Table 1. List of the 50 most significantly regulated genes in RA treated SH-SY5Y cells compared to noRA cells as identified by microarray analysis.
| SystematicName | GeneName | Description | P.Value | Fold changes | Cluster | ||
| RA D8/D1 | noRA D8/D1 | D8 RA/noRA | |||||
| NM_002923 | RGS2 | Homo sapiens regulator of G-protein signalling 2, 24 kDa | 1.10E-09 | 12.43 | 0.98 | 13.90 | 4 |
| NM_017414 | USP18 | Homo sapiens ubiquitin specific peptidase 18 | 1.10E-09 | 0.42 | 4.00 | 0.13 | 13 |
| NM_152654 | DAND5 | Homo sapiens DAN domain family, member 5 | 1.10E-09 | 0.14 | 2.67 | 0.04 | 13 |
| NM_001005339 | RGS10 | Homo sapiens regulator of G-protein signalling 10, transcript variant 1 | 3.73E-09 | 0.19 | 0.89 | 0.23 | 13 |
| NM_001496 | GFRA3 | Homo sapiens GDNF family receptor alpha 3 | 3.73E-09 | 0.26 | 3.89 | 0.05 | 13 |
| NM_001008540 | CXCR4 | Homo sapiens chemokine (C-X-C motif) receptor 4, transcript variant 1 | 6.13E-08 | 0.19 | 0.74 | 0.30 | 13 |
| NM_139314 | ANGPTL4 | Homo sapiens angiopoietin-like 4, transcript variant 1 | 6.70E-09 | 4.57 | 0.18 | 24.65 | 16 |
| NM_018712 | ELMOD1 | Homo sapiens ELMO/CED-12 domain containing 1 | 6.70E-09 | 22.20 | 0.99 | 19.34 | 3 |
| NM_000599 | IGFBP5 | Homo sapiens insulin-like growth factor binding protein 5 | 9.92E-09 | 0.10 | 0.22 | 0.44 | 13 |
| NM_033066 | MPP4 | Homo sapiens membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4) | 1.24E-08 | 7.11 | 0.80 | 8.92 | 3 |
| NM_002247 | KCNMA1 | Homo sapiens potassium large conductance calcium-activated channel, subfamily M, alpha member 1, transcript variant 2 | 1.24E-08 | 0.13 | 3.02 | 0.05 | 13 |
| NM_005461 | MAFB | Homo sapiens v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (avian) | 1.24E-08 | 2.41 | 0.39 | 5.89 | 16 |
| NM_002166 | ID2 | Homo sapiens inhibitor of DNA binding 2, dominant negative helix-loop-helix protein | 2.24E-08 | 0.77 | 0.30 | 3.00 | 17 |
| AF131762 | AF131762 | Homo sapiens clone 25218 mRNA sequence | 2.33E-08 | 5.39 | 0.75 | 6.12 | 3 |
| AK091547 | LOC730125 | Homo sapiens cDNA FLJ34228 fis, clone FCBBF3025417 | 2.33E-08 | 0.08 | 0.76 | 0.13 | 13 |
| NM_152703 | SAMD9L | Homo sapiens sterile alpha motif domain containing 9-like | 2.49E-08 | 5.26 | 0.55 | 7.06 | 4 |
| AK125162 | AK125162 | Homo sapiens cDNA FLJ43172 fis, clone FCBBF3007242 | 2.60E-08 | 0.08 | 0.52 | 0.18 | 5 |
| NM_001419 | ELAVL1 | Homo sapiens ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R) | 3.21E-08 | 0.31 | 1.23 | 0.33 | 5 |
| A_23_P170719 | A_23_P170719 | Unknown | 3.21E-08 | 4.25 | 0.31 | 13.74 | 16 |
| NM_000905 | NPY | Homo sapiens neuropeptide Y (NPY) | 3.21E-08 | 0.03 | 0.69 | 0.05 | 5 |
| NM_002849 | PTPRR | Homo sapiens protein tyrosine phosphatase, receptor type, R, transcript variant 1 | 3.66E-08 | 2.12 | 0.85 | 2.93 | 14 |
| THC2656519 | THC2656519 | Unknown | 3.66E-08 | 0.20 | 0.94 | 0.27 | 13 |
| CR618615 | CR618615 | full-length cDNA clone CL0BB018ZH05 of Neuroblastoma of Homo sapiens (human) | 4.16E-08 | 0.12 | 0.82 | 0.15 | 5 |
| NM_197966 | BID | Homo sapiens BH3 interacting domain death agonist, transcript variant 1 | 4.49E-08 | 0.28 | 1.04 | 0.29 | 13 |
| NM_007124 | UTRN | Homo sapiens utrophin | 4.92E-08 | 0.36 | 2.87 | 0.18 | 13 |
| NM_016354 | SLCO4A1 | Homo sapiens solute carrier organic anion transporter family, member 4A1 | 4.99E-08 | 0.10 | 1.24 | 0.07 | 13 |
| NM_006157 | NELL1 | Homo sapiens NEL-like 1 (chicken) | 4.99E-08 | 0.22 | 5.58 | 0.05 | 13 |
| NM_024817 | THSD4 | Homo sapiens thrombospondin, type I, domain containing 4 | 5.72E-08 | 15.75 | 0.80 | 19.77 | 3 |
| NM_003713 | PPAP2B | Homo sapiens phosphatidic acid phosphatase type 2B, transcript variant 1 | 5.72E-08 | 0.46 | 7.42 | 0.08 | 2 |
| NM_003385 | VSNL1 | Homo sapiens visinin-like 1 | 6.08E-08 | 0.26 | 4.10 | 0.09 | 13 |
| NM_018286 | TMEM100 | Homo sapiens transmembrane protein 100 | 6.85E-08 | 0.25 | 1.62 | 0.20 | 13 |
| NM_004598 | SPOCK1 | Homo sapiens sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1 | 7.77E-08 | 0.53 | 8.70 | 0.07 | 2 |
| BX648591 | BX648591 | Homo sapiens mRNA; cDNA DKFZp686G14198 (from clone DKFZp686G14198) | 7.90E-08 | 0.29 | 1.32 | 0.25 | 5 |
| NM_000507 | FBP1 | Homo sapiens fructose-1,6-bisphosphatase 1 | 9.46E-08 | 0.18 | 1.17 | 0.18 | 13 |
| NM_001034852 | SMOC1 | Homo sapiens SPARC related modular calcium binding 1, transcript variant 1 | 1.00E-07 | 3.71 | 1.31 | 4.74 | 4 |
| NM_004982 | KCNJ8 | Homo sapiens potassium inwardly-rectifying channel, subfamily J, member 8 | 1.08E-07 | 0.25 | 1.33 | 0.19 | 5 |
| NM_015150 | RFTN1 | Homo sapiens raftlin, lipid raft linker 1 | 1.08E-07 | 0.46 | 3.74 | 0.13 | 11 |
| NM_003068 | SNAI2 | Homo sapiens snail homolog 2 (Drosophila) | 1.22E-07 | 2.20 | 0.32 | 7.42 | 16 |
| NM_024645 | ZMAT4 | Homo sapiens zinc finger, matrin type 4 | 2.37E-07 | 0.66 | 0.67 | 1.28 | 11 |
| NM_003836 | DLK1 | Homo sapiens delta-like 1 homolog (Drosophila), transcript variant 1 | 2.37E-07 | 0.07 | 1.43 | 0.05 | 13 |
| NM_000087 | CNGA1 | Homo sapiens cyclic nucleotide gated channel alpha 1 | 2.37E-07 | 4.60 | 0.70 | 5.18 | 4 |
| NM_001797 | CDH11 | Homo sapiens cadherin 11, type 2, OB-cadherin (osteoblast) | 2.37E-07 | 1.48 | 0.86 | 2.01 | 18 |
| ENST00000284894 | NCAM2 | Neural cell adhesion molecule 2 precursor (N-CAM 2) | 2.37E-07 | 24.28 | 1.78 | 12.63 | 3 |
| NM_000693 | ALDH1A3 | Homo sapiens aldehyde dehydrogenase 1 family, member A3 | 2.37E-07 | 0.14 | 1.23 | 0.14 | 13 |
| THC2637644 | THC2637644 | Unknown | 2.37E-07 | 0.16 | 0.55 | 0.31 | 13 |
| NM_002615 | SERPINF1 | Homo sapiens serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1 | 2.37E-07 | 0.27 | 0.94 | 0.26 | 13 |
| NM_000845 | GRM8 | Homo sapiens glutamate receptor, metabotropic 8 | 2.37E-07 | 0.46 | 2.60 | 0.20 | 11 |
| NM_145008 | YPEL4 | Homo sapiens yippee-like 4 (Drosophila) | 2.37E-07 | 4.33 | 1.21 | 3.45 | 4 |
| NM_078481 | CD97 | Homo sapiens CD97 molecule, transcript variant 1 | 2.37E-07 | 0.20 | 1.07 | 0.23 | 13 |
| BC045679 | LOC285878 | Homo sapiens hypothetical protein LOC285878, mRNA (cDNA clone IMAGE:5299807) | 2.37E-07 | 6.94 | 0.88 | 7.55 | 3 |
Gene expression fold changes are given for the comparison of RA treated cells on day 8 (D8) versus RA day 1 (D1), noRA D8 versus noRA D1 and RA D8 versus noRA D8. The last column indicates the cluster number to which that gene is assigned based on its expression profile (see Figure S2). CXCR4 and CR618615 were represented by more than one probe in the list and the corresponding p-values and fold changes were averaged. P-values are Benjamini-Hochberg corrected. The complete list of all significantly regulated genes can be found in Table S2 in Tables S1.