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Gene: CDK5RAP3 |
Gene summary for CDK5RAP3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CDK5RAP3 | Gene ID | 80279 |
| Gene name | CDK5 regulatory subunit associated protein 3 | |
| Gene Alias | C53 | |
| Cytomap | 17q21.32 | |
| Gene Type | protein-coding | GO ID | GO:0000075 | UniProtAcc | Q96JB5 |
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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 |
| 80279 | CDK5RAP3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.15e-03 | 1.88e-01 | -0.1808 |
| 80279 | CDK5RAP3 | HTA11_78_2000001011 | Human | Colorectum | AD | 3.71e-03 | 2.30e-01 | -0.1088 |
| 80279 | CDK5RAP3 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.44e-07 | 2.32e-01 | -0.1954 |
| 80279 | CDK5RAP3 | HTA11_411_2000001011 | Human | Colorectum | SER | 2.94e-02 | 4.83e-01 | -0.2602 |
| 80279 | CDK5RAP3 | HTA11_83_2000001011 | Human | Colorectum | SER | 3.04e-03 | 1.89e-01 | -0.1526 |
| 80279 | CDK5RAP3 | HTA11_696_2000001011 | Human | Colorectum | AD | 9.34e-04 | 2.48e-01 | -0.1464 |
| 80279 | CDK5RAP3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.82e-08 | 3.86e-01 | -0.059 |
| 80279 | CDK5RAP3 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.65e-05 | 2.61e-01 | 0.096 |
| 80279 | CDK5RAP3 | HTA11_4255_2000001011 | Human | Colorectum | SER | 4.01e-03 | 2.84e-01 | 0.0446 |
| 80279 | CDK5RAP3 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 5.76e-04 | 2.95e-01 | 0.294 |
| 80279 | CDK5RAP3 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.02e-11 | 5.41e-01 | 0.3859 |
| 80279 | CDK5RAP3 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.06e-08 | 4.05e-01 | 0.3005 |
| 80279 | CDK5RAP3 | A015-C-203 | Human | Colorectum | FAP | 3.80e-06 | 3.77e-01 | -0.1294 |
| 80279 | CDK5RAP3 | A015-C-006 | Human | Colorectum | FAP | 2.12e-07 | 5.33e-01 | -0.0994 |
| 80279 | CDK5RAP3 | A015-C-104 | Human | Colorectum | FAP | 1.22e-08 | 4.20e-01 | -0.1899 |
| 80279 | CDK5RAP3 | A018-E-020 | Human | Colorectum | FAP | 6.60e-03 | 3.23e-01 | -0.2034 |
| 80279 | CDK5RAP3 | LZE2T | Human | Esophagus | ESCC | 2.94e-10 | 3.56e-01 | 0.082 |
| 80279 | CDK5RAP3 | LZE4T | Human | Esophagus | ESCC | 4.96e-12 | 2.06e-01 | 0.0811 |
| 80279 | CDK5RAP3 | LZE5T | Human | Esophagus | ESCC | 2.26e-05 | 3.10e-01 | 0.0514 |
| 80279 | CDK5RAP3 | LZE7T | Human | Esophagus | ESCC | 4.23e-11 | 6.73e-01 | 0.0667 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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 | ||
| 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:190336333 | Thyroid | ATC | negative regulation of cellular protein catabolic process | 43/6293 | 75/18723 | 2.07e-05 | 1.85e-04 | 43 |
| GO:001092117 | Thyroid | ATC | regulation of phosphatase activity | 47/6293 | 84/18723 | 2.09e-05 | 1.87e-04 | 47 |
| GO:190402921 | Thyroid | ATC | regulation of cyclin-dependent protein kinase activity | 53/6293 | 98/18723 | 2.36e-05 | 2.06e-04 | 53 |
| GO:000007921 | Thyroid | ATC | regulation of cyclin-dependent protein serine/threonine kinase activity | 51/6293 | 94/18723 | 2.97e-05 | 2.48e-04 | 51 |
| GO:001631117 | Thyroid | ATC | dephosphorylation | 179/6293 | 417/18723 | 3.88e-05 | 3.15e-04 | 179 |
| GO:001038911 | Thyroid | ATC | regulation of G2/M transition of mitotic cell cycle | 49/6293 | 94/18723 | 1.60e-04 | 1.10e-03 | 49 |
| GO:004340513 | Thyroid | ATC | regulation of MAP kinase activity | 82/6293 | 177/18723 | 2.87e-04 | 1.83e-03 | 82 |
| GO:007190122 | Thyroid | ATC | negative regulation of protein serine/threonine kinase activity | 59/6293 | 120/18723 | 2.95e-04 | 1.87e-03 | 59 |
| GO:190274911 | Thyroid | ATC | regulation of cell cycle G2/M phase transition | 51/6293 | 102/18723 | 4.45e-04 | 2.64e-03 | 51 |
| GO:004340926 | Thyroid | ATC | negative regulation of MAPK cascade | 82/6293 | 180/18723 | 5.51e-04 | 3.19e-03 | 82 |
| GO:000709511 | Thyroid | ATC | mitotic G2 DNA damage checkpoint | 21/6293 | 34/18723 | 7.12e-04 | 4.00e-03 | 21 |
| GO:004477313 | Thyroid | ATC | mitotic DNA damage checkpoint | 40/6293 | 81/18723 | 2.36e-03 | 1.10e-02 | 40 |
| GO:000007712 | Thyroid | ATC | DNA damage checkpoint | 53/6293 | 115/18723 | 3.59e-03 | 1.58e-02 | 53 |
| GO:004477411 | Thyroid | ATC | mitotic DNA integrity checkpoint | 41/6293 | 85/18723 | 3.62e-03 | 1.58e-02 | 41 |
| GO:190275011 | Thyroid | ATC | negative regulation of cell cycle G2/M phase transition | 31/6293 | 62/18723 | 5.52e-03 | 2.24e-02 | 31 |
| GO:00434333 | Thyroid | ATC | negative regulation of DNA-binding transcription factor activity | 79/6293 | 185/18723 | 5.96e-03 | 2.40e-02 | 79 |
| GO:001097211 | Thyroid | ATC | negative regulation of G2/M transition of mitotic cell cycle | 30/6293 | 60/18723 | 6.27e-03 | 2.50e-02 | 30 |
| GO:00315707 | Thyroid | ATC | DNA integrity checkpoint | 55/6293 | 123/18723 | 6.64e-03 | 2.65e-02 | 55 |
| GO:00448182 | Thyroid | ATC | mitotic G2/M transition checkpoint | 24/6293 | 46/18723 | 7.13e-03 | 2.82e-02 | 24 |
| 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 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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 |
| CDK5RAP3 | SNV | Missense_Mutation | novel | c.814N>T | p.Pro272Ser | p.P272S | Q96JB5 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A2-A0D1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxotere | SD |
| CDK5RAP3 | SNV | Missense_Mutation | novel | c.1164C>A | p.Phe388Leu | p.F388L | Q96JB5 | protein_coding | deleterious(0.03) | probably_damaging(0.997) | TCGA-A2-A3XT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | PR |
| CDK5RAP3 | SNV | Missense_Mutation | novel | c.371N>G | p.Glu124Gly | p.E124G | Q96JB5 | protein_coding | deleterious(0) | possibly_damaging(0.894) | TCGA-C8-A273-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| CDK5RAP3 | SNV | Missense_Mutation | novel | c.371N>G | p.Glu124Gly | p.E124G | Q96JB5 | protein_coding | deleterious(0) | possibly_damaging(0.894) | TCGA-E9-A1NF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD |
| CDK5RAP3 | insertion | Frame_Shift_Ins | novel | c.354_355insGGCCC | p.Met119GlyfsTer3 | p.M119Gfs*3 | Q96JB5 | protein_coding | TCGA-BH-A0DS-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
| CDK5RAP3 | insertion | Nonsense_Mutation | novel | c.355_356insGACTTTGAGAGGTCAGTCCCAT | p.Met119ArgfsTer3 | p.M119Rfs*3 | Q96JB5 | protein_coding | TCGA-BH-A0DS-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
| CDK5RAP3 | deletion | Frame_Shift_Del | novel | c.528delN | p.Ala177GlnfsTer32 | p.A177Qfs*32 | Q96JB5 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| CDK5RAP3 | SNV | Missense_Mutation | c.832C>T | p.Pro278Ser | p.P278S | Q96JB5 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-C5-A7CO-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | SD | |
| CDK5RAP3 | SNV | Missense_Mutation | c.530N>A | p.Ala177Glu | p.A177E | Q96JB5 | protein_coding | tolerated(0.94) | benign(0.148) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| CDK5RAP3 | SNV | Missense_Mutation | c.450G>T | p.Glu150Asp | p.E150D | Q96JB5 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
| Page: 1 2 3 4 |
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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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