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Gene: CDK2 |
Gene summary for CDK2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CDK2 | Gene ID | 1017 |
| Gene name | cyclin dependent kinase 2 | |
| Gene Alias | CDKN2 | |
| Cytomap | 12q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | B4DDL9 |
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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 |
| 1017 | CDK2 | LZE7T | Human | Esophagus | ESCC | 1.65e-08 | 3.67e-01 | 0.0667 |
| 1017 | CDK2 | LZE24T | Human | Esophagus | ESCC | 3.68e-10 | 2.38e-01 | 0.0596 |
| 1017 | CDK2 | LZE6T | Human | Esophagus | ESCC | 3.79e-05 | 1.72e-01 | 0.0845 |
| 1017 | CDK2 | P1T-E | Human | Esophagus | ESCC | 9.24e-04 | 3.20e-01 | 0.0875 |
| 1017 | CDK2 | P2T-E | Human | Esophagus | ESCC | 6.14e-31 | 7.28e-01 | 0.1177 |
| 1017 | CDK2 | P4T-E | Human | Esophagus | ESCC | 6.12e-12 | 3.19e-01 | 0.1323 |
| 1017 | CDK2 | P5T-E | Human | Esophagus | ESCC | 2.13e-11 | 2.09e-01 | 0.1327 |
| 1017 | CDK2 | P8T-E | Human | Esophagus | ESCC | 1.53e-19 | 3.53e-01 | 0.0889 |
| 1017 | CDK2 | P10T-E | Human | Esophagus | ESCC | 2.64e-09 | 2.27e-01 | 0.116 |
| 1017 | CDK2 | P11T-E | Human | Esophagus | ESCC | 3.14e-05 | 1.58e-01 | 0.1426 |
| 1017 | CDK2 | P12T-E | Human | Esophagus | ESCC | 1.55e-16 | 3.09e-01 | 0.1122 |
| 1017 | CDK2 | P15T-E | Human | Esophagus | ESCC | 2.66e-08 | 1.90e-01 | 0.1149 |
| 1017 | CDK2 | P16T-E | Human | Esophagus | ESCC | 4.10e-11 | 2.57e-01 | 0.1153 |
| 1017 | CDK2 | P17T-E | Human | Esophagus | ESCC | 2.91e-06 | 3.36e-01 | 0.1278 |
| 1017 | CDK2 | P19T-E | Human | Esophagus | ESCC | 2.14e-05 | 5.45e-01 | 0.1662 |
| 1017 | CDK2 | P20T-E | Human | Esophagus | ESCC | 1.42e-08 | 1.89e-01 | 0.1124 |
| 1017 | CDK2 | P21T-E | Human | Esophagus | ESCC | 5.16e-12 | 3.11e-01 | 0.1617 |
| 1017 | CDK2 | P22T-E | Human | Esophagus | ESCC | 7.55e-19 | 1.90e-01 | 0.1236 |
| 1017 | CDK2 | P23T-E | Human | Esophagus | ESCC | 1.26e-15 | 4.76e-01 | 0.108 |
| 1017 | CDK2 | P24T-E | Human | Esophagus | ESCC | 1.62e-09 | 3.35e-01 | 0.1287 |
| Page: 1 2 3 4 |
| 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 | ||
| 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:00062602 | Cervix | CC | DNA replication | 48/2311 | 260/18723 | 2.70e-03 | 1.85e-02 | 48 |
| GO:0007346 | Colorectum | AD | regulation of mitotic cell cycle | 119/3918 | 457/18723 | 4.60e-03 | 3.14e-02 | 119 |
| GO:0070507 | Colorectum | AD | regulation of microtubule cytoskeleton organization | 44/3918 | 148/18723 | 7.05e-03 | 4.31e-02 | 44 |
| GO:00073461 | Colorectum | MSS | regulation of mitotic cell cycle | 108/3467 | 457/18723 | 3.30e-03 | 2.50e-02 | 108 |
| GO:000734610 | Esophagus | HGIN | regulation of mitotic cell cycle | 98/2587 | 457/18723 | 4.39e-06 | 1.42e-04 | 98 |
| GO:00447729 | Esophagus | HGIN | mitotic cell cycle phase transition | 89/2587 | 424/18723 | 2.80e-05 | 7.21e-04 | 89 |
| GO:19019906 | Esophagus | HGIN | regulation of mitotic cell cycle phase transition | 65/2587 | 299/18723 | 1.12e-04 | 2.36e-03 | 65 |
| GO:20000456 | Esophagus | HGIN | regulation of G1/S transition of mitotic cell cycle | 36/2587 | 142/18723 | 1.74e-04 | 3.35e-03 | 36 |
| GO:00000827 | Esophagus | HGIN | G1/S transition of mitotic cell cycle | 48/2587 | 214/18723 | 3.97e-04 | 6.07e-03 | 48 |
| GO:00448437 | Esophagus | HGIN | cell cycle G1/S phase transition | 52/2587 | 241/18723 | 6.19e-04 | 8.58e-03 | 52 |
| GO:19028065 | Esophagus | HGIN | regulation of cell cycle G1/S phase transition | 39/2587 | 168/18723 | 6.60e-04 | 9.03e-03 | 39 |
| GO:20001343 | Esophagus | HGIN | negative regulation of G1/S transition of mitotic cell cycle | 23/2587 | 84/18723 | 7.90e-04 | 1.03e-02 | 23 |
| GO:00459305 | Esophagus | HGIN | negative regulation of mitotic cell cycle | 49/2587 | 235/18723 | 1.88e-03 | 2.01e-02 | 49 |
| GO:19019915 | Esophagus | HGIN | negative regulation of mitotic cell cycle phase transition | 39/2587 | 179/18723 | 2.31e-03 | 2.36e-02 | 39 |
| GO:19028073 | Esophagus | HGIN | negative regulation of cell cycle G1/S phase transition | 23/2587 | 93/18723 | 3.39e-03 | 3.18e-02 | 23 |
| GO:19019876 | Esophagus | HGIN | regulation of cell cycle phase transition | 72/2587 | 390/18723 | 5.78e-03 | 4.70e-02 | 72 |
| GO:0010498111 | Esophagus | ESCC | proteasomal protein catabolic process | 369/8552 | 490/18723 | 1.13e-41 | 1.80e-38 | 369 |
| GO:0043161111 | Esophagus | ESCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 312/8552 | 412/18723 | 3.53e-36 | 4.48e-33 | 312 |
| GO:001657015 | Esophagus | ESCC | histone modification | 323/8552 | 463/18723 | 2.61e-26 | 7.88e-24 | 323 |
| GO:0042176111 | Esophagus | ESCC | regulation of protein catabolic process | 280/8552 | 391/18723 | 8.65e-26 | 2.39e-23 | 280 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| 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 |
| hsa05166211 | Esophagus | ESCC | Human T-cell leukemia virus 1 infection | 164/4205 | 222/8465 | 8.13e-14 | 2.09e-12 | 1.07e-12 | 164 |
| hsa05169210 | Esophagus | ESCC | Epstein-Barr virus infection | 151/4205 | 202/8465 | 1.55e-13 | 3.45e-12 | 1.77e-12 | 151 |
| hsa0411524 | Esophagus | ESCC | p53 signaling pathway | 65/4205 | 74/8465 | 3.88e-12 | 6.50e-11 | 3.33e-11 | 65 |
| hsa0421829 | Esophagus | ESCC | Cellular senescence | 119/4205 | 156/8465 | 5.89e-12 | 9.40e-11 | 4.81e-11 | 119 |
| hsa0516510 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
| hsa0520325 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
| hsa052229 | Esophagus | ESCC | Small cell lung cancer | 69/4205 | 92/8465 | 5.40e-07 | 3.85e-06 | 1.97e-06 | 69 |
| hsa0521516 | Esophagus | ESCC | Prostate cancer | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
| hsa051609 | Esophagus | ESCC | Hepatitis C | 107/4205 | 157/8465 | 1.75e-06 | 1.08e-05 | 5.55e-06 | 107 |
| hsa051619 | Esophagus | ESCC | Hepatitis B | 108/4205 | 162/8465 | 7.68e-06 | 4.15e-05 | 2.12e-05 | 108 |
| hsa040689 | Esophagus | ESCC | FoxO signaling pathway | 89/4205 | 131/8465 | 1.56e-05 | 7.98e-05 | 4.09e-05 | 89 |
| hsa051629 | Esophagus | ESCC | Measles | 90/4205 | 139/8465 | 2.16e-04 | 7.87e-04 | 4.03e-04 | 90 |
| hsa041517 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
| hsa041146 | Esophagus | ESCC | Oocyte meiosis | 77/4205 | 131/8465 | 2.19e-02 | 4.80e-02 | 2.46e-02 | 77 |
| hsa0411033 | Esophagus | ESCC | Cell cycle | 126/4205 | 157/8465 | 1.34e-15 | 5.60e-14 | 2.87e-14 | 126 |
| hsa05166310 | Esophagus | ESCC | Human T-cell leukemia virus 1 infection | 164/4205 | 222/8465 | 8.13e-14 | 2.09e-12 | 1.07e-12 | 164 |
| hsa0516937 | Esophagus | ESCC | Epstein-Barr virus infection | 151/4205 | 202/8465 | 1.55e-13 | 3.45e-12 | 1.77e-12 | 151 |
| hsa0411534 | Esophagus | ESCC | p53 signaling pathway | 65/4205 | 74/8465 | 3.88e-12 | 6.50e-11 | 3.33e-11 | 65 |
| hsa0421838 | Esophagus | ESCC | Cellular senescence | 119/4205 | 156/8465 | 5.89e-12 | 9.40e-11 | 4.81e-11 | 119 |
| Page: 1 2 3 4 5 |
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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 |
| CDK2 | SNV | Missense_Mutation | novel | c.688N>T | p.Val230Phe | p.V230F | P24941 | protein_coding | deleterious(0.01) | probably_damaging(0.987) | TCGA-A2-A0CT-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cytoxan | SD |
| CDK2 | insertion | Frame_Shift_Ins | novel | c.269_270insGTCTCCTG | p.Phe90LeufsTer29 | p.F90Lfs*29 | P24941 | protein_coding | TCGA-A2-A0CQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| CDK2 | insertion | Frame_Shift_Ins | novel | c.271_272insCATTTCACCCC | p.Met91ThrfsTer29 | p.M91Tfs*29 | P24941 | protein_coding | TCGA-A2-A0CQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| CDK2 | deletion | Frame_Shift_Del | c.367delG | p.Val123SerfsTer21 | p.V123Sfs*21 | P24941 | protein_coding | TCGA-A2-A25D-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | |||
| CDK2 | SNV | Missense_Mutation | rs201353858 | c.890N>A | p.Arg297Gln | p.R297Q | P24941 | protein_coding | tolerated_low_confidence(0.21) | benign(0.015) | TCGA-EK-A2RJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| CDK2 | SNV | Missense_Mutation | c.250C>T | p.His84Tyr | p.H84Y | P24941 | protein_coding | deleterious(0.02) | benign(0.003) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CDK2 | SNV | Missense_Mutation | c.339N>T | p.Gln113His | p.Q113H | P24941 | protein_coding | deleterious(0.02) | benign(0.013) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| CDK2 | SNV | Missense_Mutation | novel | c.487N>A | p.Val163Met | p.V163M | P24941 | protein_coding | deleterious(0) | probably_damaging(0.982) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CDK2 | SNV | Missense_Mutation | c.364C>G | p.Arg122Gly | p.R122G | P24941 | protein_coding | deleterious(0.03) | probably_damaging(0.999) | TCGA-AA-3994-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | capecitabine | CR | |
| CDK2 | SNV | Missense_Mutation | rs769372167 | c.778C>T | p.Arg260Trp | p.R260W | P24941 | protein_coding | deleterious(0.03) | benign(0.069) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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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 |
| 1017 | CDK2 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | INOC-005 | |||
| 1017 | CDK2 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | Flavopiridol analog 1 | |||
| 1017 | CDK2 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | TGFBETA1 | 9794232 | ||
| 1017 | CDK2 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | inhibitor | 363894197 | CT-7001 | |
| 1017 | CDK2 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | GOSSYPETIN-8-GLUCOSIDE | CHEMBL402915 | 18063365 | |
| 1017 | CDK2 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | DEXAMETHASONE | DEXAMETHASONE | 10867026 | |
| 1017 | CDK2 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | Indole-based analog 11 | |||
| 1017 | CDK2 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | inhibitor | 328083507 | ||
| 1017 | CDK2 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | AGM-1470 | O-CHLOROACETYLCARBAMOYLFUMAGILLOL | 8012959 | |
| 1017 | CDK2 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | ALSTERPAULLONE | ALSTERPAULLONE |
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