Table 1.
Genes induced or repressed by serum deprivation that display the highest differential modulation by HDLs
| Gene symbol | Gene title | Fold change | P value | |
|---|---|---|---|---|
| Cyp4v3 | Cytochrome P450, family 4, subfamily v, polypeptide 3 | 1.15 | 0.0271 | S+ |
| Apcs | Serum amyloid P-component | 1.13 | 0.0234 | S+ |
| 4930429H24Rik | RIKEN cDNA 4930429H24 gene | 0.75 | 0.0302 | A+ |
| Fosl2 | fos-Like antigen 2 | 0.75 | 0.0019 | A+ |
| Cebpb | CCAAT/enhancer binding protein (C/EBP), β | 0.75 | 0.0145 | A+ |
| Depdc6 | DEP domain containing 6 | 0.74 | 0.0257 | A+ |
| Vldlr | Very-low-density lipoprotein receptor | 0.74 | 0.0008 | A+ |
| Crem | CAMP-responsive element modulator | 0.74 | 0.0019 | A+ |
| Cebpb | CCAAT/enhancer-binding protein (C/EBP), β | 0.72 | 0.0070 | A+ |
| Nupr1 | Nuclear protein 1 | 0.71 | 0.0019 | A+ |
| Mbd5 | Methyl-CpG-binding domain protein 5 | 0.70 | 0.0022 | A+ |
| Gpt2 | Glutamic pyruvate transaminase (alanine aminotransferase) 2 | 0.68 | 0.0019 | A+ |
| Vldlr | Very-low-density lipoprotein receptor | 0.67 | 0.0049 | A+ |
| Trim66 | Tripartite motif-containing 66 | 0.67 | 0.0345 | A+ |
| Gpt2 | Glutamic pyruvate transaminase (alanine aminotransferase) 2 | 0.64 | 0.0045 | A+ |
| Nupr1 | Nuclear protein 1 | 0.63 | 0.0015 | A+ |
| Vldlr | Very-low-density lipoprotein receptor | 0.75 | 0.0217 | A+ |
| Eif4ebp1 | Eukaryotic translation initiation factor 4E-binding protein 1 | 0.73 | 0.0128 | A+ |
| Eif4ebp1 | Eukaryotic translation initiation factor 4E-binding protein 1 | 0.73 | 0.0019 | A+ |
| LOC98434 | Hypothetical LOC98434 | 0.71 | 0.0019 | A+ |
| Trib3 | Tribbles homolog 3 (Drosophila) | 0.64 | 0.0072 | A+ |
| Trib3 | Tribbles homolog 3 (Drosophila) | 0.55 | 0.0019 | A+ |
| Apob | Apolipoprotein B | 1.23 | 0.0144 | A− |
| Rasgrp1 | RAS guanyl-releasing protein 1 | 1.23 | 0.0291 | A− |
| 4932417H02Rik | RIKEN cDNA 4932417H02 gene | 1.20 | 0.0234 | A− |
| Dusp15 | Expressed sequence AI851682 | 1.20 | 0.0118 | A− |
| Slc2a2 | Solute carrier family 2 (facilitated glucose transporter), member 2 | 1.30 | 0.0022 | A− |
| Nudt7 | Nudix (nucleoside diphosphate-linked moiety X)-type motif 7 | 1.26 | 0.0093 | A− |
| Hnrpd | Heterogeneous nuclear ribonucleoprotein D | 1.21 | 0.0301 | A− |
| Aldh1l2 | Aldehyde dehydrogenase 1 family, member L2 | 0.87 | 0.0350 | S− |
| Eif2s2 | Eukaryotic translation initiation factor 2, subunit 2 (β) | 0.85 | 0.0367 | S− |
| 6430517E21Rik | RIKEN cDNA 6430517E21 gene | 0.85 | 0.0329 | S− |
| 2700022B06Rik | RIKEN cDNA 2700022B06 gene | 0.85 | 0.0222 | S− |
| Gpc6 | Glypican 6 | 0.85 | 0.0215 | S− |
| Slc30a1 | Solute carrier family 30 (zinc transporter), member 1 | 0.82 | 0.0070 | S− |
| Egr1 | Early growth response 1 | 0.81 | 0.0106 | S− |
| 1810008K03Rik | RIKEN cDNA 1810008K03 gene | 0.74 | 0.0145 | S− |
The indicated fold changes correspond to the ratio of the (″HDL + serum deprivation″ condition/vehicle condition) values over the (serum deprivation condition/vehicle condition) values (S+, HDLs amplify the stimulation effect of serum deprivation (synergistic effect); A+, HDLs decrease the stimulation effect of serum deprivation (buffering effect); A−, HDLs decrease the inhibitory effect of serum deprivation (buffering effect); S−, HDLs increase the inhibitory effect of serum deprivation (synergistic effect). In the A+ category, only the genes associated with a HDL-induced modulation ≥25% (i.e. fold changes ≤0.75 and ≥1.25) are shown. In the A− category, only the genes associated with a HDL-induced modulation ≥20% (i.e. fold changes ≤0.80 and ≥1.20) are shown. A gene symbol can be mentioned several times if identified as significantly regulated by independent probe sets. The full list of the 262 genes induced or repressed by serum deprivation that are differentially modulated by HDLs can be found in supplemental Table 5.