Expression of genes encoding miscellaneous surface or secreted molecules in the thalamus at E18.5.

<p><i>In situ</i> hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of Astrotactin2 (<i>Astn2</i>), Contactin-associated protein-4 (<i>Cntnap4)</i>, Delta-like-1 homolog (<i>Dlk1</i>), Delta/Notch-Like EGF Repeat Containing (<i>Dner</i>), Frizzled7 (<i>Fzd7</i>), Glypican-3 (<i>Gpc3</i>), Low-density lipoprotein receptor 8 (<i>Lrp8</i>), LY6/PLAUR Domain Containing 1 (<i>Lypd1</i>) and <i>Trp53i11</i>. See text for details. A representative and equivalent section is shown for each molecule (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177977#pone.0177977.s014" target="_blank">S8 Fig</a> for details on how the sections were selected). <i>Dlk1</i> expression is shown laterally, while the other gene expression patterns are shown medially with <i>Gpc3</i> more medial than the rest (parasagittal). Scale bar in <i>Astn2</i>: 314 μm.</p

Expression of receptor tyrosine kinases and phosphatases in the thalamus at E18.5.

<p><i>In situ</i> hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of <i>Flt3</i>, <i>Kit</i>, <i>Ntrk2</i>, <i>Ntrk3</i>, <i>Ret</i> and <i>Ptpru</i>. See text for details. A representative and equivalent section of medial thalamus is shown for each gene (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177977#pone.0177977.s014" target="_blank">S8 Fig</a> for details on how the sections were selected). Scale bar in <i>Flt3</i>: 216 μm.</p

Enrichment of functional groups across clusters.

<p>Relative enrichment across clusters is shown by plotting observed/expected numbers of proteins per cluster for each of six groups: Group 1—axon guidance pathway and cell adhesion (A); Group 2—synapse (B); Group 3—receptor tyrosine kinases and their ligands, and patterning (C); Group 4—neurotransmission pathway (GPCRs, ion channels, gap junctions; D); Group 5—chromatin and transcription factor activity (E); and, Group 6—other (cytoskeleton, extracellular matrix, myelin, metabolic enzymes and signal transduction) and unannotated (F). A value of 1 indicates observed data matches expected values, whereas a value below or above 1 indicates decreased or increased counts compared to expected values, respectively. Clusters 0–9 are organized chronologically. P-values from chi square analyses are shown in upper right corner of each graph. All groups showed statistically significant deviation from expected distributions.</p

Protocadherin expression in the thalamus at E18.5.

<p><i>In situ</i> hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of <i>Protocadherin</i> (<i>Pcdh</i>) <i>1</i>, <i>10</i>, <i>11X</i>, <i>19</i> and <i>21</i>. See text for details. Two representative and equivalent sections are shown for each protocadherin, one lateral and the other medial (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177977#pone.0177977.s014" target="_blank">S8 Fig</a> for details on how the sections were selected). Scale bar in <i>Pcdh1</i>: 424 μm.</p

Netrin-G expression in the thalamus at E18.5.

<p><i>In situ</i> hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of <i>Netrin-G</i> (<i>Ntng</i>) <i>1</i> and <i>2</i>. See text for details. Two representative and equivalent sections are shown for each netrin-G, one medial and the other adjacent medially (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177977#pone.0177977.s014" target="_blank">S8 Fig</a> for details on how the sections were selected). Scale bar in <i>Ntng1</i>: 255 μm.</p

<i>In situ</i> hybridization patterns for immunoglobulin superfamily genes in dorsal thalamus at P0.

<p>Two coronal sections are shown for <i>Kirrel3</i>, <i>Igsf9b</i> and <i>Sdk2</i>, one rostral and one more caudal. The entire corresponding sections are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177977#pone.0177977.s007" target="_blank">S1 Fig</a>, for context. CL, centrolateral nucleus; DLG, dorsolateral geniculate nucleus; DM, dorosmedial hypothalamic nucleus; LD, laterodorsal nucleus; MHb, medial habenula; Po, posterior thalamic nuclear group; PV, paraventricular nucleus; Re, reuniens nucleus; Rh, rhomboid nucleus; Rt, reticular nucleus; VG, ventral geniculate nucleus; VP, ventral posterior nucleus; VPPC, ventral posterior nucleus parvicellular part. Scale bar: 500 μm.</p

Summary of expression profiles at <i>k</i> = 10.

<p>Normalised expression densities were averaged per cluster to see the trends of expression at <i>k</i> = 10. Clusters were organised chronologically with those showing early peaks of expression at the top and later peaks of expression at the bottom. Heatmap’s 3 colour scale of gene expression data: 0.2, red; 1, white; 5, blue. Number of genes per cluster is shown in the rightmost column.</p

Enrichment of protein localisation categories across clusters.

<p>Relative enrichment across clusters is shown by plotting observed/expected numbers of proteins per cluster for each of five groups: secreted proteins (A), single-pass transmembrane or GPI-anchored proteins (B), multi-pass transmembrane proteins (C), cytoplasmic proteins (D) and nuclear proteins (E). A value of 1 indicates observed data matches expected values, whereas a value below or above 1 indicates decreased or increased counts compared to expected values, respectively. The ten clusters (C0-C9) are organized according to age of peak expression, as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177977#pone.0177977.g006" target="_blank">Fig 6</a>. P-values from chi square analyses are shown in upper right corner of each graph. Genes encoding nuclear proteins are enriched in clusters defined by strong early embryonic expression, single-pass transmembrane and GPI-linked protein-encoding genes are enriched in clusters expressed at mid-embryonic stages and multi-pass transmembrane proteins are enriched in clusters expressed at postnatal stages.</p

Semaphorin expression in the thalamus at E18.5.

<p><i>In situ</i> hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of semaphorins (<i>Sema</i>) <i>Sema3F</i>, <i>Sema6A</i> and <i>Sema7A</i>. See text for details. Two representative and equivalent sections are shown for each semaphorin, one lateral and the other medial (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177977#pone.0177977.s014" target="_blank">S8 Fig</a> for details on how the sections were selected). Scale bar in <i>Sema3F</i>: 235 μm.</p

<i>In situ</i> hybridization patterns for Calsyntenin family genes in dorsal thalamus at P0.

<p>One coronal section for <i>Clstn1</i> and <i>Clstn2</i> is shown. MD, mediodorsal nucleus; VG, ventral geniculate nucleus; VM, ventromedial nucleus. Scale bar: 500 μm.</p