Table 1.
Transcripts enriched in E16.5 habenula relative to cerebral cortex and thalamus
| Gene symbol | Gene title | Microarray ratio |
ABA |
||||
|---|---|---|---|---|---|---|---|
| Hab/Ctx | Hab/Thal | Hab/other | Visual | Hab/Ctx | Hab/Thal | ||
| Complete | |||||||
| Robo3 | Roundabout homolog 3 | 294 | 103 | 152 | + | 1.7 | 0.9 |
| Pou4f1 | POU domain, class 4, transcription factor 1; Brn3a | 180 | 99 | 128 | ++ | 69 | 75 |
| Dcc | Deleted in colorectal carcinoma | 29 | 171 | 49 | ne | ||
| Gpr151 | G-protein-coupled receptor 151 | 51 | 34 | 40 | +++ | 25 | 179 |
| Irx2 | Iroquois related homeobox 2 | 118 | 22 | 38 | ++ | 29 | 68 |
| Kcnma1 | K+ large conductance Ca++-activated channel, subfamily M, α member 1 | 63 | 25 | 36 | + | 3.2 | 1.7 |
| Msi2 | Musashi homolog 2 | 32 | 34 | 33 | + | 5.7 | 4.5 |
| Dmt2 | Dorsomedial telencephalon gene 2 | 447 | 17 | 33 | nd | ||
| Gng8 | Guanine nucleotide binding protein, γ8 subunit | 146 | 18 | 32 | nd | ||
| Scube2 | Signal peptide, CUB domain, EGF-like 2 | 230 | 17 | 32 | ne | ||
| Ppnr | Per-pentamer repeat gene | 129 | 16 | 29 | + | 1.4 | 5.5 |
| Kcng4 | K+ voltage-gated channel, G4 | 28 | 27 | 27 | ++ | 9.4 | 9.7 |
| Tesc | Tescalcin | 117 | 14 | 25 | + | 8.8 | 2.1 |
| Dbx1 | Developing brain homeobox 1 | 33 | 19 | 24 | ne | ||
| Tmem16a | Transmembrane protein 16A | 29 | 19 | 23 | +++ | 52 | 123 |
| Irx5 | Iroquois related homeobox 5 | 79 | 12 | 21 | ne | ||
| Pbx3 | Pre-B-cell leukemia transcription factor 3 | 21 | 18 | 19 | ++ | 8.0 | 11 |
| Htr5b | 5-HT (serotonin) receptor 5B | 69 | 11 | 19 | +++ | 33 | 43 |
| Chrnb4 | Cholinergic receptor, nicotinic, β polypeptide 4 | 27 | 14 | 18 | +++ | 80 | 177 |
| Col2a1 | Procollagen, type II, α1 | 21 | 16 | 18 | nc | 0.7 | 1.5 |
| Irx1 | Iroquois related homeobox 1 | 55 | 10 | 17 | + | 1.7 | 1.5 |
| Robo1 | Roundabout homolog 1 | 15 | 19 | 17 | + | 3.5 | 7.8 |
| Selected | |||||||
| Ttr | Transthyretin | 14 | 17 | 15 | cp | 3.5 | 6.4 |
| 3110047P20Rik | Hematological and neurological expressed 1 | 188 | 7.6 | 15 | +++ | 32 | 15 |
| Efcbp2 | EF hand calcium binding protein 2 | 40 | 8.7 | 14 | ++ | 4 | 23 |
| Etv1 | Ets variant gene 1 | 11 | 19 | 14 | ++ | 9.5 | 2.1 |
| Vav3 | Vav 3 oncogene | 42 | 7.2 | 12 | ++ | 2.9 | 18 |
| Ntng2 | Netrin G2 | 8.0 | 26 | 12 | ++ | 1.9 | 8.5 |
| Kctd8 | Potassium channel tetramerization domain containing 8 | 23 | 8.3 | 12 | +++ | 28 | 19 |
| Nrp2 | Neuropilin 2 | 20 | 8.6 | 12 | ++ | 15 | 85 |
| Grb10 | Growth factor receptor bound protein 10 | 14 | 10 | 12 | +++ | 11 | 131 |
| Nr4a2 | Nuclear receptor subfamily 4, group A, member 2 Nurr1 | 8.1 | 22 | 12 | + | 1.3 | 0.8 |
Microarray analysis at E16.5 and bioinformatic analysis of the adult brain were used to identify habenula-enriched transcripts. Microarray values are derived from the means of two independent arrays for the habenula (Hab), cortex (Ctx), and thalamus (Thal). The ratio of habenula/other is calculated using the mean of the cortex and thalamus values. ABA data were examined by visual inspection and automated signal quantitation (see Materials and Methods).
+++, Enriched in the habenula with minimal other CNS expression;
++, enriched in the habenula with a few other CNS sites of expression;
+, enriched in the habenula with multiple other CNS sites of expression; nc, expression not correlated with habenula; ne, not expressed, little or no expression detected in any area of CNS; nd, no data in ABA; cp, highly enriched in choroid plexus.