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Gene: CDT1 |
Gene summary for CDT1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CDT1 | Gene ID | 81620 |
| Gene name | chromatin licensing and DNA replication factor 1 | |
| Gene Alias | DUP | |
| Cytomap | 16q24.3 | |
| Gene Type | protein-coding | GO ID | GO:0000070 | UniProtAcc | Q9H211 |
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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 |
| 81620 | CDT1 | P1T-E | Human | Esophagus | ESCC | 9.99e-03 | 3.60e-01 | 0.0875 |
| 81620 | CDT1 | P2T-E | Human | Esophagus | ESCC | 3.24e-19 | 6.20e-01 | 0.1177 |
| 81620 | CDT1 | P4T-E | Human | Esophagus | ESCC | 1.83e-16 | 5.22e-01 | 0.1323 |
| 81620 | CDT1 | P5T-E | Human | Esophagus | ESCC | 1.73e-35 | 7.31e-01 | 0.1327 |
| 81620 | CDT1 | P8T-E | Human | Esophagus | ESCC | 1.21e-20 | 5.12e-01 | 0.0889 |
| 81620 | CDT1 | P10T-E | Human | Esophagus | ESCC | 2.57e-02 | 9.82e-02 | 0.116 |
| 81620 | CDT1 | P12T-E | Human | Esophagus | ESCC | 7.00e-03 | 1.58e-01 | 0.1122 |
| 81620 | CDT1 | P15T-E | Human | Esophagus | ESCC | 7.75e-12 | 4.68e-01 | 0.1149 |
| 81620 | CDT1 | P16T-E | Human | Esophagus | ESCC | 3.39e-05 | 2.49e-01 | 0.1153 |
| 81620 | CDT1 | P17T-E | Human | Esophagus | ESCC | 1.39e-07 | 6.93e-01 | 0.1278 |
| 81620 | CDT1 | P21T-E | Human | Esophagus | ESCC | 5.55e-07 | 2.02e-01 | 0.1617 |
| 81620 | CDT1 | P22T-E | Human | Esophagus | ESCC | 2.80e-07 | 2.81e-01 | 0.1236 |
| 81620 | CDT1 | P23T-E | Human | Esophagus | ESCC | 1.00e-07 | 4.10e-01 | 0.108 |
| 81620 | CDT1 | P24T-E | Human | Esophagus | ESCC | 4.01e-18 | 5.36e-01 | 0.1287 |
| 81620 | CDT1 | P26T-E | Human | Esophagus | ESCC | 1.60e-10 | 4.31e-01 | 0.1276 |
| 81620 | CDT1 | P27T-E | Human | Esophagus | ESCC | 3.93e-06 | 1.94e-01 | 0.1055 |
| 81620 | CDT1 | P28T-E | Human | Esophagus | ESCC | 3.86e-18 | 4.65e-01 | 0.1149 |
| 81620 | CDT1 | P31T-E | Human | Esophagus | ESCC | 1.41e-30 | 8.94e-01 | 0.1251 |
| 81620 | CDT1 | P32T-E | Human | Esophagus | ESCC | 1.94e-21 | 4.73e-01 | 0.1666 |
| 81620 | CDT1 | P37T-E | Human | Esophagus | ESCC | 2.77e-07 | 3.34e-01 | 0.1371 |
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| 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 |
| ∗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:014001414 | Esophagus | ESCC | mitotic nuclear division | 218/8552 | 287/18723 | 6.17e-26 | 1.78e-23 | 218 |
| GO:005165617 | Esophagus | ESCC | establishment of organelle localization | 273/8552 | 390/18723 | 9.13e-23 | 1.81e-20 | 273 |
| GO:000007011 | Esophagus | ESCC | mitotic sister chromatid segregation | 138/8552 | 168/18723 | 1.37e-22 | 2.63e-20 | 138 |
| GO:00008194 | Esophagus | ESCC | sister chromatid segregation | 157/8552 | 202/18723 | 8.41e-21 | 1.33e-18 | 157 |
| GO:0051098111 | Esophagus | ESCC | regulation of binding | 251/8552 | 363/18723 | 6.73e-20 | 8.46e-18 | 251 |
| GO:1903829111 | Esophagus | ESCC | positive regulation of cellular protein localization | 199/8552 | 276/18723 | 2.99e-19 | 3.45e-17 | 199 |
| GO:003304416 | Esophagus | ESCC | regulation of chromosome organization | 145/8552 | 187/18723 | 3.80e-19 | 4.31e-17 | 145 |
| GO:000705911 | Esophagus | ESCC | chromosome segregation | 238/8552 | 346/18723 | 1.72e-18 | 1.82e-16 | 238 |
| GO:004477216 | Esophagus | ESCC | mitotic cell cycle phase transition | 281/8552 | 424/18723 | 4.63e-18 | 4.45e-16 | 281 |
| GO:0043254111 | Esophagus | ESCC | regulation of protein-containing complex assembly | 278/8552 | 428/18723 | 3.81e-16 | 2.77e-14 | 278 |
| GO:000734615 | Esophagus | ESCC | regulation of mitotic cell cycle | 293/8552 | 457/18723 | 8.00e-16 | 5.64e-14 | 293 |
| GO:00062604 | Esophagus | ESCC | DNA replication | 181/8552 | 260/18723 | 3.55e-15 | 2.05e-13 | 181 |
| GO:0031334111 | Esophagus | ESCC | positive regulation of protein-containing complex assembly | 166/8552 | 237/18723 | 2.06e-14 | 1.07e-12 | 166 |
| GO:005131011 | Esophagus | ESCC | metaphase plate congression | 58/8552 | 65/18723 | 1.81e-13 | 8.63e-12 | 58 |
| GO:005105215 | Esophagus | ESCC | regulation of DNA metabolic process | 232/8552 | 359/18723 | 2.40e-13 | 1.13e-11 | 232 |
| GO:000708011 | Esophagus | ESCC | mitotic metaphase plate congression | 47/8552 | 50/18723 | 3.15e-13 | 1.47e-11 | 47 |
| GO:00482853 | Esophagus | ESCC | organelle fission | 301/8552 | 488/18723 | 4.64e-13 | 2.12e-11 | 301 |
| GO:00988133 | Esophagus | ESCC | nuclear chromosome segregation | 187/8552 | 281/18723 | 1.00e-12 | 4.36e-11 | 187 |
| GO:005130311 | Esophagus | ESCC | establishment of chromosome localization | 67/8552 | 80/18723 | 1.92e-12 | 8.09e-11 | 67 |
| GO:005000011 | Esophagus | ESCC | chromosome localization | 68/8552 | 82/18723 | 3.37e-12 | 1.32e-10 | 68 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0411023 | Esophagus | ESCC | Cell cycle | 126/4205 | 157/8465 | 1.34e-15 | 5.60e-14 | 2.87e-14 | 126 |
| hsa0411033 | Esophagus | ESCC | Cell cycle | 126/4205 | 157/8465 | 1.34e-15 | 5.60e-14 | 2.87e-14 | 126 |
| hsa041102 | Liver | HCC | Cell cycle | 106/4020 | 157/8465 | 2.54e-07 | 3.04e-06 | 1.69e-06 | 106 |
| hsa041103 | Liver | HCC | Cell cycle | 106/4020 | 157/8465 | 2.54e-07 | 3.04e-06 | 1.69e-06 | 106 |
| hsa041108 | Oral cavity | OSCC | Cell cycle | 118/3704 | 157/8465 | 7.15e-16 | 2.66e-14 | 1.35e-14 | 118 |
| hsa0411015 | Oral cavity | OSCC | Cell cycle | 118/3704 | 157/8465 | 7.15e-16 | 2.66e-14 | 1.35e-14 | 118 |
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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 |
| CDT1 | SNV | Missense_Mutation | c.545C>A | p.Pro182Gln | p.P182Q | Q9H211 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CDT1 | SNV | Missense_Mutation | novel | c.1018G>T | p.Val340Leu | p.V340L | Q9H211 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-E2-A574-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| CDT1 | SNV | Missense_Mutation | novel | c.468G>T | p.Glu156Asp | p.E156D | Q9H211 | protein_coding | tolerated(0.13) | benign(0.007) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CDT1 | SNV | Missense_Mutation | novel | c.466N>A | p.Glu156Lys | p.E156K | Q9H211 | protein_coding | tolerated(0.35) | benign(0.007) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| CDT1 | SNV | Missense_Mutation | novel | c.466G>A | p.Glu156Lys | p.E156K | Q9H211 | protein_coding | tolerated(0.35) | benign(0.007) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CDT1 | SNV | Missense_Mutation | novel | c.641C>A | p.Pro214His | p.P214H | Q9H211 | protein_coding | deleterious(0) | possibly_damaging(0.882) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| CDT1 | SNV | Missense_Mutation | c.1621C>T | p.Arg541Cys | p.R541C | Q9H211 | protein_coding | deleterious(0.02) | possibly_damaging(0.676) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| CDT1 | SNV | Missense_Mutation | novel | c.310N>A | p.Ala104Thr | p.A104T | Q9H211 | protein_coding | tolerated(0.32) | benign(0.039) | TCGA-AP-A0LS-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CDT1 | SNV | Missense_Mutation | novel | c.1118C>T | p.Pro373Leu | p.P373L | Q9H211 | protein_coding | deleterious(0) | probably_damaging(0.948) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CDT1 | SNV | Missense_Mutation | novel | c.1065G>T | p.Glu355Asp | p.E355D | Q9H211 | protein_coding | tolerated(0.47) | benign(0.07) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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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 |
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