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Table 2 Differentially expressed genes in response to dietary LC-PUFAs in (A) hippocampus and (B) liver. Table includes gene categories discussed in the manuscript. Genes are grouped by functional category, sorted alphabetically, and annotated with NCBI LocusLink. Average difference intensity (ADI) represents gene absolute expression, and was used to calculate fold changes. Differentially expressed genes were clustered with a combined k-means/hierarchical approach. Asterisk (*) indicates ADIs significantly different from control diet, using 5% LFC gene selection model equations (LFChippocampus = 1.36 + (90/min ADI); LFCliver = 1.52+(100/min ADI)).

From: Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression

(A)
Gene Symbol Description Unigene ADI
(Average Difference Intensity)
Cluster Coordinates
    Control FUNG FISH FUNG
+
FISH
 
Nucleic Acid Binding
Ar androgen receptor Mm.4470 83 209* 136 101 H1-K2
Atoh4 atonal homolog 4 (Drosophila) Mm.42017 21 97 74 119* H1-K2
Btf3 basic transcription factor 3 Mm.1538 992 522* 475* 877 H5-K5
Dbp D site albumin promoter binding protein Mm.3459 111 206 84 154 H1-K2
Ddb1 damage specific DNA binding protein 1 Mm.29623 239 299 242 139 H4-K4
Dscr1 Down syndrome critical region homolog 1 (human) Mm.56 304 258 138* 130* H5-K3
E2f3 E2F transcription factor 3 Mm.6333 110 55 214 80 H3-K1
Elk1 ELK1, member of ETS oncogene family Mm.3064 613 425 690 402 H3-K1
Hdac1 (Rpd3) high homology to histone deacetylase 1 Mm.2602 393 231 411 353 H3-K1
Hoxd12 homeo box D12 Mm.57124 436 368 403 234* H4-K4
Idb1 inhibitor of DNA binding 1 Mm.444 148 169 344* 238 H3-K1
Idb3 inhibitor of DNA binding 3 Mm.110 41 117 156* 138 H1-K2
Nhlh1 nescient helix loop helix 1 Mm.2474 111 198 79 132 H1-K2
Pax9 paired box gene 9 Mm.5035 104 20 165 77 H3-K1
Pcbp3 poly(rC) binding protein 3 Mm.143816 187 180 52* 184 H5-K5
Purb purine rich element binding protein B Mm.154651 391 313 172* 246 H5-K3
Lipoprotein Metabolism
Apod apolipoprotein D Mm.2082 325 423 575* 456 H3-K1
Miscellaneous Genes
Htr4 5 hydroxytryptamine (serotonin) receptor 4 (5-HT) Mm.20440 20 130* 76 89 H1-K2
Pomc proopiomelanocortin Mm.21878 51 304* 80 71 H1-K2
Prkcd protein kinase C, delta (PKC) Mm.2314 461 297 353 263* H5-K3
Siat8e sialyltransferase 8 (alpha 2, 8 sialytransferase) E Mm.5173 128 207 49 20* H5-K4
Ttr transthyretin Mm.2108 304 490 157* 687* H1-K5
(B)
Gene Symbol Description Unigene ADI
(Average Difference Intensity)
Cluster Coordinates
    Control FUNG FISH FUNG
+
FISH
 
Nucleic Acid Binding
Atf4 activating transcription factor 4 Mm.641 1122 910 1045 647 H1-K4
Atf5 activating transcription factor 5 Mm.1566 870 505* 563* 281* H3-K3
Dbp D site albumin promoter binding protein Mm.3459 169 581* 174 747* H5-K5
Eef1a1 eukaryotic translation elongation factor 1 alpha 1 Mm.196614 1517 845* 1877 1642 H1-K1
Eif4a1 eukaryotic translation initiation factor 4A1 Mm.12858 125 180 68 218 H5-K5
Ercc2 excision repair cross-complementing rodent repair deficiency, complementation group 2 Mm.56990 148 142 319* 298* H1-K1
Gtf2i general transcription factor II I Mm.22593 89 47 150 20 H1-K1
HNF-3g forkhead box A3 (Foxa3) Mm.42260 411 501 454 207* H2-K4
Hoxd12 homeo box D12 Mm.57124 127 177 85 44 H2-K4
Hzf-pending hematopoietic zinc finger Mm.14099 235 328 516* 173 H1-K4
Klf13 Kruppel-like factor 13 Mm.41170 257 455 381 515* H4-K2
Miz1 Msx-interacting-zinc finger Mm.6370 283 453 429 146 H2-K4
Nfyb nuclear transcription factor-Y beta (NF-Y) Mm.3259 121 219 73 195 H4-K2
Pbx1 pre B-cell leukemia transcription factor 1 Mm.61526 1587 1039 1328 933* H3-K3
Rpo2tc1 RNA polymerase II transcriptional coactivator Mm.41746 461 560 368 292 H2-K4
Srebp-1 ethanol induced 6 (sterol regulatory element binding protein-1); Etohi6 Mm.30133 648 610 310* 370* H3-K3
Tceb1l transcription elongation factor B (SIII), polypeptide 1 (15 kDa),-like Mm.42944 420 549 672* 744* H5-K5
Tcf2 transcription factor 2 Mm.7226 151 121 244 20* H1-K4
Tcf7 transcription factor 7, T-cell specific Mm.31630 212 237 203 568* H5-K5
Tcfe3 EST highly similar to transcription factor E3 Mm.25762 114 135 203 20 H1-K4
Thrsp; Spot14 thyroid hormone responsive SPOT14 homolog (Rattus) Mm.28585 2481 2947 2353 1505* H2-K4
Usf2 upstream transcription factor 2 Mm.15781 180 209 32* 191 H5-K2
Fatty Acid Synthesis
Acas1 acetyl-Coenzyme A synthetase 1 (AMP forming) Mm.22719 497 200* 297* 113* H3-K3
Acly ATP citrate lyase (ACL) N/A 2513 939* 1117* 530* H3-K3
Acly ATP citrate lyase (ACL) N/A 3197 1568* 1754* 878* H3-K3
Acly ATP citrate lyase (ACL) N/A 456 115* 64* 51* H3-K3
Acly ATP citrate lyase (ACL) N/A 603 278* 252* 163* H3-K3
Elovl2; Ssc2 elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2 Mm.2567 3010 2291 1780* 1690* H3-K3
Elovl3; Cig30 elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 3 Mm.21806 517 421 983* 317 H1-K1
Facl2 fatty acid Coenzyme A ligase, long chain 2 Mm.28962 514 709 677 926* H5-K5
Fasn fatty acid synthase (FAS) Mm.3760 5214 2715* 4104 966* H1-K5
Scd1 stearoyl-Coenzyme A desaturase 1 Mm.140785 9783 8749 9493 5541* H1-K4
Fatty Acid Oxidation
Acadm acetyl-Coenzyme A dehydrogenase, medium chain (MCAD) Mm.10530 1364 2014 1774 2261* H4-K2
Aldh1a1 aldehyde dehydrogenase family 1, subfamily A1 Mm.4514 2387 3917* 4274* 4091* H4-K2
Aldh1a7 aldehyde dehydrogenase family 1, subfamily A7 Mm.14609 1717 1977 3208* 2264 H1-K1
Cpt1a carnitine palmitoyltransferase 1, liver Mm.18522 734 1285* 1058 1272* H4-K2
Cpt2 carnitine palmitoyltransferase 2 Mm.29499 418 673 791* 690* H4-K1
Crat carnitine acetyltransferase Mm.20396 58 82 190* 71 H1-K1
Ech1 enoyl coenzyme A hydratase 1 (delta 3,5-delta 2,4-dienoyl-CoA isomerase) Mm.2112 1239 1388 2031* 1731 H1-K1
Carbohydrate Metabolism
Camk2b calcium/calmodulin-dependent protein kinase II, beta Mm.4857 152 139 20* 84 H3-K3
Cam-Pde 1c calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1c N/A 98 61 75 584* H5-K5
G6pc glucose-6-phosphatase, catalytic (G6Pase) Mm.18064 1065 1224 1669* 553* H1-K4
Got1 glutamate oxaloacetate transaminase 1, soluble Mm.19039 976 798 656 467* H3-K3
Gpam glycerol-3-phosphate acyltransferase, mitochondrial (GPAT) Mm.87773 1184 683* 989 526* H3-K4
Hspa5 heat shock 70kD protein 5 (glucose-regulated protein, 78kD) Mm.918 2802 1996 3014 1820* H1-K4
Pck1 phosphoenolpyruvate carboxykinase 1, cytosolic (PEPCK) Mm.42246 1376 2913* 2198* 2369* H4-K2
Pck1 phosphoenolpyruvate carboxykinase 1, cytosolic (PEPCK) Mm.42246 964 1550 1352 1652* H4-K2
Pck1 phosphoenolpyruvate carboxykinase 1, cytosolic (PEPCK) Mm.42246 243 647* 452* 633* H4-K2
Pck1 phosphoenolpyruvate carboxykinase 1, cytosolic (PEPCK) Mm.42246 320 660* 564* 744* H4-K2
Cytochrome P450 Metabolism
Cyp1a2 cytochrome P450, 1a2, aromatic compound inducible Mm.15537 3952 5021 2839* 4187 H2-K2
Cyp2a4 cytochrome P450, 2a4 Mm.14781 922 2682* 1100 2362* H4-K2
Cyp2b9 cytochrome P450, 2b9, phenobarbitol inducible type a Mm.876 57 161 241* 146 H4-K1
Cyp3a11 cytochrome P450, steroid inducible 3a11 Mm.21193 4777 7297 8429* 6542 H4-K1
Cyp3a16 cytochrome P450, 3a16 Mm.30303 1438 2805* 2835* 2282* H4-K2
Cyp4a10 cytochrome P450, 4a10 Mm.10742 335 894* 1566* 1010* H4-K1
Cyp4a14 cytochrome P450, 4a14 Mm.7459 20 160* 385* 51 H1-K1
Cypf13 cytochrome P450 CYP4F13 Mm.22045 600 834 529 439 H2-K2
Por P450 (cytochrome) oxidoreductase Mm.3863 54 208* 119 232* H4-K2
Transport
Abca1 ATP-binding cassette, sub-family A (ABC1) member 1 Mm.369 550 121* 217* 270* H3-K3
Abca7 ATP-binding cassette, sub-family A (ABC1) member 7 Mm.103351 20 20 20 144* H5-K5
Abce1 ATP-binding cassette, sub-family E (OABP)member 1 Mm.5831 118 116 310* 124 H1-K1
Cd36 CD36 antigen Mm.18628 247 223 591* 170 H1-K1
Fabp5 fatty acid binding protein 5, epidermal (E-FABP) Mm.741 3236 593* 384* 238* H3-K3
Slc10a1 solute carrier family 10 (sodium/bile acid cotransporter family), member 1 (Ntcp) Mm.104295 845 877 534* 1005 H5-K5
Sterol Metabolism
Fpps farnesyl pyrophosphate synthase Mm.39472 794 327* 510* 421* H3-K3
Hmgcs2 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2, mitochondrial (HMG-CoA2) Mm.10633 3592 4491 4590 5822* H5-K5
Lipoprotein Metabolism
Apoa4 apolipoprotein A-IV Mm.4533 2011 781* 629* 117* H3-K3
Apoa4 apolipoprotein A-IV precursor Mm.4533 194 60* 46* 20* H3-K3
ApoB-100 EST highly similar to apolipoprotein B-100 precursor Mm.29123 2675 5710* 5005* 5395* H4-K2
Apoc1 apolipoprotein CI Mm.182440 5719 3465* 6337 5953 H1-K1
Apoc2 apolipoprotein CII Mm.28394 3199 2511 2143* 2005* H3-K3
Apoe apolipoprotein E Mm.138866 6425 6438 9632* 5253 H1-K1