Harmonizome 3.0

clock circadian regulator

The protein encoded by this gene plays a central role in the regulation of circadian rhythms. The protein encodes a transcription factor of the basic helix-loop-helix (bHLH) family and contains DNA binding histone acetyltransferase activity. The encoded protein forms a heterodimer with ARNTL (BMAL1) that binds E-box enhancer elements upstream of Period (PER1, PER2, PER3) and Cryptochrome (CRY1, CRY2) genes and activates transcription of these genes. PER and CRY proteins heterodimerize and repress their own transcription by interacting in a feedback loop with CLOCK/ARNTL complexes. Polymorphisms in this gene may be associated with behavioral changes in certain populations and with obesity and metabolic syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

CLOCK-interacting pacemaker

Predicted to be involved in negative regulation of DNA-templated transcription and negative regulation of circadian rhythm. Located in cytosol; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Mar 2025]

period circadian clock 3

This gene is a member of the Period family of genes and is expressed in a circadian pattern in the suprachiasmatic nucleus, the primary circadian pacemaker in the mammalian brain. Genes in this family encode components of the circadian rhythms of locomotor activity, metabolism, and behavior. This gene is upregulated by CLOCK/ARNTL heterodimers but then represses this upregulation in a feedback loop using PER/CRY heterodimers to interact with CLOCK/ARNTL. Polymorphisms in this gene have been linked to sleep disorders. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2014]

period circadian clock 2

This gene is a member of the Period family of genes and is expressed in a circadian pattern in the suprachiasmatic nucleus, the primary circadian pacemaker in the mammalian brain. Genes in this family encode components of the circadian rhythms of locomotor activity, metabolism, and behavior. This gene is upregulated by CLOCK/ARNTL heterodimers but then represses this upregulation in a feedback loop using PER/CRY heterodimers to interact with CLOCK/ARNTL. Polymorphisms in this gene may increase the risk of getting certain cancers and have been linked to sleep disorders. [provided by RefSeq, Jan 2014]

period circadian clock 1

This gene is a member of the Period family of genes and is expressed in a circadian pattern in the suprachiasmatic nucleus, the primary circadian pacemaker in the mammalian brain. Genes in this family encode components of the circadian rhythms of locomotor activity, metabolism, and behavior. This gene is upregulated by CLOCK/ARNTL heterodimers but then represses this upregulation in a feedback loop using PER/CRY heterodimers to interact with CLOCK/ARNTL. Polymorphisms in this gene may increase the risk of getting certain cancers. Alternative splicing has been observed in this gene; however, these variants have not been fully described. [provided by RefSeq, Jan 2014]

period circadian clock 3 pseudogene

cryptochrome circadian clock 2

This gene encodes a flavin adenine dinucleotide-binding protein that is a key component of the circadian core oscillator complex, which regulates the circadian clock. This gene is upregulated by CLOCK/ARNTL heterodimers but then represses this upregulation in a feedback loop using PER/CRY heterodimers to interact with CLOCK/ARNTL. Polymorphisms in this gene have been associated with altered sleep patterns. The encoded protein is widely conserved across plants and animals. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2014]

timeless circadian clock

The protein encoded by this gene is highly conserved and is involved in cell survival after damage or stress, increase in DNA polymerase epsilon activity, maintenance of telomere length, and epithelial cell morphogenesis. The encoded protein also plays a role in the circadian rhythm autoregulatory loop, interacting with the PERIOD genes (PER1, PER2, and PER3) and others to downregulate activation of PER1 by CLOCK/ARNTL. Changes in this gene or its expression may promote prostate cancer, lung cancer, breast cancer, and mental disorders. [provided by RefSeq, Feb 2014]

cryptochrome circadian clock 1

This gene encodes a flavin adenine dinucleotide-binding protein that is a key component of the circadian core oscillator complex, which regulates the circadian clock. This gene is upregulated by CLOCK/ARNTL heterodimers but then represses this upregulation in a feedback loop using PER/CRY heterodimers to interact with CLOCK/ARNTL. Polymorphisms in this gene have been associated with altered sleep patterns. The encoded protein is widely conserved across plants and animals. Loss of the related gene in mouse results in a shortened circadian cycle in complete darkness. [provided by RefSeq, Jan 2014]

From ChEA Transcription Factor Binding Site Profiles

genes with transcription factor binding evidence in the CLOCK-20551151-293T-HUMAN transcription factor binding site profile from the CHEA Transcription Factor Binding Site Profiles dataset.

From ChEA Transcription Factor Targets 2022

target genes of the CLOCK-20551151-293T-HUMAN transcription factor in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.

From Biocarta Pathways

proteins participating in the segmentation clock pathway from the Biocarta Pathways dataset.

From ChEA Transcription Factor Targets

target genes of the CLOCK transcription factor in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.

From GeneRIF Biological Term Annotations

genes co-occuring with the biological term clock in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.

From GO Biological Process Annotations 2015

genes participating in the entrainment of circadian clock biological process from the curated GO Biological Process Annotations 2015 dataset.

From GO Biological Process Annotations 2015

genes participating in the entrainment of circadian clock by photoperiod biological process from the curated GO Biological Process Annotations 2015 dataset.

From MPO Gene-Phenotype Associations

gene mutations causing the prolonged somite segmentation clock period phenotype in transgenic mice from the MPO Gene-Phenotype Associations dataset.

From MPO Gene-Phenotype Associations

gene mutations causing the abnormal somite segmentation clock phenotype in transgenic mice from the MPO Gene-Phenotype Associations dataset.

From NURSA Protein Complexes

proteins in the BL9468 (CLOCK) protein complex recovered by IP-MS from the NURSA Protein Complexes dataset.

From PANTHER Pathways

proteins participating in the Circadian clock system pathway from the PANTHER Pathways dataset.

From Pathway Commons Protein-Protein Interactions

interacting proteins for CLOCK from the Pathway Commons Protein-Protein Interactions dataset.

From Reactome Pathways 2014

proteins participating in the BMAL1:CLOCK,NPAS2 activates circadian gene expression pathway from the Reactome Pathways dataset.

From Reactome Pathways 2014

proteins participating in the Circadian Clock pathway from the Reactome Pathways dataset.

From GO Biological Process Annotations 2023

genes participating in the entrainment of circadian clock by photoperiod biological process from the curated GO Biological Process Annotations 2023 dataset.

From GO Cellular Component Annotations 2023

proteins localized to the CLOCK-BMAL transcription complex cellular component from the curated GO Cellular Component Annotations 2023 dataset.

From MGI Mouse Phenotype Associations 2023

gene mutations causing the abnormal somite segmentation clock phenotype in transgenic mice from the MGI Mouse Phenotype Associations 2023 dataset.

From MGI Mouse Phenotype Associations 2023

gene mutations causing the prolonged somite segmentation clock period phenotype in transgenic mice from the MGI Mouse Phenotype Associations 2023 dataset.

From LINCS L1000 CMAP CRISPR Knockout Consensus Signatures

genes differentially expressed following the CLOCK gene perturbation from the LINCS L1000 CMAP CRISPR Knockout Consensus Signatures dataset.

From WikiPathways Pathways 2024

proteins participating in the Clock controlled autophagy in bone metabolism pathway from the WikiPathways Pathways 2024 dataset.

From Reactome Pathways 2024

proteins participating in the BMAL1:CLOCK,NPAS2 activates circadian gene expression pathway from the Reactome Pathways 2024 dataset.

From Reactome Pathways 2024

proteins participating in the Circadian Clock pathway from the Reactome Pathways 2024 dataset.

From GO Biological Process Annotations 2025

genes participating in the entrainment of circadian clock by photoperiod biological process from the curated GO Biological Process Annotations 2025 dataset.

From GO Cellular Component Annotations 2025

proteins localized to the CLOCK-BMAL transcription complex cellular component from the curated GO Cellular Component Annotations 2025 dataset.

From COMPARTMENTS Curated Protein Localization Evidence Scores 2025

proteins localized to the CLOCK-BMAL transcription complex cellular component from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.

From COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025

proteins co-occuring with the CLOCK-BMAL transcription complex cellular component in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.

From JASPAR Predicted Human Transcription Factor Targets 2025

target genes of the CLOCK transcription factor predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset.

From CM4AI KOLF21J CRISPRi Gene Perturbation Atlas

genes differentially expressed following the CLOCK gene perturbation from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas.