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| Gene symbol and name | PANTHER GO Biological Process (GO BP Complete) | Circadian phase (hours) | LD phase (hours) | Fluctuating in LD |
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| Dlx2 (distal-less homeobox 2) | cerebral cortex GABAergic interneuron differentiation and fate commitment, negative regulation of Notch signaling pathway | ND | 8 | No |
| Dlx6 (distal-less homeobox 6) | inner ear morphogenesis, epithelial cell differentiation, positive regulation of epithelial cell proliferation | ND | 8 | Yes |
| Foxd1 (forkhead box D1) | axon guidance, positive regulation of kidney development, positive regulation of bone morphogenetic protein signaling | ND | 6 | No |
| Lhx1 (LIM homeobox protein 1) | nervous system development, cerebellar Purkinje cell differentiation, cell-cell signaling, embryonic retina morphogenesis in camera-type eye | ND | 6 | No |
| Nr2f2 (nuclear receptor subfamily 2, group F, member 2) | neuron migration, forebrain development, anterior/posterior pattern specification | 10 | 6 | Yes |
| Rora (RAR-related orphan receptor alpha) | cerebellar granule cell precursor proliferation, cerebellar Purkinje cell differentiation, circadian regulation of gene expression, cellular response to tumor necrosis factor, regulation of smoothened signaling pathway, negative regulation of fat cell differentiation, muscle cell differentiation, T-helper 17 cell differentiation | (7) | 6 | Yes |
| Rorb (RAR-related orphan receptor beta) | amacrine cell differentiation, retina development in camera-type eye, regulation of circadian rhythm | 6 | 0 | Yes |
| Six3 (sine oculis-related homeobox 3) | negative regulation of neuron differentiation, circadian behavior, neuroblast differentiation and migration, negative regulation of Wnt signaling pathway | ND | 6 | Yes |
| Sox1 (SRY (sex determining region Y)-box 1) | neuron migration, forebrain neuron differentiation, nervous system, development | ND | 6 | Yes |
| Sox11 (SRY (sex determining region Y)-box 11) | positive regulation of neuron differentiation, glial cell development, positive regulation of neurogenesis, positive regulation of hippo signaling, positive regulation of stem cell proliferation | (15.5) | 6 | No |
| Tle4 (transducin-like enhancer of split 4) | Wnt signaling pathway | ND | 2 | Yes |
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