Figure 3.

Microarray and bioinformatic analysis of habenula gene expression in the embryonic and adult brain. A, Microarray analysis of the E16.5 habenula, cortex, and thalamus revealed 112 unique transcripts with >10-fold enriched expression in the habenula compared with the mean expression level in the cortex/thalamus. Of these transcripts, 91 had available data in the ABA. Quantitative analysis of the ABA data showed that 42 of these transcripts also had enriched expression in the adult brain, whereas 30 were expressed but not enriched and 19 were not detectable. Microarray enrichment of transcripts in all three categories were verified by quantitative RT-PCR (qPCR; mean and SD of 3 assays are shown). B, Control transcripts were identified in the microarray analysis that had equal expression in the habenula and cortex/thalamus. Of 88 control transcripts, 82 had available data in the ABA. Three of the control transcripts exhibited habenula-enriched expression in the adult brain, whereas 50 did not show enriched expression and 29 were not detected. C, Characteristic expression patterns of habenula-enriched transcripts. Recurring patterns observed included MH plus LH (Pou4f1, Vav2), MH only (Tac2), and the ventral part of the MH only (Slc18a3). Enriched expression in the dorsal half of the MH or in the LH alone was much less frequently observed (Nhlh2, Prokr2). See also data for ChAT and SP/Tac1 in Figure 2. Hab, habenula; cortex, Ctx; Thal, thalamus; Pou4f1, Brn3a; Vav2, Vav2 oncogene; Tac2, Tachykinin 2; Slc18a3, solute carrier family 18, member 3/vescicular acetylcholine transporter; Nhlh2, nescient helix loop helix 2; Prokr2, Prokineticin receptor 2. ISH data are derived from the ABA. Scale bar, 200 μm.