Table 1.
Differentially Expressed Genes in the Liver of Lrat−/− Mice vs WTa
| gene symbol | gene description | accession no. | fold change Lrat−/− WT |
|---|---|---|---|
| upregulated in Lrat−/− mice vs WT | |||
| Ugt1a9 | UDP-glucuronosyltransferase 1 family A9 | S57479 | 7.9 |
| Apoa4 | apolipoprotein A-IV | M64249 | 6.0 |
| Mt1 | metallothionein 1 | BC027262 | 4.4 |
| Alas1 | aminolevulinate synthase 1 | M63245 | 4.4 |
| Gdpd3 | Glycerophosphodiester phosphodiesterase domain containing 3 | NM_024228 | 3.6 |
| Cxcl14 | chemokine (C-X-C motif) ligand 14 | AF352785 | 3.3 |
| Hspa8 | heat shock protein 8 | X05837 | 3.1 |
| Serpina4-ps1 | serpin A4, pseudogene 1 | BC024071 | 3.0 |
| Hsp110 | heat shock protein 110 | AK075731 | 3.0 |
| Dhtkd1 | dehydrogenase E1 and transketolase domain containing 1 | AK050057 | 2.7 |
| Hspa1b | heat shock protein 1B | M12573 | 2.5 |
| Lcn13 | Lipocalin 13 | NM_153558 | 2.5 |
| Cap1 | adenylate cyclase-associated protein 1 | NM_007598 | 2.4 |
| Tppp | tubulin polymerization-promoting protein | NM_182839 | 2.3 |
| Tsc22d3 | TSC22-related inducible leucine zipper 3 | AF024519 | 2.3 |
| downregulated in Lrat−/− mice vs WT | |||
| Clec2h | C-type lectin domain family 2, member h | NM_053165 | 0.49 |
| MGC60813 | Unknown | BC058613 | 0.45 |
| Tubb2a | tubulin, beta 2 a | NM_009450 | 0.44 |
| Cml5 | camello-like 5 | AK007530 | 0.43 |
| Cg10671 | Cg10671 like | BC048823 | 0.43 |
| Mm.2121 | Unknown | NM_026790 | 0.38 |
| Tiam2 | T-cell lymphoma invasion and metastasis 2 | NM_011878 | 0.38 |
| Cebpe | CCAAT/enhancer binding protein epsilon | NM_207131 | 0.37 |
| Hsd3b5 | Hydroxy-delta-5-steroid dehydrogenase | NM_008295 | 0.32 |
| Camk2b | calcium/calmodulin-dependent protein kinase II, beta | AK083344 | 0.19 |
| Gadd45g | growth arrest and DNA-damage-inducible 45 gamma | AK002237 | 0.15 |
Total RNA from the three livers of 3 month old Lrat−/− (or WT) mice maintained on a standard diet were pooled to generate one sample. We used two different pools of hepatic RNA from Lrat−/− mice to compare them with two different pools of WT mice. Each sample of pooled RNA was detection-labeled and hybridized in duplicate on a mouse genomic microarray using a service provided by NimbleGen System, Inc. (Madison, WI) as described previously (139). The microarray contained 37,364 genes and covered the entire mouse transcriptome as represented by the University of California, Santa Cruz database (build HG 17), using a minimum of 11 probes per gene. The expression of genes was normalized according to the probe signal, and the average signal for each gene was normalized for each sample replicate. Array data for samples across the whole study were normalized by NimbleGen Systems, Inc. (Madison, WI), using the robust multichip analysis feature of the data analysis package found at http://www.bioconductor.org. Project-wide spreadsheets of robust multichip analysis results were exported to Microsoft Excel. Expression level ratios for all of the possible pairwise comparisons, comprising a four-way comparison of two Lrat−/− and two WT samples, were calculated. These pairwise ratios were imported to Microsoft Access and mined for credible fold changes. Changes in gene expression greater than or equal to 2-fold in at least three of the four comparisons were considered significant.