Table 1.
Candidate connectivity labels.
Fig 1.
In situ hybridization patterns for immunoglobulin superfamily genes in dorsal thalamus at P0.
Two coronal sections are shown for Kirrel3, Igsf9b and Sdk2, one rostral and one more caudal. The entire corresponding sections are shown in S1 Fig, 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.
Fig 2.
In situ hybridization patterns for Odz family genes in dorsal thalamus at P0.
Two coronal sections are shown for Odz1, Odz2, Odz3 and Odz4, one rostral and one more caudal. The entire corresponding sections are shown in S2 Fig, for context. AM, anteromedial nucleus; DLG, dorsolateral geniculate nucleus; LD, laterodorsal nucleus; MD, mediodorsal nucleus; Po, posterior thalamic nuclear group; Re, reuniens nucleus; Rt, reticular nucleus; VA, ventral anterior nucleus; VG, ventral geniculate nucleus; VM, ventromedial nucleus; VP, ventral posterior nucleus. Scale bar: 500 μm.
Fig 3.
In situ hybridization patterns for Neto family genes in dorsal thalamus at P0.
Three coronal sections are shown for Neto1 and Neto2, one rostral, one at an intermediate level (mid) and one more caudal. The entire corresponding sections are shown in S5 Fig, for context. Expression of the Neto genes is notably complementary in some places (compare mid sections) and overlapping in others (e.g., PF). DLG, dorsolateral geniculate nucleus; LD, laterodorsal nucleus; MD, mediodorsal nucleus; PF, parafscicular nucleus; Po, posterior thalamic nuclear group; STh, subthalamic nucleus; VM, ventromedial nucleus; VP, ventral posterior nucleus; ZIR, zona incerta rostral part. Scale bar: 500 μm.
Fig 4.
In situ hybridization patterns for Calsyntenin family genes in dorsal thalamus at P0.
One coronal section for Clstn1 and Clstn2 is shown. MD, mediodorsal nucleus; VG, ventral geniculate nucleus; VM, ventromedial nucleus. Scale bar: 500 μm.
Fig 5.
Excerpt of k-means clustering analyses.
Clustering of a small subset of genes is shown to illustrate the method. Gene names are shown in column 1. Columns 2 to 8 show normalised expression densities per gene per time-point. Heatmap’s 3 colour scale of gene expression data: 0.2, red; 1, white; 5, blue. Columns 9 to 14 show cluster numbers assigned under k = 10 to k = 15 clustering, with clusters colour-coded to facilitate visualisation. Clusters are sorted at k = 10, followed by k = 11, followed by k = 12 and so on until k = 15. As the input value of k increases, clusters tend to get subdivided as opposed to reshuffled, giving a roughly hierarchical organisation. A clear difference in expression pattern between clusters 8 and 9 at k = 10 is evident, with cluster 8 showing peak expression at P4, and cluster 9 showing peak expression at P14. Within cluster 8, additional subclusters become apparent at k = 12 and above. The full clustering output for all 1996 genes is shown in S3 Table.
Fig 6.
Summary of expression profiles at k = 10.
Normalised expression densities were averaged per cluster to see the trends of expression at k = 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.
Fig 7.
Enrichment of protein localisation categories across clusters.
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 Fig 6. 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.
Fig 8.
Enrichment of functional groups across clusters.
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.
Table 2.
Enrichment analyses per localisation.
Table 3.
Enrichment analyses per group.
Fig 9.
Ephrin and Eph-receptor expression in the thalamus at E18.5.
In situ hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of Eph-receptor (Eph) A1, A3, A4, A6, A8, A10, B1, B2, B6, and Ephrin (Efn) A2, A5 and B3. See text for details. A representative and equivalent section of medial thalamus is shown for each gene (see S8 Fig for details on how the sections were selected). Scale bar in EphA1: 317 μm.
Fig 10.
Cadherin expression in the thalamus at E18.5.
In situ hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of Cadherin (Cdh) 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 24 and Fat3. See text for details. A representative and equivalent section of medial thalamus is shown for each cadherin (see S8 Fig for details on how the sections were selected). Scale bar in Cdh2: 351 μm.
Fig 11.
Protocadherin expression in the thalamus at E18.5.
In situ hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of Protocadherin (Pcdh) 1, 10, 11X, 19 and 21. See text for details. Two representative and equivalent sections are shown for each protocadherin, one lateral and the other medial (see S8 Fig for details on how the sections were selected). Scale bar in Pcdh1: 424 μm.
Fig 12.
Semaphorin expression in the thalamus at E18.5.
In situ hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of semaphorins (Sema) Sema3F, Sema6A and Sema7A. See text for details. Two representative and equivalent sections are shown for each semaphorin, one lateral and the other medial (see S8 Fig for details on how the sections were selected). Scale bar in Sema3F: 235 μm.
Fig 13.
Plexin expression in the thalamus at E18.5.
In situ hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of plexins (Plxn) PlxnA1, PlxnA2 and PlxnC1. See text for details. Two representative and equivalent sections are shown for each plexin, one lateral and the other medial (see S8 Fig for details on how the sections were selected). Scale bar in PlxnA1: 248 μm.
Fig 14.
Expression of receptor tyrosine kinases and phosphatases in the thalamus at E18.5.
In situ hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of Flt3, Kit, Ntrk2, Ntrk3, Ret and Ptpru. See text for details. A representative and equivalent section of medial thalamus is shown for each gene (see S8 Fig for details on how the sections were selected). Scale bar in Flt3: 216 μm.
Fig 15.
Expression of immunoglobulin superfamily molecules in the thalamus at E18.5.
In situ hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of Alcam, Cadm1, Cd47, Cntn6 and Mdga1. See text for details. Two representative and equivalent sections are shown for each gene, one lateral and the other medial (see S8 Fig for details on how the sections were selected). Scale bar in Alcam: 386 μm.
Fig 16.
Expression of leucine-rich repeat superfamily members in the thalamus at E18.5.
In situ hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of Lgi2, Lrrn3 and Rtn4rl1. See text for details. Two representative and equivalent sections are shown for each gene, one lateral and the other medial (see S8 Fig for details on how the sections were selected). Scale bar in Lgi2: 256 μm.
Fig 17.
Calsyntenin and cerebellin expression in the thalamus at E18.5.
In situ hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of Calsyntenin (Clstn) 1 and 2, and Cerebellin (Cbln) 2 and 4. See text for details. Two representative and equivalent sections are shown for each gene, one lateral and the other medial (see S8 Fig for details on how the sections were selected). Scale bar in Clstn1: 332 μm.
Fig 18.
Netrin-G expression in the thalamus at E18.5.
In situ hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of Netrin-G (Ntng) 1 and 2. See text for details. Two representative and equivalent sections are shown for each netrin-G, one medial and the other adjacent medially (see S8 Fig for details on how the sections were selected). Scale bar in Ntng1: 255 μm.
Fig 19.
Expression of genes encoding miscellaneous surface or secreted molecules in the thalamus at E18.5.
In situ hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of Astrotactin2 (Astn2), Contactin-associated protein-4 (Cntnap4), Delta-like-1 homolog (Dlk1), Delta/Notch-Like EGF Repeat Containing (Dner), Frizzled7 (Fzd7), Glypican-3 (Gpc3), Low-density lipoprotein receptor 8 (Lrp8), LY6/PLAUR Domain Containing 1 (Lypd1) and Trp53i11. See text for details. A representative and equivalent section is shown for each molecule (see S8 Fig for details on how the sections were selected). Dlk1 expression is shown laterally, while the other gene expression patterns are shown medially with Gpc3 more medial than the rest (parasagittal). Scale bar in Astn2: 314 μm.
Fig 20.
Expression of growth factors and receptors in the thalamus at E18.5.
In situ hybridization data from sagittal sections of the thalamus at E18.5 obtained from the devABA revealed differential patterns of expression of Gfra1 and Gfra2 (GDNF Family Receptor Alpha 1 and 2), Vgf (VGF nerve growth factor inducible), Bmp3 (Bone morphogenetic protein-3), Igfbp5 (Insulin-like growth factor binding protein 5), Inhba (Inhibin/Activin, beta A subunit), Nrn (Neuritin or Neuritin-1/Nrn1), Tgfb2 (Transforming growth factor, beta 2) and Wif1 (WNT inhibitory factor 1). See text for details. A representative section is shown for each gene (see S8 Fig for details on how the sections were selected). Gfra1, Gfra2 and Vgf expression is shown laterally, while the other gene expression patterns are shown medially. Scale bar in Gfra1: 299 μm.