 is unclear.