Table I ERE complex proteins with significant changes after a 24-h E2 stimulation

Proteins marked in bold were identified by both Experiments 1 and 2. TR, transcription regulation; B, binding; SDR, short-chain dehydrogenases/reductases; TRAP, thyroid hormone receptor-associated protein; UBX, domain present in ubiquitin-regulatory proteins; —, not applicable.

Swiss-Prot accession no.Protein nameMean ± S.D.No. of peptidesMolecular massCommentsRefs.
Da
1. Only ERα-related
    Q9NXB9Elongation of very long chain fatty acids protein 20.957 ± 0.054234,803TR25
    Q96JQ0Protocadherin-16 precursor1.3331346,712TR26
    Q14980Nuclear mitotic apparatus protein 10.5991239,214TR27
    P19012Keratin, type I cytoskeletal 151.006 ± 0.1131949,365TR27
    P08727Keratin, type I cytoskeletal 191.102 ± 0.23715544,065TR25
2. Only c-Myc-related
    P6208140 S ribosomal protein S71.200 ± 0.116422,113TR26
    P081954F2 cell surface antigen heavy chain0.905 ± 0.002258,023TR28
    Q9Y3U860 S ribosomal protein L360.786 ± 0.001212,303TR29
    P6242460 S ribosomal protein L7a1.085 ± 0.096330,148TR30
    P68133Actin, α skeletal muscle1.100 ± 0.0541442,366TR26
    Q9HDC9Adipocyte plasma membrane-associated protein1.037 ± 0.120846,622TR31
    P07355Annexin A21.095 ± 0.301438,808TR28
    P24539ATP synthase B chain1.498128,947TR29
    P25705ATP synthase subunit α1.103 ± 0.1012159,828TR28
    P06576ATP synthase subunit β1.099 ± 0.2343456,525TR29
    P53618Coatomer subunit β0.906 ± 0.0544108,214TR26
    Q9Y394Dehydrogenase/reductase SDR family member 7 precursor1.658138,673TR31
    P54886Δ1-Pyrroline-5-carboxylate synthetase1.064 ± 0.151387,989B32
    Q16531DNA damage-binding protein 11.224 ± 0.0022128,142TR28
    P39656Dolichyl-diphosphooligosaccharide-protein glycosyltransferase 48-kDa subunit precursor0.961 ± 0.125848,893TR28
    P50402Emerin1.204 ± 0.137429,033TR33
    P15311Ezrin (p81)1.350 ± 0.029269,484TR28
    Q06787Fragile X mental retardation 1 protein0.941 ± 0.006271,473TR34
    P62826Androgen receptor-associated protein 241.259 ± 0.063224,579TR28
    P61978Transformation up-regulated nuclear protein1.095 ± 0.193651,230TR32
    P52272Heterogeneous nuclear ribonucleoprotein M1.067 ± 0.060577,749TR31
    P05783Keratin, type I cytoskeletal 181.100 ± 0.39044948,029TR28
    Q96AG4Leucine-rich repeat-containing protein 591.257 ± 0.337535,308TR35
    Q08722Leukocyte surface antigen CD47 precursor1.957135,590TR28
    Q13724Mannosyl-oligosaccharide glucosidase0.980 ± 0.039292,032B32
    P67812Microsomal signal peptidase 18-kDa subunit2.597 ± 0.298220,612TR31
    Q8TCT9Signal peptide peptidase1.197 ± 0.153241,747TR31
    Q9Y6C9Mitochondrial carrier homolog 20.671 ± 0.072233,936TR29
    P35580Myosin heavy chain 101.333 ± 0.4444229,824TR28
    O94832Myosin-Id0.5791116,927TR29
    Q9Y2X3Nucleolar protein NOP51.632 ± 0.000260,054TR36
    Q14160Protein LAP41.9571175,794TR29
    Q86UE4Astrocyte elevated gene 1 protein1.022 ± 0.046463,856TR28
    P46940Ras GTPase-activating-like protein IQGAP10.994 ± 0.1383189,761TR31
    P61026Ras-related protein Rab-100.945 ± 0.148722,755TR31
    Q14257E6-binding protein0.964 ± 0.017336,911TR28
    Q9NW13RNA-binding protein 281.425186,198TR31
    P05023Sodium/potassium-transporting ATPase α-1 chain precursor1.100 ± 0.13017114,135TR35
    P50991T-complex protein 1 subunit δ1.164 ± 0.124258,401TR32
    Q5JTV8Torsin-1A-interacting protein 10.876 ± 0.002266,379TR31
    Q15363Transmembrane emp24 domain-containing protein 2 precursor1.672122,860TR28
    P40939Trifunctional enzyme subunit α1.288 ± 0.407883,688TR31
    Q9NYL9Tropomodulin-3 (ubiquitous tropomodulin)1.837139,741TR37
    Q9NZB2UPF0318 protein FAM120A0.927 ± 0.0833117,711TR28
    Q96A26E2-induced gene 5 protein2.3 ± 0.1217,559TR29
Da
    Q8WY22Cervical cancer 1 proto-oncogene-binding protein KG191.393127,932TR38
    Q15005Signal peptidase complex subunit 21.315 ± 0.034425,272TR28
3. Both ERα− and c-Myc-related
    P6310414-3-3 protein ζ/δ (protein kinase C inhibitor protein 1)1.372127,899TR26, 28
    P091103-Ketoacyl-CoA thiolase1.148 ± 0.018244,834TR28, 39
    P6227740 S ribosomal protein S131.042 ± 0.105417,212TR26, 33
    P6226340 S ribosomal protein S141.180 ± 0.003216,434TR28, 40
    P6224940 S ribosomal protein S161.211 ± 0.005316,549TR33, 41
    P0870840 S ribosomal protein S171.326115,597TR26, 33
    P6226940 S ribosomal protein S181.083 ± 0.137217,708TR26, 30
    P6124740 S ribosomal protein S3a1.038 ± 0.052930,154TR26
    P62753Phosphoprotein NP331.174 ± 0.001228,834TR26, 42
    P6224140 S ribosomal protein S81.271 ± 0.067224,475TR26, 28
    P1080960-kDa heat shock protein1.041 ± 0.108861,187TR26, 43
    P6291360 S ribosomal protein L111.292 ± 0.248320,468TR26, 44
    P26373Breast basic conserved protein 11.020 ± 0.049224,304TR26, 33
    P4677660 S ribosomal protein L27a1.089 ± 0.082216,665TR26, 45
    Q02878TAX-responsive enhancer element-binding protein 1070.898 ± 0.001232,765TR26, 33
    P1812460 S ribosomal protein L71.062 ± 0.001229,264TR26, 28
    P3296960 S ribosomal protein L91.173 ± 0.138421,964TR26, 33
    P60709Actin, cytoplasmic 1 (β-actin)1.087 ± 0.1072442,052B, TR26, 46
    P05141ADP/ATP translocase 21.020 ± 0.221533,102TR26, 28
    P12956Thyroid-lupus autoantigen (CTC box-binding factor 75-kDa subunit)1.066 ± 0.298470,084B, TR33, 40
    Q9NYF8Bcl-2-associated transcription factor 1 (Btf)1.177 ± 0.0022106,173TR23, 28
    P27824Calnexin precursor1.187 ± 0.101567,982TR26, 28
    O14976Cyclin G-associated kinase1.212 ± 0.1532144,583TR26, 33
    P04844Dolichyl-diphosphooligosaccharide1.045 ± 0.1321869,355B, TR26, 32
    P49411Elongation factor Tu1.181 ± 0.491649,852TR26, 28
    P14625Endoplasmin precursor1.342192,696TR33, 40
    Q92616GCN1-like protein 10.929 ± 0.0494294,953TR26, 35
    P04406Glyceraldehyde-3-phosphate dehydrogenase1.113 ± 0.258336,201TR28, 40
    P11142Heat shock cognate 71-kDa protein1.029 ± 0.253571,082TR, B42, 47
    P07900Heat shock protein HSP 90-α1.088 ± 0.087285,006TR, B28, 48
    P08238Heat shock protein HSP 90-β1.029 ± 0.004283,554TR, B28, 49
    P09651Heterogeneous nuclear ribonucleoprotein A11.069 ± 0.171538,936TR40, 45
    P51991Heterogeneous nuclear ribonucleoprotein A31.008 ± 0.197539,799TR35, 40
    P14866Heterogeneous nuclear ribonucleoprotein L0.998 ± 0.124360,719TR29, 40
    O60506Heterogeneous nuclear ribonucleoprotein Q1.374169,788TR26, 28
    P07910Heterogeneous nuclear ribonucleoproteins C1/C21.096 ± 0.1831933,707TR35, 40
    P16401Histone H1.51.047 ± 0.160822,566TR29, 40
    Q71UI9Histone H2AV1.067 ± 0.1103313,501TR26, 28
    P62807Histone H2B type 1-C/E/F/G/I1.170 ± 0.4585813,811TR33, 41
    Q16836Hydroxyacyl-coenzyme A dehydrogenase1.331 ± 0.178234,313TR26, 28
    P08779Keratin, type I cytoskeletal 161.099 ± 0.3792551,578TR26
    Q96G23Tumor metastasis suppressor gene 1 protein0.971 ± 0.001244,961TR25, 35
    P02545Lamin-A/C1.084 ± 0.144974,380TR26, 42
    P20700Lamin-B11.204 ± 0.2211066,653TR26, 28
    Q16891Proliferation-inducing gene 4 protein1.033 ± 0.115484,026TR26, 28
    P60660Myosin light polypeptide 61.272 ± 0.001217,090TR26, 50
    P35579Myosin-90.966 ± 0.19317227,646TR31, 40
    O43795Myosin-Ib0.955 ± 0.1083132,928TR26, 51
    Q15758Neutral amino acid transporter B(0)1.098 ± 0.113357,018TR26, 28
    P06748Nucleophosmin (NPM) (nucleolar phosphoprotein B23)0.996 ± 0.019432,726TR40, 43
    P26599Polypyrimidine tract-binding protein 11.020 ± 0.296657,357TR28, 39
    Q6P2Q9Pre-mRNA processing-splicing factor 81.030 ± 0.0924274,738B40, 51
    P35232Prohibitin1.012 ± 0.147729,843TR, B52, 53
Da
    Q99623Prohibitin-2 (repressor of estrogen receptor activity)1.144 ± 0.197733,276TR, B33, 40
    Q15084Protein-disulfide isomerase A6 precursor1.243 ± 0.027248,490TR26, 28
    Q9BSJ8Protein FAM62A0.982 ± 0.0406123,293TR26, 40
    O43143Putative pre-mRNA splicing factor ATP-dependent RNA helicase DHX151.558191,673TR26, 32
    Q15050Ribosome biogenesis regulatory protein homolog1.322141,225TR28, 54
    Q9H3N1Thioredoxin domain-containing protein 1 precursor1.235 ± 0.222232,170TR26, 35
    Q13263Transcription intermediary factor 1-β (nuclear corepressor KAP-1)1.083 ± 0.094290,261TR, B32, 40
    Q9UNL2Translocon-associated protein subunit γ (TRAP-γ)1.151 ± 0.001221,067TR25, 35
    P68363Tubulin α ubiquitous chain0.950 ± 0.27110350,804B28, 55
    P07437Tubulin β chain1.015 ± 0.1953850,095TR, B26, 55
    P68371Tubulin β-2C chain1.021 ± 0.1863950,255TR26
    Q9P0L0Vesicle-associated membrane protein-associated protein A0.921 ± 0.002228,103TR26, 33
    O95292Vesicle-associated membrane protein-associated protein B/C0.921 ± 0.002227,439TR26, 31
    O75396Vesicle-trafficking protein SEC22b0.897 ± 0.022224,896TR26, 31
    P21796Voltage-dependent anion-selective channel protein 11.168 ± 0.3792630,868TR26, 35
    Q9Y277Voltage-dependent anion-selective channel protein 31.045 ± 0.043330,981TR26, 28
    P68104Elongation factor 1-α 11.159 ± 0.065350,451TR26, 28
    O94972Tripartite motif-containing protein 371.8821109,491TR
    P22626Heterogeneous nuclear ribonucleoproteins A2/B11.032 ± 0.1731637,464TR33, 40
    P33778Histone H2B type 1-B1.177 ± 0.4555813,942TR29, 40
    P84243Histone H3.31.393 ± 1.1002815,376TR28, 40
    O75367Core histone macro-H2A.11.2 ± 0.4839,764TR26, 33
4. Others
    Q15008Breast cancer-associated protein SGA-113 m0.985 ± 0.112645,787
    Q16352α-Internexin (α-Inx)0.366 ± 0.068655,528
    P00403Cytochrome c oxidase subunit 20.983 ± 0.095425,719
    P15924Desmoplakin (DP)1.008 ± 0.0615334,02156
    Q14315Filamin-C2.7281293,344
    P20671Histone H2A type 11.063 ± 0.2004714,099
    Q71DI3Histone H3.20.970 ± 0.2013115,436
    P62805Histone H41.004 ± 0.19616211,36057
    P04264Keratin, type II cytoskeletal 10.987 ± 0.08615766,14958
    P02538Keratin, type II cytoskeletal 6A1.215 ± 0.3461960,29359
    P05787Keratin, type II cytoskeletal 81.072 ± 0.44756553,67160
    Q7Z406Myosin-141.014 ± 0.2084228,889
    P16435NADPH-cytochrome P450 reductase0.913 ± 0.000277,097
    Q9H0U4Ras-related protein Rab-1B1.149 ± 0.112522,328
    P62834Ras-related protein Rap-1A precursor0.956 ± 0.085321,31661
    Q96HR9Receptor expression-enhancing protein 61.004 ± 0.178420,89162
    O94901Sad1/unc-84 protein-like 11.180 ± 0.045290,806
    P04350Tubulin β-4 chain0.943 ± 0.1531750,01063
    Q96CS3UBX domain-containing protein 80.998 ± 0.035352,93364