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Gene: CDKN2A |
Gene summary for CDKN2A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CDKN2A | Gene ID | 1029 |
| Gene name | cyclin dependent kinase inhibitor 2A | |
| Gene Alias | ARF | |
| Cytomap | 9p21.3 | |
| Gene Type | protein-coding | GO ID | GO:0000079 | UniProtAcc | K7PML8 |
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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 |
| 1029 | CDKN2A | C06 | Human | Oral cavity | OSCC | 3.31e-18 | 4.29e+00 | 0.2699 |
| 1029 | CDKN2A | C07 | Human | Oral cavity | OSCC | 7.85e-11 | 3.50e+00 | 0.2491 |
| 1029 | CDKN2A | C08 | Human | Oral cavity | OSCC | 7.28e-72 | 1.51e+00 | 0.1919 |
| 1029 | CDKN2A | C86 | Human | Oral cavity | OSCC | 8.43e-13 | 3.00e+00 | 0.161 |
| 1029 | CDKN2A | C09 | Human | Oral cavity | OSCC | 3.49e-28 | 1.05e+00 | 0.1431 |
| 1029 | CDKN2A | LN22 | Human | Oral cavity | OSCC | 4.51e-31 | 4.69e+00 | 0.1733 |
| 1029 | CDKN2A | LN46 | Human | Oral cavity | OSCC | 1.45e-87 | 3.98e+00 | 0.1666 |
| 1029 | CDKN2A | LP15 | Human | Oral cavity | LP | 9.99e-20 | 3.40e+00 | 0.2174 |
| 1029 | CDKN2A | LP17 | Human | Oral cavity | LP | 5.26e-16 | 2.50e+00 | 0.2349 |
| 1029 | CDKN2A | SYSMH1 | Human | Oral cavity | OSCC | 1.18e-88 | 1.56e+00 | 0.1127 |
| 1029 | CDKN2A | SYSMH2 | Human | Oral cavity | OSCC | 5.94e-45 | 2.39e+00 | 0.2326 |
| 1029 | CDKN2A | SYSMH3 | Human | Oral cavity | OSCC | 2.98e-59 | 2.29e+00 | 0.2442 |
| 1029 | CDKN2A | GSM5252130_BPH340PrGF_Via | Human | Prostate | BPH | 2.25e-11 | 6.87e-01 | -0.1972 |
| 1029 | CDKN2A | GSM5252131_BPH340PrSF_Via | Human | Prostate | BPH | 6.73e-23 | 8.62e-01 | -0.2126 |
| 1029 | CDKN2A | GSM5252132_BPH389PrGF | Human | Prostate | BPH | 3.49e-04 | 8.43e-01 | -0.2247 |
| 1029 | CDKN2A | GSM5252134_BPH511PrG_Fcol_3GEX | Human | Prostate | BPH | 3.79e-08 | 5.67e-01 | -0.1433 |
| 1029 | CDKN2A | GSM5252135_BPH511PrPUr_Fcol_3GEX | Human | Prostate | BPH | 2.93e-02 | 4.82e-01 | -0.1833 |
| 1029 | CDKN2A | GSM5252137_BPH556PrGA2_Fcol | Human | Prostate | BPH | 5.95e-16 | 6.48e-01 | -0.23 |
| 1029 | CDKN2A | 048752_1579-all-cells | Human | Prostate | BPH | 3.80e-05 | 1.62e-01 | 0.1008 |
| 1029 | CDKN2A | 052095_1628-all-cells | Human | Prostate | BPH | 5.65e-06 | 2.21e-01 | 0.1032 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:00075688 | Breast | Precancer | aging | 41/1080 | 339/18723 | 5.95e-06 | 1.71e-04 | 41 |
| GO:00160497 | Breast | Precancer | cell growth | 46/1080 | 482/18723 | 5.63e-04 | 7.16e-03 | 46 |
| GO:00075694 | Breast | Precancer | cell aging | 17/1080 | 132/18723 | 1.55e-03 | 1.59e-02 | 17 |
| GO:00015587 | Breast | Precancer | regulation of cell growth | 39/1080 | 414/18723 | 1.81e-03 | 1.78e-02 | 39 |
| GO:00903423 | Breast | Precancer | regulation of cell aging | 10/1080 | 61/18723 | 2.40e-03 | 2.21e-02 | 10 |
| GO:00513489 | Breast | Precancer | negative regulation of transferase activity | 27/1080 | 268/18723 | 3.49e-03 | 2.90e-02 | 27 |
| GO:0033028 | Breast | Precancer | myeloid cell apoptotic process | 6/1080 | 29/18723 | 5.49e-03 | 4.01e-02 | 6 |
| GO:0006925 | Breast | Precancer | inflammatory cell apoptotic process | 5/1080 | 21/18723 | 5.93e-03 | 4.21e-02 | 5 |
| GO:2000106 | Breast | Precancer | regulation of leukocyte apoptotic process | 11/1080 | 81/18723 | 6.65e-03 | 4.57e-02 | 11 |
| GO:000756813 | Breast | IDC | aging | 52/1434 | 339/18723 | 1.14e-06 | 5.10e-05 | 52 |
| GO:005134814 | Breast | IDC | negative regulation of transferase activity | 39/1434 | 268/18723 | 7.89e-05 | 1.56e-03 | 39 |
| GO:00459369 | Breast | IDC | negative regulation of phosphate metabolic process | 53/1434 | 441/18723 | 7.21e-04 | 8.79e-03 | 53 |
| GO:00105639 | Breast | IDC | negative regulation of phosphorus metabolic process | 53/1434 | 442/18723 | 7.60e-04 | 9.25e-03 | 53 |
| GO:001604913 | Breast | IDC | cell growth | 56/1434 | 482/18723 | 1.16e-03 | 1.26e-02 | 56 |
| GO:000155813 | Breast | IDC | regulation of cell growth | 49/1434 | 414/18723 | 1.55e-03 | 1.55e-02 | 49 |
| GO:00071625 | Breast | IDC | negative regulation of cell adhesion | 37/1434 | 303/18723 | 3.27e-03 | 2.75e-02 | 37 |
| GO:000756912 | Breast | IDC | cell aging | 19/1434 | 132/18723 | 5.63e-03 | 4.08e-02 | 19 |
| GO:00108109 | Breast | IDC | regulation of cell-substrate adhesion | 28/1434 | 221/18723 | 5.88e-03 | 4.24e-02 | 28 |
| GO:00903421 | Breast | IDC | regulation of cell aging | 11/1434 | 61/18723 | 6.10e-03 | 4.36e-02 | 11 |
| GO:00064699 | Breast | IDC | negative regulation of protein kinase activity | 27/1434 | 212/18723 | 6.30e-03 | 4.47e-02 | 27 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa042189 | Breast | Precancer | Cellular senescence | 29/684 | 156/8465 | 1.66e-05 | 1.69e-04 | 1.30e-04 | 29 |
| hsa0516618 | Breast | Precancer | Human T-cell leukemia virus 1 infection | 33/684 | 222/8465 | 4.29e-04 | 3.31e-03 | 2.53e-03 | 33 |
| hsa0516316 | Breast | Precancer | Human cytomegalovirus infection | 32/684 | 225/8465 | 1.13e-03 | 7.57e-03 | 5.80e-03 | 32 |
| hsa052196 | Breast | Precancer | Bladder cancer | 9/684 | 41/8465 | 4.65e-03 | 2.72e-02 | 2.08e-02 | 9 |
| hsa052036 | Breast | Precancer | Viral carcinogenesis | 27/684 | 204/8465 | 7.19e-03 | 4.06e-02 | 3.11e-02 | 27 |
| hsa0421814 | Breast | Precancer | Cellular senescence | 29/684 | 156/8465 | 1.66e-05 | 1.69e-04 | 1.30e-04 | 29 |
| hsa0516619 | Breast | Precancer | Human T-cell leukemia virus 1 infection | 33/684 | 222/8465 | 4.29e-04 | 3.31e-03 | 2.53e-03 | 33 |
| hsa0516317 | Breast | Precancer | Human cytomegalovirus infection | 32/684 | 225/8465 | 1.13e-03 | 7.57e-03 | 5.80e-03 | 32 |
| hsa0521913 | Breast | Precancer | Bladder cancer | 9/684 | 41/8465 | 4.65e-03 | 2.72e-02 | 2.08e-02 | 9 |
| hsa0520312 | Breast | Precancer | Viral carcinogenesis | 27/684 | 204/8465 | 7.19e-03 | 4.06e-02 | 3.11e-02 | 27 |
| hsa0421824 | Breast | IDC | Cellular senescence | 35/867 | 156/8465 | 5.49e-06 | 7.43e-05 | 5.56e-05 | 35 |
| hsa0516624 | Breast | IDC | Human T-cell leukemia virus 1 infection | 40/867 | 222/8465 | 2.52e-04 | 2.21e-03 | 1.66e-03 | 40 |
| hsa0516324 | Breast | IDC | Human cytomegalovirus infection | 39/867 | 225/8465 | 6.66e-04 | 5.41e-03 | 4.05e-03 | 39 |
| hsa0520322 | Breast | IDC | Viral carcinogenesis | 34/867 | 204/8465 | 2.82e-03 | 1.86e-02 | 1.39e-02 | 34 |
| hsa041157 | Breast | IDC | p53 signaling pathway | 16/867 | 74/8465 | 2.86e-03 | 1.86e-02 | 1.39e-02 | 16 |
| hsa052147 | Breast | IDC | Glioma | 16/867 | 75/8465 | 3.30e-03 | 2.10e-02 | 1.57e-02 | 16 |
| hsa0521921 | Breast | IDC | Bladder cancer | 10/867 | 41/8465 | 7.07e-03 | 3.54e-02 | 2.65e-02 | 10 |
| hsa0522010 | Breast | IDC | Chronic myeloid leukemia | 15/867 | 76/8465 | 9.24e-03 | 4.37e-02 | 3.27e-02 | 15 |
| hsa0421834 | Breast | IDC | Cellular senescence | 35/867 | 156/8465 | 5.49e-06 | 7.43e-05 | 5.56e-05 | 35 |
| hsa0516634 | Breast | IDC | Human T-cell leukemia virus 1 infection | 40/867 | 222/8465 | 2.52e-04 | 2.21e-03 | 1.66e-03 | 40 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
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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 |
| CDKN2A | deletion | Frame_Shift_Del | novel | c.235_236delAC | p.Thr79ProfsTer40 | p.T79Pfs*40 | P42771 | protein_coding | TCGA-LQ-A4E4-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | PD | ||
| CDKN2A | SNV | Missense_Mutation | c.395N>T | p.Ala132Val | p.A132V | P42771 | protein_coding | tolerated(0.07) | benign(0.012) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| CDKN2A | SNV | Missense_Mutation | c.437N>G | p.Asp146Gly | p.D146G | P42771 | protein_coding | tolerated_low_confidence(0.08) | benign(0.001) | TCGA-C5-A2LT-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | |
| CDKN2A | SNV | Missense_Mutation | novel | c.23N>T | p.Ser8Ile | p.S8I | P42771 | protein_coding | deleterious_low_confidence(0.03) | possibly_damaging(0.73) | TCGA-C5-A905-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| CDKN2A | SNV | Missense_Mutation | c.22N>C | p.Ser8Arg | p.S8R | P42771 | protein_coding | tolerated_low_confidence(0.18) | possibly_damaging(0.64) | TCGA-C5-A905-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| CDKN2A | SNV | Missense_Mutation | c.262N>A | p.Glu88Lys | p.E88K | P42771 | protein_coding | deleterious(0.04) | possibly_damaging(0.485) | TCGA-EK-A2PM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CDKN2A | SNV | Missense_Mutation | c.383N>A | p.Arg128Gln | p.R128Q | P42771 | protein_coding | tolerated(0.36) | benign(0.001) | TCGA-AD-6901-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD | |
| CDKN2A | SNV | Missense_Mutation | rs755927351 | c.391N>T | p.Arg131Cys | p.R131C | P42771 | protein_coding | deleterious(0) | probably_damaging(0.978) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| CDKN2A | SNV | Missense_Mutation | rs876659307 | c.443N>T | p.Ala148Val | p.A148V | P42771 | protein_coding | tolerated_low_confidence(0.1) | benign(0) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| CDKN2A | SNV | Missense_Mutation | c.500C>T | p.Ala167Val | p.A167V | P42771 | protein_coding | unknown(0) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
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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 |
| 1029 | CDKN2A | CLINICALLY ACTIONABLE, DRUG RESISTANCE, KINASE, TUMOR SUPPRESSOR | ON-01910 | RIGOSERTIB | 25156567 | |
| 1029 | CDKN2A | CLINICALLY ACTIONABLE, DRUG RESISTANCE, KINASE, TUMOR SUPPRESSOR | LY2835219 | ABEMACICLIB | ||
| 1029 | CDKN2A | CLINICALLY ACTIONABLE, DRUG RESISTANCE, KINASE, TUMOR SUPPRESSOR | Alvocidib | ALVOCIDIB | 12777976 | |
| 1029 | CDKN2A | CLINICALLY ACTIONABLE, DRUG RESISTANCE, KINASE, TUMOR SUPPRESSOR | Palbociclib | PALBOCICLIB | ||
| 1029 | CDKN2A | CLINICALLY ACTIONABLE, DRUG RESISTANCE, KINASE, TUMOR SUPPRESSOR | BAY1000394 | |||
| 1029 | CDKN2A | CLINICALLY ACTIONABLE, DRUG RESISTANCE, KINASE, TUMOR SUPPRESSOR | LETROZOLE | LETROZOLE | 26715889 | |
| 1029 | CDKN2A | CLINICALLY ACTIONABLE, DRUG RESISTANCE, KINASE, TUMOR SUPPRESSOR | VEMURAFENIB | VEMURAFENIB | 24265155 | |
| 1029 | CDKN2A | CLINICALLY ACTIONABLE, DRUG RESISTANCE, KINASE, TUMOR SUPPRESSOR | PD 0332991 | |||
| 1029 | CDKN2A | CLINICALLY ACTIONABLE, DRUG RESISTANCE, KINASE, TUMOR SUPPRESSOR | ZK304709 | 18829975 | ||
| 1029 | CDKN2A | CLINICALLY ACTIONABLE, DRUG RESISTANCE, KINASE, TUMOR SUPPRESSOR | Sapanisertib | SAPANISERTIB | 25261369 |
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