Table 2.
Tbr1 deletion alters expression of genes with layer- or region-specific distribution in the cerebral cortex.
| Gene symbol* | Gene name | Layer | Region |
|---|---|---|---|
| Bhlhb5 (BHLHE22) | Basic helix-loop-helix family, member e22 | L5 | Caudomedial |
| Calb2 | Calbindin 2 | Cajal–Retzius | All |
| Cdh8* | Cadherin 8, type 2 | L5 | Rostral + caudal |
| Cdh9 | Cadherin 9, type 2 (T1-cadherin) | L6 | Rostral |
| Cntn3 | Contactin 3 (plasmacytoma associated) | L5 | Caudal |
| Cntn6* | Contactin 6 | L5 SCPN | Caudal |
| Cplx3 | Complexin 3 | Cajal–Retzius | All |
| Crim1* | Cysteine rich transmembrane BMP regulator 1 (chordin-like) | L5 corticospinal motor neuron | All |
| Crym | Crystallin, mu | L5 corticospinal motor neuron | Caudal |
| Ctgf* | Connective tissue growth factor | Subplate | All |
| Ctip2 (Bcl11b) | B-cell CLL/lymphoma 11B (zinc finger protein) | L5 SCPN | All |
| Cux1 | Cut-like homeobox 1 | L2–4 | All |
| Cux2 | Cut-like homeobox 2 | L2–4 | All |
| Dkk3 | Dickkopf WNT signaling pathway inhibitor 3 | CPN | Caudomedial |
| Drd1a* | Dopamine receptor D1 | L6 | All |
| Dtx4 | Deltex 4, E3 ubiquitin ligase | L2–4 | All |
| Etv1 (Er81) | Ets variant 1 | L5 | All |
| Fezf2 | FEZ family zinc finger 2 | L5 SCPN | All |
| Flrt3* | Fibronectin leucine rich transmembrane protein 3 | L2–3 | Caudal |
| Foxp1 | Forkhead box P1 | L5 | All |
| Foxp2 | Forkhead box P2 | L6 | All |
| Inhba | Inhibin, beta A | L2–4, CPN | All |
| Lhx5 | LIM homeobox 5 | Cajal–Retzius | All |
| Limch1 | LIM and calponin homology domains 1 | L2–3, CPN | All |
| Mdga1 | MAM domain containing glycosylphosphatidylinositol anchor 1 | L2–3 | Caudal |
| Mef2c | Myocyte enhancer factor 2C | L2–3 | All |
| Nefm* | Neurofilament, medium polypeptide | L2–3 | Caudal |
| Nfe2l3 | Nuclear factor, erythroid 2-like 3 | L6 | All |
| Ngfr | Nerve growth factor receptor | L6 | Caudal |
| Nhlh2* | Nescient helix loop helix 2 | Cajal–Retzius | All |
| Npy | Neuropeptide Y | L6 | All |
| Nr4a2 (Nurr1)* | Nuclear receptor subfamily 4, group A, member 2 | L6 | Caudal |
| Nr4a3 | Nuclear receptor subfamily 4, group A, member 3 | L6 | Caudal |
| Nrgn* | Neurogranin | L2–4 | All |
| Nxph4 | Neurexophilin 4 | Subplate | All |
| Oma1 | OMA1 zinc metallopeptidase | L5 SCPN | All |
| Pcdh11x | Protocadherin 11 X-linked | L2–4 | All |
| Pcdh19 | Protocadherin 19 | L5 | All |
| Pcdh20 | Protocadherin 20 | L2–4 | Rostral |
| Pcdh8 | Protocadherin 8 | L2–3 | Caudal |
| Pcp4 | Purkinje cell protein 4 | L5 | All |
| Pou3f2 (Brn-2) | POU class 3 homeobox 2 | L2–4 | All |
| Pou3f3 (Brn-1) | POU class 3 homeobox 3 | L2–4 | All |
| Ppp1r1b* | Protein phosphatase 1, regulatory (inhibitor) subunit 1B | L6 | Rostral |
| Ptn | Pleiotrophin | CPN | All |
| Ptprz1 | Protein tyrosine phosphatase, receptor-type, Z polypeptide 1 | L2–3 | Caudal |
| Pvrl3 | Poliovirus receptor-related 3 | L2–3, CPN | Caudomedial |
| Reln* | Reelin | Cajal–Retzius | All |
| Rgs8 | Regulator of G-protein signaling 8 | L2–3 | All |
| Rorb* | RAR-related orphan receptor B | L4 | Rostral |
| S100a10 | S100 calcium binding protein A10 | L5 corticospinal motor neuron | All |
| Satb2 | SATB homeobox 2 | CPN | All |
| Sorl1 | Sortilin-related receptor, L(DLR class) A repeats containing | L2–3 | All |
| Sox5* | SRY (sex determining region Y)-box 5 | L6 | All |
| Tle1 | Transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila) | L2–3 | All |
| Tle4* | Transducin-like enhancer of split 4 | L6 | All |
| Tox | Thymocyte selection-associated high mobility group box | L5 | Rostromedial |
| Trp73 | Tumor protein p73 | Cajal–Retzius | All |
| Unc5c | Unc-5 homolog C (C. elegans) | L4 | All |
| Unc5d (Svet1) | Unc-5 homolog D (C. elegans) | L2–4 | All |
| Wnt7b* | Wingless-type MMTV integration site family, member 7B | L6 | All |
| Wscd1 | WSC domain containing 1 | L6 | Rostral |
| Zfpm2 (FOG2) | Zinc finger protein, FOG family member 2 | L6 | All |
*
Genes also identified in our microarray analysis (Huang et al., 2014). CPN, callosal projection neurons; SCPN, subcerebral projection neurons.