Table 3.

EKLF-dependent genes in the fetal liver

Intensity
Gene description
Common abbreviation
Accession no.
Ratio, —/— to +/+
EKLF—/—
EKLF+/+
Downregulated genes      
   Cytoskeleton       
      Erythrocyte protein band 4.9/dematin  Epb4.9* NM_013514  0.0507   372   7 233  
      Hect domain and RCC1 (CHC1)-like domain (RLD) 2  rjs  AF061529   0.079   95   741  
      Talin 1  Tln1  AK006088   0.0864   1 021   11 849  
      Cables  Cables,ik3-1  AF133208   0.137   571   4 207  
      P120-catenin  Catns NM_007615  0.224   142   587  
      Parvin, gamma  Parvg  AF312712   0.265   181   671  
      Alpha 1 spectrin  Spna-1 NM_011465  0.749   5 607   7 401  
   Transmembrane/blood group antigens/receptors       
      Solute carrier family 2, glucose transporter  Slc2a4; Glut4 NM_009204  0.0249   21   696  
      Solute carrier family 22; mitochondrial anion exchange  Slc22a4 OCTN1 NM_019687  0.0346   33   785  
      Lysophosphatidic acid-operated K+ channel; TRAAK  Kcnk4 NM_008431  0.0624   108   1 831  
      Rhodopsin, olfactory receptor  Rhod  AL133159   0.0862   281   3 661  
      Mus musculus olfactory receptor 65  Olfr65 NM_013617  0.0893   115   639  
      Calcium channel, voltage-dep, L type, alpha 1C subunit  Cacna1c NM_009781  0.097   110   668  
      Neurexophilin 4  Nxph4  AK004130   0.099   189   1 912  
      Duffy blood group  Dfy* NM_010045  0.108   1 432   13 104  
      ICAM 4, LW blood group  ICAM-4, Cd242*  AF296282   0.219   3 518   16 029  
      Roundabout homolog 3 (Drosophila)  Robo3 NM_011248  0.28   338.3   1 111  
      Erythroblast membrane-associated protein  Ermap* NM_013848  0.309   12 719   40 085  
      Transferrin receptor  Tfrc; CD71*  AK011596   0.31   7 367   23 487  
      Activin A receptor, type II-like 1  Acvrl1 NM_009612  0.326   1 301   3 480  
      Lectin, galactose binding, soluble 1  Lgals1; d-Gal1* NM_008495  0.335   11 570   33 382  
      Rhesus blood group CDE  Rhced* NM_011270  0.40   9 880   24 273  
      Glycophorin A  Gypa† NM_010369  0.572   14 932   25 518  
      CD59a antigen  Cd59a† NM_007652  0.626   4 744   7 127  
      CD47 antigen, Rh-related antigen  Cd47† NM_010581  0.647   9 620   14 890  
   Transcription factors and other nuclear proteins       
      Orphan nuclear receptor subfamily 0, group B, mem 1  Nr0b1; Dax NM_007430  0.0784   200   1 717  
      Retinoic acid receptor, gamma  Rarg, RARγ   M32071   0.123   160   1 240  
      Fanconi anemia, compl group D2  2410150O07Ri  AK019136   0.215   467   2 099  
      SMC2 structural maintenance of chromosomes 2-like 1  Smc2l1; CAP  AK017747   0.27   411   1 500  
      Homeo box B3  Hox-2.7  X66177   0.278   586   2 156  
      Zinc finger protein 297; Bing 1  Zfp297, Bing1 NM_020625  0.284   1 000   3 516  
      CBFA2T1, ETO, MTG8  Cbfa2t1h, Eto NM_009822  0.319   126   381  
      Zinc finger protein 1, Y-linked  Zfy1 NM_009570  0.329   180   451  
      Retinoic acid receptor, alpha  Rara, RARα   X56570   0.33   434   1 059  
      Zinc finger protein 162  Zfp162 NM_011750  0.335   159   446  
   Zinc finger and BTB domain containing 7  Zbtb7; Pokemon  AK018596   0.349   1 662   4 817  
      Kruppel-like factor 3  Klf3 NM_008453  0.38   389   910  
      Btebp1; Kruppel-like factor 9  Bteb1; Klf9 NM_010638  0.474   250   540  
      LIM domain only 2  Lmo2* NM_008505  0.483   4 807   9 776  
      GLI-Kruppel family member GLI3  Gli3 NM_008130  0.51   362   690  
      Hemogen  Hemgn  AF269248   0.539   7 947   15 065  
      TBP-associated factor 140  TAF140  AJ292189   0.539   818.5   1 359  
   Others       
      RIKEN cDNA 1190001M18 - EST  1190001M18Ri  AK004435   0.0594   128   1 522  
      RIKEN cDNA 4930518C09 gene  4930518C09Rik  AK015822   0.0762   119   836  
      Keratin complex 1, acidic, gene 15  Krt1-15 NM_008469  0.0457   149   1 858  
      Reelin  Reln  U72343   0.0458   100   3 690  
      Sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1  Spock1 NM_009262  0.0503   56   632  
      Chaperonin subunit 6b (zeta)  Cct6b NM_009839  0.0578   66   505  
      IL-3; interleukin-3  IL3  S59969   0.081   268   3 479  
      RIKEN cDNA 1700011M02 gene  1700011M02Ri  AK005877   0.0831   300   2 917  
      Male wolffian duct clone: 6720484C15  6720484C15Rik  AK020173   0.0845   419   4 694  
      RIKEN cDNA 4933401L05 gene  4933401L05Rik  AK016606   0.0918   125   1 587  
      RIKEN cDNA 4933421O10 gene  4933421O10Ri  AK016866   0.0934   224   2 456  
      RIKEN cDNA 3110006O06 gene  3110006O06Ri  AK014014   0.0969   207   759  
      Tripartite motif-containing 59  Trim59 NM_025863  0.358   289   795  
      Synuclein, alpha  Snca* NM_009221  0.395   9 863   24 559  
   Nonheme enzymes       
      Fructosamine 3 kinase  FN3K  AJ404616   0.0746   346   4 573  
      ATPase, AAA domain containing 3A  Atad3a  AF343079   0.085   347   4 253  
      Mitochondrial gst 3  Mgst3* NM_025569  0.12   1 279   10 724  
      Pyruvate kinase  Pklr NM_013631  0.267   308.9   1 128  
      Protein tyrosine phosphatase 4a3  Ptp4a3, Acp5* NM_008975  0.268   3 153   11 465  
      Diacylglycerol O-acyltransferase 1  Dgat1 NM_010046  0.388   1 339   3 414  
      Pyruvate carboxylase  Pcx NM_008797  0.436   1 086   2 471  
      Ubiquitin-conjugating enzyme E2C  Ube2c  AK003722   0.461   12 446   26 672  
      Cathepsin B  Ctsb NM_007798  0.536   752.1   1 419  
   Globin and heme synthesis       
      Alpha hemoglobin-stabilizing protein  AHSP, EDRF*  AF060220   0.0426   3 666   78 235  
      β-Globin   β-major*  AF071431   0.199   13 941   72 270  
      Benzodiazepine receptor, peripheral  Bzrp* NM_009775  0.487   3 691   7 488  
      Interferon-stimulated protein  Isg20 NM_020583  0.501   1 432   2 890  
      Biliverdin reductase B  Blvrb  BC006617   0.524   15 936   29 989  
      Protoporphyrinogen oxidase  Ppox NM_008911  0.555   1 644   2 999  
      Hydroxymethylbilane synthase  Hmbs, PBGD  BC003861   0.693   30 672   42 426  
      Aminolevulinic acid synthase 2, erythroid  ALAS-E  M63244   0.711   38 138   53 271  
      Similar to Cpo protein  Cpox† NM_007757  0.752   684   
      Uroporphyrinogen decarboxylase  Urod† NM_009478  0.768   22 428   28 536  
      Ferrochelatase  Fech† NM_007998  1.195   20 752   17 629  
      Aminolevulinic acid synthase 1  ALAS-H†  M63245   1.394   846.2   625  
      Uroporphyrinogen III synthase  Uros† NM_009479  1.392   17 625   12 695  
Upregulated genes      
   Carbonic anhydrase 1  Car1 NM_009799  12.39   24 734   2 155  
   BCL2/adenovirus E1B 19-kDa interacting protein 1, NIP3  Bnip3 NM_009760  5.834   9 525   1 678  
   Neoplastic progression 3  Npn3; Srx; TX01  Z31362   4.732   3 036   686  
   RIKEN cDNA 9630039A02 gene  Cntnap2 NM_025771  4.651   1 571   388  
   Tnf receptor-associated factor 5  Traf5 NM_011633  4.464   778   367  
   Trafficking protein particle complex 2  Trappc2 NM_025432  4.039   880   344  
   RIKEN cDNA 3110040M04 gene  3110040M04Ri  AK014162   3.973   2 038   577  
   Glutathione transferase zeta 1  Tmed8; Gm1184  AK018286   3.909   2 717   690  
   Ubiquitin-conjugating enzyme E2E 1, UBC4/5 homolog  Ube2e1 NM_009455  3.842   4 706   2 774  
   Formin homology 2 domain containing 3  Fhod3  AK020839   3.558   1 508   498  
   RIKEN cDNA 1500010M24 gene  1500010M24Ri  AK005193   3.532   1 505   468.2  
   Interferon, alpha-inducible protein  G1p2 NM_015783  3.444   2 849   968.3  
   SH3 domain and nuclear localization signals, 1  Samsn1; Hacs1  AF222928   3.44   2 597   757  
   Phosphoglycerate kinase 1  Pgk1 NM_008828  3.367   14 878   5 269  
   ST3 beta-galactoside alpha-2,3-sialyltransferase 6  St3gal6 NM_018784  3.365   4 880   1 578  
   G kinase anchoring protein 1  Gkap1 NM_019832  3.29   803   460  
   Tuftelin 1  Tuft1 NM_011656  3.145   3 052   966  
   Kruppel-like factor 6  Klf6  AF072403   2.843   736   302  
   Retinoblastoma-like 2  Rbl2 NM_011250  2.793   812   346  
   Musashi homolog 2 (Drosophila)  msi2  AB056103   2.775   1 205   449  
   Annexin A6  Anxa6 NM_013472  2.622   575.2   317.8  
   Annexin A5  Anxa5 NM_009673  2.62   6 065   2 436  
   Phosphoglycerate mutase 1
 		Pgam1
 		 AF283667
 		 2.46
 		 23 283
 		 9 548
 
Intensity
Gene description
Common abbreviation
Accession no.
Ratio, —/— to +/+
EKLF—/—
EKLF+/+
Downregulated genes      
   Cytoskeleton       
      Erythrocyte protein band 4.9/dematin  Epb4.9* NM_013514  0.0507   372   7 233  
      Hect domain and RCC1 (CHC1)-like domain (RLD) 2  rjs  AF061529   0.079   95   741  
      Talin 1  Tln1  AK006088   0.0864   1 021   11 849  
      Cables  Cables,ik3-1  AF133208   0.137   571   4 207  
      P120-catenin  Catns NM_007615  0.224   142   587  
      Parvin, gamma  Parvg  AF312712   0.265   181   671  
      Alpha 1 spectrin  Spna-1 NM_011465  0.749   5 607   7 401  
   Transmembrane/blood group antigens/receptors       
      Solute carrier family 2, glucose transporter  Slc2a4; Glut4 NM_009204  0.0249   21   696  
      Solute carrier family 22; mitochondrial anion exchange  Slc22a4 OCTN1 NM_019687  0.0346   33   785  
      Lysophosphatidic acid-operated K+ channel; TRAAK  Kcnk4 NM_008431  0.0624   108   1 831  
      Rhodopsin, olfactory receptor  Rhod  AL133159   0.0862   281   3 661  
      Mus musculus olfactory receptor 65  Olfr65 NM_013617  0.0893   115   639  
      Calcium channel, voltage-dep, L type, alpha 1C subunit  Cacna1c NM_009781  0.097   110   668  
      Neurexophilin 4  Nxph4  AK004130   0.099   189   1 912  
      Duffy blood group  Dfy* NM_010045  0.108   1 432   13 104  
      ICAM 4, LW blood group  ICAM-4, Cd242*  AF296282   0.219   3 518   16 029  
      Roundabout homolog 3 (Drosophila)  Robo3 NM_011248  0.28   338.3   1 111  
      Erythroblast membrane-associated protein  Ermap* NM_013848  0.309   12 719   40 085  
      Transferrin receptor  Tfrc; CD71*  AK011596   0.31   7 367   23 487  
      Activin A receptor, type II-like 1  Acvrl1 NM_009612  0.326   1 301   3 480  
      Lectin, galactose binding, soluble 1  Lgals1; d-Gal1* NM_008495  0.335   11 570   33 382  
      Rhesus blood group CDE  Rhced* NM_011270  0.40   9 880   24 273  
      Glycophorin A  Gypa† NM_010369  0.572   14 932   25 518  
      CD59a antigen  Cd59a† NM_007652  0.626   4 744   7 127  
      CD47 antigen, Rh-related antigen  Cd47† NM_010581  0.647   9 620   14 890  
   Transcription factors and other nuclear proteins       
      Orphan nuclear receptor subfamily 0, group B, mem 1  Nr0b1; Dax NM_007430  0.0784   200   1 717  
      Retinoic acid receptor, gamma  Rarg, RARγ   M32071   0.123   160   1 240  
      Fanconi anemia, compl group D2  2410150O07Ri  AK019136   0.215   467   2 099  
      SMC2 structural maintenance of chromosomes 2-like 1  Smc2l1; CAP  AK017747   0.27   411   1 500  
      Homeo box B3  Hox-2.7  X66177   0.278   586   2 156  
      Zinc finger protein 297; Bing 1  Zfp297, Bing1 NM_020625  0.284   1 000   3 516  
      CBFA2T1, ETO, MTG8  Cbfa2t1h, Eto NM_009822  0.319   126   381  
      Zinc finger protein 1, Y-linked  Zfy1 NM_009570  0.329   180   451  
      Retinoic acid receptor, alpha  Rara, RARα   X56570   0.33   434   1 059  
      Zinc finger protein 162  Zfp162 NM_011750  0.335   159   446  
   Zinc finger and BTB domain containing 7  Zbtb7; Pokemon  AK018596   0.349   1 662   4 817  
      Kruppel-like factor 3  Klf3 NM_008453  0.38   389   910  
      Btebp1; Kruppel-like factor 9  Bteb1; Klf9 NM_010638  0.474   250   540  
      LIM domain only 2  Lmo2* NM_008505  0.483   4 807   9 776  
      GLI-Kruppel family member GLI3  Gli3 NM_008130  0.51   362   690  
      Hemogen  Hemgn  AF269248   0.539   7 947   15 065  
      TBP-associated factor 140  TAF140  AJ292189   0.539   818.5   1 359  
   Others       
      RIKEN cDNA 1190001M18 - EST  1190001M18Ri  AK004435   0.0594   128   1 522  
      RIKEN cDNA 4930518C09 gene  4930518C09Rik  AK015822   0.0762   119   836  
      Keratin complex 1, acidic, gene 15  Krt1-15 NM_008469  0.0457   149   1 858  
      Reelin  Reln  U72343   0.0458   100   3 690  
      Sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1  Spock1 NM_009262  0.0503   56   632  
      Chaperonin subunit 6b (zeta)  Cct6b NM_009839  0.0578   66   505  
      IL-3; interleukin-3  IL3  S59969   0.081   268   3 479  
      RIKEN cDNA 1700011M02 gene  1700011M02Ri  AK005877   0.0831   300   2 917  
      Male wolffian duct clone: 6720484C15  6720484C15Rik  AK020173   0.0845   419   4 694  
      RIKEN cDNA 4933401L05 gene  4933401L05Rik  AK016606   0.0918   125   1 587  
      RIKEN cDNA 4933421O10 gene  4933421O10Ri  AK016866   0.0934   224   2 456  
      RIKEN cDNA 3110006O06 gene  3110006O06Ri  AK014014   0.0969   207   759  
      Tripartite motif-containing 59  Trim59 NM_025863  0.358   289   795  
      Synuclein, alpha  Snca* NM_009221  0.395   9 863   24 559  
   Nonheme enzymes       
      Fructosamine 3 kinase  FN3K  AJ404616   0.0746   346   4 573  
      ATPase, AAA domain containing 3A  Atad3a  AF343079   0.085   347   4 253  
      Mitochondrial gst 3  Mgst3* NM_025569  0.12   1 279   10 724  
      Pyruvate kinase  Pklr NM_013631  0.267   308.9   1 128  
      Protein tyrosine phosphatase 4a3  Ptp4a3, Acp5* NM_008975  0.268   3 153   11 465  
      Diacylglycerol O-acyltransferase 1  Dgat1 NM_010046  0.388   1 339   3 414  
      Pyruvate carboxylase  Pcx NM_008797  0.436   1 086   2 471  
      Ubiquitin-conjugating enzyme E2C  Ube2c  AK003722   0.461   12 446   26 672  
      Cathepsin B  Ctsb NM_007798  0.536   752.1   1 419  
   Globin and heme synthesis       
      Alpha hemoglobin-stabilizing protein  AHSP, EDRF*  AF060220   0.0426   3 666   78 235  
      β-Globin   β-major*  AF071431   0.199   13 941   72 270  
      Benzodiazepine receptor, peripheral  Bzrp* NM_009775  0.487   3 691   7 488  
      Interferon-stimulated protein  Isg20 NM_020583  0.501   1 432   2 890  
      Biliverdin reductase B  Blvrb  BC006617   0.524   15 936   29 989  
      Protoporphyrinogen oxidase  Ppox NM_008911  0.555   1 644   2 999  
      Hydroxymethylbilane synthase  Hmbs, PBGD  BC003861   0.693   30 672   42 426  
      Aminolevulinic acid synthase 2, erythroid  ALAS-E  M63244   0.711   38 138   53 271  
      Similar to Cpo protein  Cpox† NM_007757  0.752   684   
      Uroporphyrinogen decarboxylase  Urod† NM_009478  0.768   22 428   28 536  
      Ferrochelatase  Fech† NM_007998  1.195   20 752   17 629  
      Aminolevulinic acid synthase 1  ALAS-H†  M63245   1.394   846.2   625  
      Uroporphyrinogen III synthase  Uros† NM_009479  1.392   17 625   12 695  
Upregulated genes      
   Carbonic anhydrase 1  Car1 NM_009799  12.39   24 734   2 155  
   BCL2/adenovirus E1B 19-kDa interacting protein 1, NIP3  Bnip3 NM_009760  5.834   9 525   1 678  
   Neoplastic progression 3  Npn3; Srx; TX01  Z31362   4.732   3 036   686  
   RIKEN cDNA 9630039A02 gene  Cntnap2 NM_025771  4.651   1 571   388  
   Tnf receptor-associated factor 5  Traf5 NM_011633  4.464   778   367  
   Trafficking protein particle complex 2  Trappc2 NM_025432  4.039   880   344  
   RIKEN cDNA 3110040M04 gene  3110040M04Ri  AK014162   3.973   2 038   577  
   Glutathione transferase zeta 1  Tmed8; Gm1184  AK018286   3.909   2 717   690  
   Ubiquitin-conjugating enzyme E2E 1, UBC4/5 homolog  Ube2e1 NM_009455  3.842   4 706   2 774  
   Formin homology 2 domain containing 3  Fhod3  AK020839   3.558   1 508   498  
   RIKEN cDNA 1500010M24 gene  1500010M24Ri  AK005193   3.532   1 505   468.2  
   Interferon, alpha-inducible protein  G1p2 NM_015783  3.444   2 849   968.3  
   SH3 domain and nuclear localization signals, 1  Samsn1; Hacs1  AF222928   3.44   2 597   757  
   Phosphoglycerate kinase 1  Pgk1 NM_008828  3.367   14 878   5 269  
   ST3 beta-galactoside alpha-2,3-sialyltransferase 6  St3gal6 NM_018784  3.365   4 880   1 578  
   G kinase anchoring protein 1  Gkap1 NM_019832  3.29   803   460  
   Tuftelin 1  Tuft1 NM_011656  3.145   3 052   966  
   Kruppel-like factor 6  Klf6  AF072403   2.843   736   302  
   Retinoblastoma-like 2  Rbl2 NM_011250  2.793   812   346  
   Musashi homolog 2 (Drosophila)  msi2  AB056103   2.775   1 205   449  
   Annexin A6  Anxa6 NM_013472  2.622   575.2   317.8  
   Annexin A5  Anxa5 NM_009673  2.62   6 065   2 436  
   Phosphoglycerate mutase 1
 		Pgam1
 		 AF283667
 		 2.46
 		 23 283
 		 9 548
 

Gene names are in full description and common abbreviations with a GenBank accession number. The ratio is the normalized mean of the relative expression in EKLF–/– versus EKLF+/+ fetal liver RNA (n = 6). The mean absolute intensities of each gene are given.

*

Genes verified by real-time RT-PCR

†

Genes that do not have expression fold differences that are enough for listing as possible EKLF targets but are included for comparison and discussion

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