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 |
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