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Table 1 List of putative ER target genes

From: Discovery of estrogen receptor α target genes and response elements in breast tumor cells

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]
  1. *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.