Research Article

A Meta-Analysis Characterizing Stem-Like Gene Expression in the Suprachiasmatic Nucleus and Its Circadian Clock

Table 1

Genes expressed in adult mouse SCN selected from the Fine Structure Search.

Gene symbol and namePANTHER GO Biological Process (GO BP Complete)FSS rankingCircadian phase in SCN (hours)LD phase in SCN (hours)Fluctuating in LD

Lhx1 (LIM homeobox protein 1)nervous system development, cell-cell signaling2ND16No2
Rorb (RAR-related orphan receptor beta)3regulation of circadian rhythm, amacrine cell differentiation, retina development in camera-type eye, negative regulation of osteoblast differentiation660Yes
Rora (RAR-related orphan receptor alpha)3regulation of circadian rhythm, regulation of smoothened signaling pathway, cerebellar Purkinje cell differentiation, negative regulation of fat cell differentiation10(7)6Yes
Flrt3 (fibronectin leucine rich transmembrane protein 3)neuron projection development, synapse organization, fibroblast growth factor receptor signaling pathway, axon guidance, cell adhesion, response to axon injury, synapse assembly, embryonic morphogenesis, neuron projection extension, cell-cell adhesion via plasma-membrane adhesion molecules, positive regulation of synapse assembly1380Yes
Zic1 (zinc finger protein of the cerebellum 1)nervous system development, regulation of smoothened signaling pathway, spinal cord development, adult walking behavior, central nervous system development, cell differentiation14(8)5No
Btg1 (B cell translocation gene 1, anti-proliferative)positive regulation of myoblast differentiation, positive regulation of endothelial cell differentiation16(5)8Yes
Spon1 (spondin 1, extracellular matrix protein)cell adhesion19ND9No
Dlk1 (delta-like1 homolog Drosophila)post-embryonic development, negative regulation of fat cell differentiation, negative regulation of Notch signaling pathway, osteoblast differentiation21ND0Yes
Neurod2 (neurogenic differentiation2)4regulation of synapse maturation, nervous system development, positive regulation of neuron differentiation, regulation of neuron differentiation, associative learning, cerebellar cortex development, behavioral fear response, positive regulation of synaptic plasticity, cell differentiation, cellular response to electrical stimulus22ND13Yes
Igfbp5 (insulin-like growth factor binding protein 5)negative regulation of muscle tissue development, negative regulation of osteoblast differentiation, striated muscle cell differentiation, osteoblast differentiation, negative regulation of cell migration24(10)6Yes
Thsd7b (thrombospondin, type I, domain containing 7B)anatomical structure morphogenesis, ectoderm development526ND22Yes
Msi2 (musashi RNA-binding protein 2)6stem cell development32ND8No
Nkd1 (naked cuticle 1 homolog Drosophila)positive and negative regulation of canonical Wnt signaling pathway, spermatogenesis, cell differentiation34ND2No
Myt1 (myelin transcription factor 1)post-embryonic development, nervous system development, cell differentiation, endocrine pancreas development35ND20No
Zfhx3 (zinc finger homeobox 3)nervous system development, cerebellar Purkinje cell differentiation, embryonic retina morphogenesis in camera-type eye, cell-cell signaling3616No
Cdh13 (cadherin 13)calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules, endothelial cell migration, positive regulation of cell-matrix adhesion, positive regulation of cell migration461020No
Pcsk2 (proprotein convertase
subtilisin/kexin type 2)
nervous system development49ND13No

Boldface indicates a gene also present in Table 2. 1Lhx1 expression shows a 32-hour rhythm in the mouse SCN by JTK analysis (CircaDB). Acceptable circadian periods in this study were 19-30 hours. 2Lhx1 is suppressed by light [38]. 3Circadian clock-related or core clock gene. 4Neuronal differentiation marker. 5Only the GO slim annotation was available. 6Stem cell marker. ND = no significant rhythm detected in CircaDB using the JTK test. () = average phase when phases from multiple experiments with circadian rhythms in the SCN were reported in CircaDB.