Tissue | Expression Dynamics | Abbreviation |
Esophagus | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Esophagus/CLOCK_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
Liver | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Liver/CLOCK_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
Lung | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Lung/CLOCK_pca_on_diff_genes.png) | AAH: Atypical adenomatous hyperplasia |
AIS: Adenocarcinoma in situ |
IAC: Invasive lung adenocarcinoma |
MIA: Minimally invasive adenocarcinoma |
Skin | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Skin/CLOCK_pca_on_diff_genes.png) | AK: Actinic keratosis |
cSCC: Cutaneous squamous cell carcinoma |
SCCIS:squamous cell carcinoma in situ |
Thyroid | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Thyroid/CLOCK_pca_on_diff_genes.png) | ATC: Anaplastic thyroid cancer |
HT: Hashimoto's thyroiditis |
PTC: Papillary thyroid cancer |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00331433 | Liver | NAFLD | regulation of intracellular steroid hormone receptor signaling pathway | 15/1882 | 74/18723 | 6.18e-03 | 4.62e-02 | 15 |
GO:00900874 | Liver | NAFLD | regulation of peptide transport | 32/1882 | 202/18723 | 6.42e-03 | 4.69e-02 | 32 |
GO:00102123 | Liver | NAFLD | response to ionizing radiation | 25/1882 | 148/18723 | 6.67e-03 | 4.74e-02 | 25 |
GO:00093066 | Liver | NAFLD | protein secretion | 51/1882 | 359/18723 | 7.17e-03 | 4.96e-02 | 51 |
GO:001049822 | Liver | HCC | proteasomal protein catabolic process | 351/7958 | 490/18723 | 6.92e-40 | 1.46e-36 | 351 |
GO:004316122 | Liver | HCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 299/7958 | 412/18723 | 7.82e-36 | 8.27e-33 | 299 |
GO:001657021 | Liver | HCC | histone modification | 283/7958 | 463/18723 | 2.68e-16 | 2.33e-14 | 283 |
GO:00182052 | Liver | HCC | peptidyl-lysine modification | 230/7958 | 376/18723 | 1.51e-13 | 8.32e-12 | 230 |
GO:003052222 | Liver | HCC | intracellular receptor signaling pathway | 171/7958 | 265/18723 | 3.00e-13 | 1.61e-11 | 171 |
GO:00064732 | Liver | HCC | protein acetylation | 135/7958 | 201/18723 | 1.20e-12 | 5.92e-11 | 135 |
GO:00435432 | Liver | HCC | protein acylation | 157/7958 | 243/18723 | 2.40e-12 | 1.12e-10 | 157 |
GO:00183942 | Liver | HCC | peptidyl-lysine acetylation | 116/7958 | 169/18723 | 5.11e-12 | 2.23e-10 | 116 |
GO:004854522 | Liver | HCC | response to steroid hormone | 206/7958 | 339/18723 | 6.81e-12 | 2.92e-10 | 206 |
GO:00064752 | Liver | HCC | internal protein amino acid acetylation | 107/7958 | 160/18723 | 3.77e-10 | 1.23e-08 | 107 |
GO:00183932 | Liver | HCC | internal peptidyl-lysine acetylation | 105/7958 | 158/18723 | 9.48e-10 | 2.90e-08 | 105 |
GO:00165732 | Liver | HCC | histone acetylation | 101/7958 | 152/18723 | 1.99e-09 | 5.63e-08 | 101 |
GO:007138322 | Liver | HCC | cellular response to steroid hormone stimulus | 128/7958 | 204/18723 | 3.92e-09 | 1.04e-07 | 128 |
GO:007121421 | Liver | HCC | cellular response to abiotic stimulus | 183/7958 | 331/18723 | 1.59e-06 | 2.26e-05 | 183 |
GO:010400421 | Liver | HCC | cellular response to environmental stimulus | 183/7958 | 331/18723 | 1.59e-06 | 2.26e-05 | 183 |
GO:19019871 | Liver | HCC | regulation of cell cycle phase transition | 211/7958 | 390/18723 | 2.11e-06 | 2.89e-05 | 211 |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
CLOCK | CD8TEX | Breast | DCIS | DHX30,BCAS3,MTMR4, etc. | 3.82e-02 | ![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.](images/gene_regulatory/Breast/Str/TF_DCIS/regulons_activity_in_dotplot.png) |
CLOCK | CD4TN | Breast | Healthy | DHX30,BCAS3,MTMR4, etc. | 2.09e-02 | ![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.](images/gene_regulatory/Breast/Str/TF_Healthy/regulons_activity_in_dotplot.png) |
CLOCK | CD8TEX | Breast | IDC | DHX30,BCAS3,MTMR4, etc. | 3.95e-02 | ![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.](images/gene_regulatory/Breast/Str/TF_IDC/regulons_activity_in_dotplot.png) |
CLOCK | KER | Esophagus | ADJ | KRT13,KRT5,TMEM165, etc. | 2.21e-01 | ![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.](images/gene_regulatory/Esophagus/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
CLOCK | CD8TEXP | Esophagus | ADJ | SMIM10L2B,CDC42SE2,CLEC7A, etc. | 4.89e-02 | ![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.](images/gene_regulatory/Esophagus/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
CLOCK | CD8TEXP | Esophagus | ESCC | SMIM10L2B,CDC42SE2,CLEC7A, etc. | 7.66e-02 | ![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.](images/gene_regulatory/Esophagus/Str/TF_ESCC/regulons_activity_in_dotplot.png) |
CLOCK | INMON | Esophagus | ESCC | SMIM10L2B,CDC42SE2,CLEC7A, etc. | 8.35e-02 | ![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.](images/gene_regulatory/Esophagus/Str/TF_ESCC/regulons_activity_in_dotplot.png) |
CLOCK | AT2L | Lung | MIAC | TMEM165,SYT8,SPTSSA, etc. | 6.38e-01 | ![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.](images/gene_regulatory/Lung/Str/TF_MIAC/regulons_activity_in_dotplot.png) |
CLOCK | CD8TEXINT | Lung | AAH | TICAM2,HSPA1B,ZHX3, etc. | 3.56e-01 | ![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.](images/gene_regulatory/Lung/Str/TF_AAH/regulons_activity_in_dotplot.png) |
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.](images/gene_regulatory/OralCavity/Str/TF_EOLP/regulons_activity_in_dotplot.png) |
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 |