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:007121412 | Lung | AIS | cellular response to abiotic stimulus | 51/1849 | 331/18723 | 9.10e-04 | 1.21e-02 | 51 |
GO:010400412 | Lung | AIS | cellular response to environmental stimulus | 51/1849 | 331/18723 | 9.10e-04 | 1.21e-02 | 51 |
GO:000975512 | Lung | AIS | hormone-mediated signaling pathway | 33/1849 | 190/18723 | 9.44e-04 | 1.25e-02 | 33 |
GO:005109011 | Lung | AIS | regulation of DNA-binding transcription factor activity | 64/1849 | 440/18723 | 1.04e-03 | 1.36e-02 | 64 |
GO:005109111 | Lung | AIS | positive regulation of DNA-binding transcription factor activity | 41/1849 | 260/18723 | 1.77e-03 | 2.01e-02 | 41 |
GO:000007711 | Lung | AIS | DNA damage checkpoint | 22/1849 | 115/18723 | 1.82e-03 | 2.05e-02 | 22 |
GO:001021212 | Lung | AIS | response to ionizing radiation | 26/1849 | 148/18723 | 2.64e-03 | 2.68e-02 | 26 |
GO:00094162 | Lung | AIS | response to light stimulus | 47/1849 | 320/18723 | 3.72e-03 | 3.48e-02 | 47 |
GO:00315701 | Lung | AIS | DNA integrity checkpoint | 22/1849 | 123/18723 | 4.32e-03 | 3.86e-02 | 22 |
GO:000206423 | Lung | AAH | epithelial cell development | 17/613 | 220/18723 | 9.62e-04 | 2.94e-02 | 17 |
GO:000931421 | Lung | AAH | response to radiation | 27/613 | 456/18723 | 2.33e-03 | 4.92e-02 | 27 |
GO:007147922 | Lung | AAH | cellular response to ionizing radiation | 8/613 | 72/18723 | 2.39e-03 | 4.98e-02 | 8 |
GO:001049827 | Skin | AK | proteasomal protein catabolic process | 97/1910 | 490/18723 | 9.65e-11 | 1.54e-08 | 97 |
GO:004851119 | Skin | AK | rhythmic process | 67/1910 | 298/18723 | 3.47e-10 | 4.37e-08 | 67 |
GO:004316127 | Skin | AK | proteasome-mediated ubiquitin-dependent protein catabolic process | 84/1910 | 412/18723 | 3.96e-10 | 4.88e-08 | 84 |
GO:004854528 | Skin | AK | response to steroid hormone | 73/1910 | 339/18723 | 4.51e-10 | 5.24e-08 | 73 |
GO:000762320 | Skin | AK | circadian rhythm | 51/1910 | 210/18723 | 2.80e-09 | 2.40e-07 | 51 |
GO:000206425 | Skin | AK | epithelial cell development | 51/1910 | 220/18723 | 1.50e-08 | 9.13e-07 | 51 |
GO:007121420 | Skin | AK | cellular response to abiotic stimulus | 67/1910 | 331/18723 | 3.15e-08 | 1.71e-06 | 67 |
GO:010400420 | Skin | AK | cellular response to environmental stimulus | 67/1910 | 331/18723 | 3.15e-08 | 1.71e-06 | 67 |
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 |