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Gene: TIMELESS |
Gene summary for TIMELESS |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TIMELESS | Gene ID | 8914 |
| Gene name | timeless circadian regulator | |
| Gene Alias | TIM | |
| Cytomap | 12q13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000018 | UniProtAcc | Q9UNS1 |
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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 |
| 8914 | TIMELESS | LZE2T | Human | Esophagus | ESCC | 2.18e-04 | 3.61e-01 | 0.082 |
| 8914 | TIMELESS | LZE7T | Human | Esophagus | ESCC | 1.62e-04 | 2.47e-01 | 0.0667 |
| 8914 | TIMELESS | LZE22T | Human | Esophagus | ESCC | 1.48e-05 | 3.61e-01 | 0.068 |
| 8914 | TIMELESS | LZE24T | Human | Esophagus | ESCC | 4.35e-08 | 2.17e-01 | 0.0596 |
| 8914 | TIMELESS | P1T-E | Human | Esophagus | ESCC | 1.09e-04 | 3.46e-01 | 0.0875 |
| 8914 | TIMELESS | P2T-E | Human | Esophagus | ESCC | 3.95e-30 | 6.64e-01 | 0.1177 |
| 8914 | TIMELESS | P4T-E | Human | Esophagus | ESCC | 1.49e-09 | 2.71e-01 | 0.1323 |
| 8914 | TIMELESS | P5T-E | Human | Esophagus | ESCC | 2.03e-09 | 2.08e-01 | 0.1327 |
| 8914 | TIMELESS | P8T-E | Human | Esophagus | ESCC | 4.12e-11 | 2.51e-01 | 0.0889 |
| 8914 | TIMELESS | P9T-E | Human | Esophagus | ESCC | 2.30e-02 | 1.06e-01 | 0.1131 |
| 8914 | TIMELESS | P10T-E | Human | Esophagus | ESCC | 9.20e-06 | 2.10e-01 | 0.116 |
| 8914 | TIMELESS | P11T-E | Human | Esophagus | ESCC | 4.74e-03 | 1.45e-01 | 0.1426 |
| 8914 | TIMELESS | P12T-E | Human | Esophagus | ESCC | 1.78e-03 | 1.39e-01 | 0.1122 |
| 8914 | TIMELESS | P15T-E | Human | Esophagus | ESCC | 7.99e-08 | 2.18e-01 | 0.1149 |
| 8914 | TIMELESS | P16T-E | Human | Esophagus | ESCC | 4.40e-09 | 2.53e-01 | 0.1153 |
| 8914 | TIMELESS | P17T-E | Human | Esophagus | ESCC | 8.50e-05 | 2.04e-01 | 0.1278 |
| 8914 | TIMELESS | P19T-E | Human | Esophagus | ESCC | 4.64e-06 | 4.32e-01 | 0.1662 |
| 8914 | TIMELESS | P20T-E | Human | Esophagus | ESCC | 2.18e-03 | 1.32e-01 | 0.1124 |
| 8914 | TIMELESS | P21T-E | Human | Esophagus | ESCC | 9.44e-07 | 1.79e-01 | 0.1617 |
| 8914 | TIMELESS | P22T-E | Human | Esophagus | ESCC | 9.56e-08 | 1.92e-01 | 0.1236 |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:00062604 | Esophagus | ESCC | DNA replication | 181/8552 | 260/18723 | 3.55e-15 | 2.05e-13 | 181 |
| GO:005105215 | Esophagus | ESCC | regulation of DNA metabolic process | 232/8552 | 359/18723 | 2.40e-13 | 1.13e-11 | 232 |
| GO:005105417 | Esophagus | ESCC | positive regulation of DNA metabolic process | 139/8552 | 201/18723 | 1.20e-11 | 4.33e-10 | 139 |
| GO:190198713 | Esophagus | ESCC | regulation of cell cycle phase transition | 242/8552 | 390/18723 | 3.86e-11 | 1.26e-09 | 242 |
| GO:00457865 | Esophagus | ESCC | negative regulation of cell cycle | 236/8552 | 385/18723 | 3.62e-10 | 9.93e-09 | 236 |
| GO:00000754 | Esophagus | ESCC | cell cycle checkpoint | 117/8552 | 169/18723 | 4.47e-10 | 1.17e-08 | 117 |
| GO:2001020110 | Esophagus | ESCC | regulation of response to DNA damage stimulus | 145/8552 | 219/18723 | 5.97e-10 | 1.50e-08 | 145 |
| GO:00062612 | Esophagus | ESCC | DNA-dependent DNA replication | 100/8552 | 151/18723 | 2.61e-07 | 3.94e-06 | 100 |
| GO:00109484 | Esophagus | ESCC | negative regulation of cell cycle process | 177/8552 | 294/18723 | 3.26e-07 | 4.59e-06 | 177 |
| GO:00315705 | Esophagus | ESCC | DNA integrity checkpoint | 83/8552 | 123/18723 | 8.17e-07 | 1.06e-05 | 83 |
| GO:19019883 | Esophagus | ESCC | negative regulation of cell cycle phase transition | 151/8552 | 249/18723 | 1.28e-06 | 1.57e-05 | 151 |
| GO:00063024 | Esophagus | ESCC | double-strand break repair | 152/8552 | 251/18723 | 1.33e-06 | 1.62e-05 | 152 |
| GO:190165319 | Esophagus | ESCC | cellular response to peptide | 208/8552 | 359/18723 | 1.68e-06 | 2.01e-05 | 208 |
| GO:00062754 | Esophagus | ESCC | regulation of DNA replication | 73/8552 | 107/18723 | 1.97e-06 | 2.28e-05 | 73 |
| GO:20010228 | Esophagus | ESCC | positive regulation of response to DNA damage stimulus | 69/8552 | 105/18723 | 2.66e-05 | 2.22e-04 | 69 |
| GO:00062826 | Esophagus | ESCC | regulation of DNA repair | 82/8552 | 130/18723 | 4.65e-05 | 3.66e-04 | 82 |
| GO:00457395 | Esophagus | ESCC | positive regulation of DNA repair | 49/8552 | 73/18723 | 1.74e-04 | 1.14e-03 | 49 |
| GO:00063101 | Esophagus | ESCC | DNA recombination | 168/8552 | 305/18723 | 5.58e-04 | 3.05e-03 | 168 |
| GO:004851118 | Esophagus | ESCC | rhythmic process | 164/8552 | 298/18723 | 6.80e-04 | 3.57e-03 | 164 |
| GO:000762319 | Esophagus | ESCC | circadian rhythm | 119/8552 | 210/18723 | 8.47e-04 | 4.36e-03 | 119 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| ∗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 |
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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 |
| TIMELESS | SNV | Missense_Mutation | rs780706303 | c.2110G>A | p.Val704Ile | p.V704I | Q9UNS1 | protein_coding | deleterious(0.04) | benign(0.001) | TCGA-A8-A06O-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | letrozole | SD |
| TIMELESS | SNV | Missense_Mutation | c.2530N>T | p.Asp844Tyr | p.D844Y | Q9UNS1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AN-A0AS-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| TIMELESS | SNV | Missense_Mutation | rs780869332 | c.1169N>A | p.Arg390Gln | p.R390Q | Q9UNS1 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AN-A0FT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TIMELESS | SNV | Missense_Mutation | c.2404N>C | p.Glu802Gln | p.E802Q | Q9UNS1 | protein_coding | deleterious(0.02) | probably_damaging(0.996) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
| TIMELESS | SNV | Missense_Mutation | rs751726906 | c.319C>T | p.Arg107Trp | p.R107W | Q9UNS1 | protein_coding | deleterious(0.01) | probably_damaging(0.981) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD |
| TIMELESS | SNV | Missense_Mutation | rs199809988 | c.721N>T | p.Arg241Cys | p.R241C | Q9UNS1 | protein_coding | deleterious(0.01) | probably_damaging(0.93) | TCGA-E9-A6HE-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | CR |
| TIMELESS | SNV | Missense_Mutation | rs374201861 | c.2879C>T | p.Ala960Val | p.A960V | Q9UNS1 | protein_coding | tolerated(0.26) | benign(0.025) | TCGA-EW-A1IZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | SD |
| TIMELESS | insertion | Nonsense_Mutation | novel | c.1142_1143insGTGTCGGTCTCCAGATCCATAAAGTTGGGATTGTGACAGTTG | p.Ala381_Leu382insCysArgSerProAspProTerSerTrpAspCysAspSerCys | p.A381_L382insCRSPDP*SWDCDSC | Q9UNS1 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| TIMELESS | insertion | Frame_Shift_Ins | novel | c.3343_3344insCAGCTCTCTGGAGATTTAGTTCTCTTCTTCTAGGAACC | p.Val1115AlafsTer33 | p.V1115Afs*33 | Q9UNS1 | protein_coding | TCGA-B6-A0I6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
| TIMELESS | deletion | Frame_Shift_Del | novel | c.956delN | p.Pro319LeufsTer20 | p.P319Lfs*20 | Q9UNS1 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
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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 |
| Page: 1 |
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