Transcription factor landscape - Brain region - Neuronal cells

Transcriptome analysis shows that 78% (n=15733) of all human proteins (n=20162) are detected in neuronal cells and 1782 of these genes show an elevated expression in any neuronal cells compared to other brain cell types. Learn more about genes with elevated expression in neuronal cells here. In-depth analysis of transcription factor genes expressed in neuronal cells highlights 173 transcription factors with elevated expression in neuronal cells compared to other cell types. In total, 57 transcription factors are classified as enriched in neuronal cells.

Here we provide the expression overview of all transcription factors that show enriched expression levels in neuronal clusters compared to other brain cluster types.

Enriched transcription factors
Gene Expression
TLX3
Cell type enriched (Upper rhombic lip)
LHX3
Cell type enriched (Splatter)
BARHL2
Cell type enriched (Upper rhombic lip)
LBX1
Cell type enriched (Cerebellar inhibitory)
NEUROD1
Cell type enriched (Upper rhombic lip)
PHOX2B
Cell type enriched (Splatter)
SP8
Cell type enriched (Cge interneuron)
BHLHE22
Cell type enriched (Cerebellar inhibitory)
PAX2
Cell type enriched (Cerebellar inhibitory)
DMBX1
Cell type enriched (Midbrain-derived inhibitory)
HOXB8
Cell type enriched (Splatter)
HOXC4
Cell type enriched (Lower rhombic lip)
PITX2
Cell type enriched (Mammillary body)
POU4F2
Cell type enriched (Lower rhombic lip)
SHOX2
Cell type enriched (Thalamic excitatory)
SIM1
Cell type enriched (Mammillary body)
SOX14
Cell type enriched (Midbrain-derived inhibitory)
TFAP2A
Cell type enriched (Cerebellar inhibitory)
TFAP2B
Cell type enriched (Cerebellar inhibitory)

Enriched transcription factors
Gene Expression
BARHL1
Group enriched (Lower rhombic lip, Upper rhombic lip)
CRX
Group enriched (Choroid plexus epithelial cell, Upper rhombic lip)
OTP
Group enriched (Amygdala excitatory, Splatter)
NR2E1
Group enriched (Astrocyte, Cge interneuron, Choroid plexus epithelial cell)
EN2
Group enriched (Cerebellar inhibitory, Upper rhombic lip)
NR1I3
Group enriched (Eccentric medium spiny neuron, Medium spiny neuron)
NEUROG3
Group enriched (Hippocampal ca4, Hippocampal dentate gyrus)
OTX2
Group enriched (Choroid plexus epithelial cell, Midbrain-derived inhibitory)
DRGX
Group enriched (Lower rhombic lip, Splatter)
NKX2-1
Group enriched (Lamp5-lhx6 and chandelier, Mammillary body)
VSX1
Group enriched (Astrocyte, Bergmann glia, Oligodendrocyte precursor cell, Upper rhombic lip)
GBX1
Group enriched (Eccentric medium spiny neuron, Fibroblast, Splatter)
PAX6
Group enriched (Astrocyte, Bergmann glia, Ependymal cell, Upper rhombic lip)
VAX2
Group enriched (Committed oligodendrocyte precursor, Hippocampal dentate gyrus, Oligodendrocyte precursor cell, Upper rhombic lip)
EOMES
Group enriched (Leukocyte, Upper rhombic lip)
FOXB1
Group enriched (Astrocyte, Ependymal cell, Mammillary body)
LHX2
Group enriched (Amygdala excitatory, Astrocyte, Deep-layer intratelencephalic, Hippocampal ca1-3, Hippocampal ca4, Hippocampal dentate gyrus, Lamp5-lhx6 and chandelier, Miscellaneous, Thalamic excitatory, Upper-layer intratelencephalic)
RORB
Group enriched (Astrocyte, Bergmann glia, Deep-layer intratelencephalic, Midbrain-derived inhibitory, Thalamic excitatory, Upper-layer intratelencephalic)
SATB2
Group enriched (Choroid plexus epithelial cell, Deep-layer corticothalamic and 6b, Deep-layer intratelencephalic, Deep-layer near-projecting, Ependymal cell, Hippocampal ca1-3, Miscellaneous, Upper-layer intratelencephalic)
LMX1B
Group enriched (Ependymal cell, Splatter)
MYB
Group enriched (Ependymal cell, Lamp5-lhx6 and chandelier, Medium spiny neuron)
NKX2-8
Group enriched (Lamp5-lhx6 and chandelier, Lower rhombic lip, Mammillary body, Oligodendrocyte)
DLX6
Group enriched (Cge interneuron, Eccentric medium spiny neuron, Lamp5-lhx6 and chandelier, Medium spiny neuron, Mge interneuron, Splatter)
ELK3
Group enriched (Central nervous system macrophage, Endothelial cell, Leukocyte, Upper rhombic lip)
GATA3
Group enriched (Leukocyte, Midbrain-derived inhibitory)
IRX1
Group enriched (Astrocyte, Bergmann glia, Ependymal cell, Lower rhombic lip, Oligodendrocyte precursor cell)
ISL1
Group enriched (Medium spiny neuron, Splatter)
LHX8
Group enriched (Ependymal cell, Splatter)
MAFB
Group enriched (Central nervous system macrophage, Cge interneuron, Lamp5-lhx6 and chandelier, Leukocyte, Mge interneuron)
NR2F2
Group enriched (Fibroblast, Midbrain-derived inhibitory, Pericyte, Vascular associated smooth muscle cell)
ONECUT2
Group enriched (Mammillary body, Medium spiny neuron)
POU4F1
Group enriched (Astrocyte, Committed oligodendrocyte precursor, Splatter)
SIX3
Group enriched (Choroid plexus epithelial cell, Eccentric medium spiny neuron, Ependymal cell, Medium spiny neuron)
SMAD9
Group enriched (Astrocyte, Bergmann glia, Endothelial cell, Hippocampal dentate gyrus, Midbrain-derived inhibitory)
SOX4
Group enriched (Committed oligodendrocyte precursor, Midbrain-derived inhibitory, Oligodendrocyte precursor cell)
SP5
Group enriched (Cerebellar inhibitory, Fibroblast, Midbrain-derived inhibitory)
ZNF556
Group enriched (Central nervous system macrophage, Cerebellar inhibitory, Hippocampal ca4, Upper rhombic lip)
ZNF648
Group enriched (Choroid plexus epithelial cell, Fibroblast, Lamp5-lhx6 and chandelier)

Enriched transcription factors
Gene Expression
RBPJL
Cell type enhanced (Miscellaneous)
NEUROD6
Cell type enhanced (Hippocampal ca4, Miscellaneous)
NEUROD2
Cell type enhanced (Upper rhombic lip)
YBX2
Cell type enhanced (Hippocampal ca4)
TBR1
Cell type enhanced (Deep-layer corticothalamic and 6b, Deep-layer intratelencephalic)
SCRT2
Cell type enhanced (Cerebellar inhibitory)
LHX1
Cell type enhanced (Cerebellar inhibitory, Mammillary body, Upper rhombic lip)
LHX5
Cell type enhanced (Cerebellar inhibitory, Mammillary body, Midbrain-derived inhibitory)
TBX22
Cell type enhanced (Ependymal cell, Thalamic excitatory)
ZIC4
Cell type enhanced (Bergmann glia, Fibroblast, Pericyte, Upper rhombic lip)
UNCX
Cell type enhanced (Midbrain-derived inhibitory, Upper rhombic lip)
ZNF729
Cell type enhanced (Hippocampal ca4)
DLX1
Cell type enhanced (Cge interneuron, Lamp5-lhx6 and chandelier, Mge interneuron)
ETV3L
Cell type enhanced (Medium spiny neuron)
GBX2
Cell type enhanced (Bergmann glia, Ependymal cell, Thalamic excitatory)
NKX6-3
Cell type enhanced (Cerebellar inhibitory, Lamp5-lhx6 and chandelier, Mge interneuron, Upper rhombic lip)
SOHLH1
Cell type enhanced (Hippocampal ca1-3)
VAX1
Cell type enhanced (Cge interneuron, Eccentric medium spiny neuron, Mge interneuron)
POU2F3
Cell type enhanced (Deep-layer near-projecting)
POU3F1
Cell type enhanced (Bergmann glia, Hippocampal ca1-3, Miscellaneous)
ZIC2
Cell type enhanced (Endothelial cell, Fibroblast, Upper rhombic lip)
PROP1
Cell type enhanced (Cge interneuron, Hippocampal dentate gyrus)
ZNF99
Cell type enhanced (Hippocampal ca4)
NPAS4
Cell type enhanced (Medium spiny neuron)
ARX
Cell type enhanced (Cge interneuron, Lamp5-lhx6 and chandelier, Mge interneuron)
ATOH7
Cell type enhanced (Deep-layer near-projecting)
EGR4
Cell type enhanced (Medium spiny neuron)
EMX1
Cell type enhanced (Hippocampal ca4, Upper-layer intratelencephalic)
FEZF2
Cell type enhanced (Deep-layer corticothalamic and 6b, Deep-layer near-projecting, Hippocampal ca1-3)
HOXD3
Cell type enhanced (Lower rhombic lip, Splatter)
LHX9
Cell type enhanced (Ependymal cell, Splatter, Thalamic excitatory)
NHLH2
Cell type enhanced (Thalamic excitatory)
ONECUT1
Cell type enhanced (Cerebellar inhibitory, Oligodendrocyte precursor cell)
SALL3
Cell type enhanced (Astrocyte, Ependymal cell, Mammillary body, Oligodendrocyte precursor cell)
SP9
Cell type enhanced (Cge interneuron, Eccentric medium spiny neuron, Lamp5-lhx6 and chandelier, Mge interneuron)
TOX
Cell type enhanced (Mammillary body)
ZIC5
Cell type enhanced (Bergmann glia, Choroid plexus epithelial cell, Endothelial cell, Upper rhombic lip)
HOXB7
Cell type enhanced (Ependymal cell, Splatter)
MNX1
Cell type enhanced (Cerebellar inhibitory, Upper rhombic lip)
PROX1
Cell type enhanced (Cge interneuron, Hippocampal dentate gyrus, Oligodendrocyte)
RFX6
Cell type enhanced (Hippocampal ca1-3)
SATB1
Cell type enhanced (Deep-layer near-projecting, Mge interneuron)
AHR
Cell type enhanced (Hippocampal dentate gyrus)
AIRE
Cell type enhanced (Deep-layer near-projecting, Fibroblast)
ARGFX
Cell type enhanced (Upper-layer intratelencephalic)
BACH1
Cell type enhanced (Midbrain-derived inhibitory)
BARX2
Cell type enhanced (Choroid plexus epithelial cell, Deep-layer near-projecting, Ependymal cell)
BHLHA9
Cell type enhanced (Lower rhombic lip)
BMAL2
Cell type enhanced (Deep-layer near-projecting)
CASZ1
Cell type enhanced (Eccentric medium spiny neuron)
CREB3L1
Cell type enhanced (Deep-layer corticothalamic and 6b, Oligodendrocyte precursor cell)
CUX2
Cell type enhanced (Choroid plexus epithelial cell, Mammillary body, Upper-layer intratelencephalic)
DLX2
Cell type enhanced (Cge interneuron, Eccentric medium spiny neuron, Lamp5-lhx6 and chandelier, Mge interneuron)
DLX5
Cell type enhanced (Cge interneuron, Lamp5-lhx6 and chandelier, Mge interneuron)
EBF2
Cell type enhanced (Fibroblast, Splatter)
EBF3
Cell type enhanced (Fibroblast, Splatter)
EGR3
Cell type enhanced (Upper-layer intratelencephalic)
ETV1
Cell type enhanced (Upper rhombic lip)
FEZF1
Cell type enhanced (Amygdala excitatory, Astrocyte, Ependymal cell, Splatter)
FOXD4
Cell type enhanced (Upper rhombic lip)
FOXP2
Cell type enhanced (Eccentric medium spiny neuron)
HES7
Cell type enhanced (Cerebellar inhibitory)
HMGA2
Cell type enhanced (Astrocyte, Deep-layer near-projecting, Ependymal cell)
HNF1B
Cell type enhanced (Hippocampal ca4)
HOPX
Cell type enhanced (Hippocampal ca4)
HOXA2
Cell type enhanced (Ependymal cell, Lower rhombic lip)
HOXA3
Cell type enhanced (Ependymal cell, Lower rhombic lip)
HOXB2
Cell type enhanced (Fibroblast, Leukocyte, Lower rhombic lip)
HOXB3
Cell type enhanced (Ependymal cell, Lower rhombic lip, Splatter)
INSM1
Cell type enhanced (Midbrain-derived inhibitory, Upper rhombic lip)
INSM2
Cell type enhanced (Mammillary body, Midbrain-derived inhibitory)
IRF6
Cell type enhanced (Cerebellar inhibitory, Endothelial cell, Ependymal cell)
IRX2
Cell type enhanced (Bergmann glia, Lower rhombic lip)
IRX6
Cell type enhanced (Medium spiny neuron)
KLF5
Cell type enhanced (Fibroblast, Medium spiny neuron)
LHX6
Cell type enhanced (Lamp5-lhx6 and chandelier, Mge interneuron)
MEIS1
Cell type enhanced (Bergmann glia, Oligodendrocyte, Upper rhombic lip)
MEIS2
Cell type enhanced (Eccentric medium spiny neuron, Medium spiny neuron)
MKX
Cell type enhanced (Ependymal cell, Mammillary body)
MSC
Cell type enhanced (Hippocampal ca4, Pericyte, Vascular associated smooth muscle cell)
MYC
Cell type enhanced (Lower rhombic lip)
MYCN
Cell type enhanced (Midbrain-derived inhibitory, Oligodendrocyte precursor cell)
NEUROG2
Cell type enhanced (Cerebellar inhibitory, Hippocampal ca4)
NPAS1
Cell type enhanced (Cge interneuron, Mge interneuron)
ONECUT3
Cell type enhanced (Splatter)
OSR1
Cell type enhanced (Fibroblast, Hippocampal ca4)
PBX3
Cell type enhanced (Eccentric medium spiny neuron)
POU6F2
Cell type enhanced (Deep-layer corticothalamic and 6b, Deep-layer intratelencephalic, Oligodendrocyte precursor cell)
PRDM1
Cell type enhanced (Central nervous system macrophage, Leukocyte, Mge interneuron)
PRDM8
Cell type enhanced (Cerebellar inhibitory, Hippocampal ca4)
RARB
Cell type enhanced (Eccentric medium spiny neuron, Medium spiny neuron)
RFX3
Cell type enhanced (Ependymal cell, Hippocampal dentate gyrus)
RORA
Cell type enhanced (Cerebellar inhibitory)
RXRG
Cell type enhanced (Eccentric medium spiny neuron, Medium spiny neuron)
SOX11
Cell type enhanced (Midbrain-derived inhibitory)
SP7
Cell type enhanced (Cge interneuron)
TBX5
Cell type enhanced (Astrocyte, Lower rhombic lip)
TCF21
Cell type enhanced (Fibroblast, Hippocampal dentate gyrus)
TCF7L2
Cell type enhanced (Committed oligodendrocyte precursor, Thalamic excitatory)
TFAP2D
Cell type enhanced (Amygdala excitatory, Deep-layer intratelencephalic, Splatter)