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Gene: CLOCK |
Gene summary for CLOCK |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CLOCK | Gene ID | 9575 |
| Gene name | clock circadian regulator | |
| Gene Alias | KAT13D | |
| Cytomap | 4q12 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | O15516 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 9575 | CLOCK | LZE7T | Human | Esophagus | ESCC | 3.67e-02 | 3.49e-01 | 0.0667 |
| 9575 | CLOCK | LZE24T | Human | Esophagus | ESCC | 1.39e-10 | 1.05e-01 | 0.0596 |
| 9575 | CLOCK | P1T-E | Human | Esophagus | ESCC | 2.82e-08 | 4.13e-01 | 0.0875 |
| 9575 | CLOCK | P2T-E | Human | Esophagus | ESCC | 3.42e-16 | 2.87e-01 | 0.1177 |
| 9575 | CLOCK | P4T-E | Human | Esophagus | ESCC | 3.37e-10 | 2.44e-01 | 0.1323 |
| 9575 | CLOCK | P5T-E | Human | Esophagus | ESCC | 1.34e-03 | 7.07e-02 | 0.1327 |
| 9575 | CLOCK | P8T-E | Human | Esophagus | ESCC | 2.60e-19 | 3.46e-01 | 0.0889 |
| 9575 | CLOCK | P9T-E | Human | Esophagus | ESCC | 1.56e-06 | 1.17e-01 | 0.1131 |
| 9575 | CLOCK | P10T-E | Human | Esophagus | ESCC | 3.17e-10 | 1.65e-01 | 0.116 |
| 9575 | CLOCK | P11T-E | Human | Esophagus | ESCC | 6.32e-03 | 1.71e-01 | 0.1426 |
| 9575 | CLOCK | P12T-E | Human | Esophagus | ESCC | 7.28e-13 | 2.50e-01 | 0.1122 |
| 9575 | CLOCK | P15T-E | Human | Esophagus | ESCC | 8.50e-10 | 1.54e-01 | 0.1149 |
| 9575 | CLOCK | P20T-E | Human | Esophagus | ESCC | 1.08e-08 | 1.72e-01 | 0.1124 |
| 9575 | CLOCK | P21T-E | Human | Esophagus | ESCC | 5.73e-10 | 2.97e-01 | 0.1617 |
| 9575 | CLOCK | P22T-E | Human | Esophagus | ESCC | 3.43e-18 | 2.44e-01 | 0.1236 |
| 9575 | CLOCK | P23T-E | Human | Esophagus | ESCC | 5.65e-14 | 3.16e-01 | 0.108 |
| 9575 | CLOCK | P24T-E | Human | Esophagus | ESCC | 1.37e-12 | 1.03e-01 | 0.1287 |
| 9575 | CLOCK | P26T-E | Human | Esophagus | ESCC | 4.82e-17 | 2.01e-01 | 0.1276 |
| 9575 | CLOCK | P27T-E | Human | Esophagus | ESCC | 9.54e-14 | 1.93e-01 | 0.1055 |
| 9575 | CLOCK | P28T-E | Human | Esophagus | ESCC | 5.67e-26 | 6.06e-01 | 0.1149 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00510914 | Lung | IAC | positive regulation of DNA-binding transcription factor activity | 50/2061 | 260/18723 | 5.87e-05 | 1.29e-03 | 50 |
| GO:00434017 | Lung | IAC | steroid hormone mediated signaling pathway | 31/2061 | 136/18723 | 6.00e-05 | 1.31e-03 | 31 |
| GO:00093147 | Lung | IAC | response to radiation | 77/2061 | 456/18723 | 8.59e-05 | 1.74e-03 | 77 |
| GO:00457861 | Lung | IAC | negative regulation of cell cycle | 67/2061 | 385/18723 | 9.74e-05 | 1.93e-03 | 67 |
| GO:00000773 | Lung | IAC | DNA damage checkpoint | 27/2061 | 115/18723 | 1.03e-04 | 2.02e-03 | 27 |
| GO:00714784 | Lung | IAC | cellular response to radiation | 38/2061 | 186/18723 | 1.19e-04 | 2.25e-03 | 38 |
| GO:19019881 | Lung | IAC | negative regulation of cell cycle phase transition | 47/2061 | 249/18723 | 1.53e-04 | 2.80e-03 | 47 |
| GO:00109481 | Lung | IAC | negative regulation of cell cycle process | 53/2061 | 294/18723 | 2.05e-04 | 3.58e-03 | 53 |
| GO:0051092 | Lung | IAC | positive regulation of NF-kappaB transcription factor activity | 32/2061 | 152/18723 | 2.25e-04 | 3.90e-03 | 32 |
| GO:00712146 | Lung | IAC | cellular response to abiotic stimulus | 58/2061 | 331/18723 | 2.30e-04 | 3.96e-03 | 58 |
| GO:01040046 | Lung | IAC | cellular response to environmental stimulus | 58/2061 | 331/18723 | 2.30e-04 | 3.96e-03 | 58 |
| GO:00427526 | Lung | IAC | regulation of circadian rhythm | 27/2061 | 121/18723 | 2.53e-04 | 4.24e-03 | 27 |
| GO:00102124 | Lung | IAC | response to ionizing radiation | 31/2061 | 148/18723 | 3.07e-04 | 4.89e-03 | 31 |
| GO:00331434 | Lung | IAC | regulation of intracellular steroid hormone receptor signaling pathway | 19/2061 | 74/18723 | 3.15e-04 | 4.98e-03 | 19 |
| GO:00315703 | Lung | IAC | DNA integrity checkpoint | 27/2061 | 123/18723 | 3.34e-04 | 5.24e-03 | 27 |
| GO:00331445 | Lung | IAC | negative regulation of intracellular steroid hormone receptor signaling pathway | 12/2061 | 38/18723 | 5.35e-04 | 7.54e-03 | 12 |
| GO:00000752 | Lung | IAC | cell cycle checkpoint | 33/2061 | 169/18723 | 7.51e-04 | 9.82e-03 | 33 |
| GO:00182053 | Lung | IAC | peptidyl-lysine modification | 62/2061 | 376/18723 | 7.55e-04 | 9.82e-03 | 62 |
| GO:00097557 | Lung | IAC | hormone-mediated signaling pathway | 36/2061 | 190/18723 | 7.95e-04 | 1.02e-02 | 36 |
| GO:00321033 | Lung | IAC | positive regulation of response to external stimulus | 65/2061 | 427/18723 | 4.28e-03 | 3.41e-02 | 65 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa047105 | Esophagus | ESCC | Circadian rhythm | 24/4205 | 34/8465 | 1.09e-02 | 2.51e-02 | 1.29e-02 | 24 |
| hsa0471012 | Esophagus | ESCC | Circadian rhythm | 24/4205 | 34/8465 | 1.09e-02 | 2.51e-02 | 1.29e-02 | 24 |
| hsa04710 | Lung | IAC | Circadian rhythm | 10/1053 | 34/8465 | 6.70e-03 | 2.76e-02 | 1.83e-02 | 10 |
| hsa047101 | Lung | IAC | Circadian rhythm | 10/1053 | 34/8465 | 6.70e-03 | 2.76e-02 | 1.83e-02 | 10 |
| hsa047102 | Lung | AIS | Circadian rhythm | 11/961 | 34/8465 | 9.22e-04 | 7.11e-03 | 4.55e-03 | 11 |
| hsa047103 | Lung | AIS | Circadian rhythm | 11/961 | 34/8465 | 9.22e-04 | 7.11e-03 | 4.55e-03 | 11 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| CLOCK | CD8TEX | Breast | DCIS | DHX30,BCAS3,MTMR4, etc. | 3.82e-02 |  |
| CLOCK | CD4TN | Breast | Healthy | DHX30,BCAS3,MTMR4, etc. | 2.09e-02 |  |
| CLOCK | CD8TEX | Breast | IDC | DHX30,BCAS3,MTMR4, etc. | 3.95e-02 |  |
| CLOCK | KER | Esophagus | ADJ | KRT13,KRT5,TMEM165, etc. | 2.21e-01 |  |
| CLOCK | CD8TEXP | Esophagus | ADJ | SMIM10L2B,CDC42SE2,CLEC7A, etc. | 4.89e-02 | |
| CLOCK | CD8TEXP | Esophagus | ESCC | SMIM10L2B,CDC42SE2,CLEC7A, etc. | 7.66e-02 |  |
| CLOCK | INMON | Esophagus | ESCC | SMIM10L2B,CDC42SE2,CLEC7A, etc. | 8.35e-02 | |
| CLOCK | AT2L | Lung | MIAC | TMEM165,SYT8,SPTSSA, etc. | 6.38e-01 |  |
| CLOCK | CD8TEXINT | Lung | AAH | TICAM2,HSPA1B,ZHX3, etc. | 3.56e-01 |  |
| CLOCK | ECM | Oral cavity | EOLP | GLIS2,LUZP2,AL078604.4, etc. | 0.00e+00 |  |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 2 3 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| CLOCK | SNV | Missense_Mutation | c.496N>A | p.Val166Ile | p.V166I | O15516 | protein_coding | tolerated(0.13) | benign(0.042) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CLOCK | SNV | Missense_Mutation | c.49N>T | p.Asp17Tyr | p.D17Y | O15516 | protein_coding | deleterious(0) | possibly_damaging(0.526) | TCGA-AR-A256-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD | |
| CLOCK | SNV | Missense_Mutation | c.35N>T | p.Ser12Leu | p.S12L | O15516 | protein_coding | deleterious(0.03) | benign(0.001) | TCGA-EW-A1IZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | SD | |
| CLOCK | insertion | Nonsense_Mutation | novel | c.1840_1841insTAATTT | p.Gly614delinsValIleTer | p.G614delinsVI* | O15516 | protein_coding | TCGA-B6-A0IB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| CLOCK | insertion | Frame_Shift_Ins | novel | c.1839_1840insCACGTTCCCACCAGCAGTGT | p.Gly614HisfsTer16 | p.G614Hfs*16 | O15516 | protein_coding | TCGA-B6-A0IB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| CLOCK | SNV | Missense_Mutation | novel | c.677N>G | p.Ser226Cys | p.S226C | O15516 | protein_coding | deleterious(0) | possibly_damaging(0.447) | TCGA-C5-A907-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| CLOCK | SNV | Missense_Mutation | novel | c.142N>A | p.Asp48Asn | p.D48N | O15516 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-ZJ-AAX8-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
| CLOCK | SNV | Missense_Mutation | novel | c.1174N>A | p.Glu392Lys | p.E392K | O15516 | protein_coding | deleterious(0.04) | benign(0.043) | TCGA-ZJ-AAXU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| CLOCK | SNV | Missense_Mutation | c.2355N>G | p.Phe785Leu | p.F785L | O15516 | protein_coding | tolerated(0.08) | benign(0.007) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| CLOCK | SNV | Missense_Mutation | rs779397098 | c.1460N>T | p.Ser487Phe | p.S487F | O15516 | protein_coding | deleterious(0.01) | possibly_damaging(0.887) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 8 |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| 9575 | CLOCK | ENZYME, TRANSCRIPTION FACTOR, NUCLEAR HORMONE RECEPTOR, TRANSCRIPTION FACTOR COMPLEX | salbutamol | ALBUTEROL | 23508266 | |
| 9575 | CLOCK | ENZYME, TRANSCRIPTION FACTOR, NUCLEAR HORMONE RECEPTOR, TRANSCRIPTION FACTOR COMPLEX | lithium | LITHIUM | 21047205 |
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