Table I Candidate estrogen-regulated proteins verified by SRM assay. 4-OHT, 4-hydroxytamoxifen. *See notes in the supplemental Table S3
Gene symbolProtein symbolUniProt accessionProtein nameERESILAC fold change 36 hSRM fold change 36 hResponse to 4-OHTCategory of response
Candidates identified by SILAC in three biological replicates (adjusted p < 0.05)
    TFF1TFF1P04155Trefoil factor 1+4.56.6YesPrimary
    MCM6MCM6Q14566DNA replication licensing factor MCM6+1.52.7YesPrimary
    KPNA2IMA1P52292Importin subunit alpha-1+3.12.5YesPrimary
    TSTTHTRQ16762Thiosulfate sulfurtransferase+1.71.9YesPrimary
    BCL2L11B2L11O43521Bcl-2-like protein 11+1.51.7YesPrimary
    ASNSASNSP08243Asparagine synthetase [glutamine-hydrolyzing]+1.71.5YesPrimary
    CDK2CDK2P24941Cyclin-dependent kinase 2+1.61.4YesPrimary
    RAB31RAB31Q13636Ras-related protein Rab-31+1.51.3WeakTransient
    TPM1TPM1P09493–3Isoform 3 of Tropomyosin alpha-1 chain+1.71.1WeakTransient
    DNAJA1DNJA1P31689DnaJ homolog subfamily A member 1+1.71.1WeakTransient
    DUTDUTP33316Deoxyuridine 5Ȳ-triphosphate nucleotidohydrolase1.83.5YesSecondary
    CDK1CDK1P06493Cyclin-dependent kinase 1n/a2.8YesSecondary
    NAB2NAB2Q15742NGFI-A-binding protein 21.81.9YesSecondary
    TOP2ATOP2AP11388DNA topoisomerase 2-alpha3.71.5YesSecondary
    HSP90AB1*HS90BP08238Heat shock protein HSP 90-beta1.71.3YesSecondary
    ESR1ESR1P03372Estrogen receptor0.40.7YesSecondary
    LXNLXNQ9BS40Latexin1.50.5YesSecondary
    SLC9A3R1NHRF1O14745Na(+)/H(+) exchange regulatory cofactor NHE-RF11.61.3NoIndirect
    ACACAACACAQ13085Acetyl-CoA carboxylase 11.50.9WeakFalse
Controls for hypoxia
    SLC2A1GTR1P11166Solute carrier family 2, facilitated glucose transporter member 1+1.41.8Weak
    ALDOAALDOAP04075Fructose-bisphosphate aldolase A231.11.1No
    ALDOCALDOCP09972Fructose-bisphosphate aldolase C231.21.2No
Housekeeping proteins used for normalization of SRM data
    ACTBACTBP60709Actin, cytoplasmic 1+1.01.0No
    CSCISYO75390Citrate synthase, mitochondrial+1.11.0No
    IDH2IDHPP48735Isocitrate dehydrogenase [NADP], mitochondrial+1.01.1No
    TALDO1TALDOP37837Transaldolase+0.91.1No
    ENO1ENOAP06733Alpha-enolase0.90.8No
    GAPDHG3PP04406Glyceraldehyde-3-phosphate dehydrogenase1.10.9No
    PKMKPYMP14618Pyruvate kinase PKM1.21.0No
    PKM/PKLRKPYM/KPYRP14618/P30613Pyruvate kinase PKM/Pyruvate kinase PKLR1.21.0No
    RPL27ARL27AP4677660S ribosomal protein L27a1.11.1No
    RPL30RL30P6288860S ribosomal protein L300.91.2Weak
    RPS3RS3P2339640S ribosomal protein S31.21.1No
    TUBBTBB5P07437Tubulin beta chain1.21.2Weak
    UBBUBP0CG47Polyubiquitin-B1.01.1No