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Gene: CDK5RAP2 |
Gene summary for CDK5RAP2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CDK5RAP2 | Gene ID | 55755 |
| Gene name | CDK5 regulatory subunit associated protein 2 | |
| Gene Alias | C48 | |
| Cytomap | 9q33.2 | |
| Gene Type | protein-coding | GO ID | GO:0000070 | UniProtAcc | B9EG74 |
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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 |
| 55755 | CDK5RAP2 | P49T-E | Human | Esophagus | ESCC | 6.51e-03 | 1.32e+00 | 0.1768 |
| 55755 | CDK5RAP2 | P52T-E | Human | Esophagus | ESCC | 3.93e-19 | 4.44e-01 | 0.1555 |
| 55755 | CDK5RAP2 | P54T-E | Human | Esophagus | ESCC | 2.56e-04 | 1.49e-01 | 0.0975 |
| 55755 | CDK5RAP2 | P57T-E | Human | Esophagus | ESCC | 1.03e-15 | 3.24e-01 | 0.0926 |
| 55755 | CDK5RAP2 | P61T-E | Human | Esophagus | ESCC | 1.53e-05 | 1.62e-01 | 0.099 |
| 55755 | CDK5RAP2 | P62T-E | Human | Esophagus | ESCC | 3.09e-13 | 3.35e-01 | 0.1302 |
| 55755 | CDK5RAP2 | P65T-E | Human | Esophagus | ESCC | 2.47e-03 | 1.00e-01 | 0.0978 |
| 55755 | CDK5RAP2 | P74T-E | Human | Esophagus | ESCC | 2.07e-21 | 6.52e-01 | 0.1479 |
| 55755 | CDK5RAP2 | P75T-E | Human | Esophagus | ESCC | 1.64e-21 | 4.35e-01 | 0.1125 |
| 55755 | CDK5RAP2 | P76T-E | Human | Esophagus | ESCC | 1.32e-12 | 2.35e-01 | 0.1207 |
| 55755 | CDK5RAP2 | P79T-E | Human | Esophagus | ESCC | 1.64e-15 | 2.06e-01 | 0.1154 |
| 55755 | CDK5RAP2 | P80T-E | Human | Esophagus | ESCC | 1.75e-20 | 5.63e-01 | 0.155 |
| 55755 | CDK5RAP2 | P82T-E | Human | Esophagus | ESCC | 7.66e-13 | 3.82e-01 | 0.1072 |
| 55755 | CDK5RAP2 | P83T-E | Human | Esophagus | ESCC | 4.29e-23 | 8.30e-01 | 0.1738 |
| 55755 | CDK5RAP2 | P89T-E | Human | Esophagus | ESCC | 1.32e-11 | 5.69e-01 | 0.1752 |
| 55755 | CDK5RAP2 | P91T-E | Human | Esophagus | ESCC | 1.60e-07 | 8.66e-01 | 0.1828 |
| 55755 | CDK5RAP2 | P104T-E | Human | Esophagus | ESCC | 2.02e-03 | 3.32e-01 | 0.0931 |
| 55755 | CDK5RAP2 | P107T-E | Human | Esophagus | ESCC | 3.43e-31 | 8.34e-01 | 0.171 |
| 55755 | CDK5RAP2 | P126T-E | Human | Esophagus | ESCC | 2.78e-02 | 4.52e-01 | 0.1125 |
| 55755 | CDK5RAP2 | P127T-E | Human | Esophagus | ESCC | 3.48e-03 | 2.06e-01 | 0.0826 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| 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 |
| 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:00071639 | Cervix | CC | establishment or maintenance of cell polarity | 63/2311 | 218/18723 | 4.25e-11 | 8.76e-09 | 63 |
| GO:190290310 | Cervix | CC | regulation of supramolecular fiber organization | 92/2311 | 383/18723 | 1.49e-10 | 2.48e-08 | 92 |
| GO:004325410 | Cervix | CC | regulation of protein-containing complex assembly | 96/2311 | 428/18723 | 2.91e-09 | 3.05e-07 | 96 |
| GO:00300108 | Cervix | CC | establishment of cell polarity | 42/2311 | 143/18723 | 4.30e-08 | 2.62e-06 | 42 |
| GO:005125810 | Cervix | CC | protein polymerization | 70/2311 | 297/18723 | 5.20e-08 | 3.11e-06 | 70 |
| GO:003227110 | Cervix | CC | regulation of protein polymerization | 57/2311 | 233/18723 | 2.37e-07 | 1.03e-05 | 57 |
| GO:00447725 | Cervix | CC | mitotic cell cycle phase transition | 89/2311 | 424/18723 | 2.70e-07 | 1.12e-05 | 89 |
| GO:003133410 | Cervix | CC | positive regulation of protein-containing complex assembly | 55/2311 | 237/18723 | 2.25e-06 | 6.73e-05 | 55 |
| GO:190290510 | Cervix | CC | positive regulation of supramolecular fiber organization | 50/2311 | 209/18723 | 2.55e-06 | 7.54e-05 | 50 |
| GO:00073466 | Cervix | CC | regulation of mitotic cell cycle | 88/2311 | 457/18723 | 1.26e-05 | 2.60e-04 | 88 |
| GO:19019903 | Cervix | CC | regulation of mitotic cell cycle phase transition | 63/2311 | 299/18723 | 1.27e-05 | 2.60e-04 | 63 |
| GO:005149510 | Cervix | CC | positive regulation of cytoskeleton organization | 50/2311 | 226/18723 | 2.53e-05 | 4.29e-04 | 50 |
| GO:00516567 | Cervix | CC | establishment of organelle localization | 76/2311 | 390/18723 | 3.17e-05 | 5.21e-04 | 76 |
| GO:00106399 | Cervix | CC | negative regulation of organelle organization | 68/2311 | 348/18723 | 7.40e-05 | 1.03e-03 | 68 |
| GO:19019873 | Cervix | CC | regulation of cell cycle phase transition | 74/2311 | 390/18723 | 9.80e-05 | 1.27e-03 | 74 |
| GO:003227310 | Cervix | CC | positive regulation of protein polymerization | 33/2311 | 138/18723 | 1.23e-04 | 1.53e-03 | 33 |
| GO:00514948 | Cervix | CC | negative regulation of cytoskeleton organization | 37/2311 | 163/18723 | 1.57e-04 | 1.88e-03 | 37 |
| GO:19021153 | Cervix | CC | regulation of organelle assembly | 40/2311 | 186/18723 | 2.92e-04 | 3.15e-03 | 40 |
| GO:00705074 | Cervix | CC | regulation of microtubule cytoskeleton organization | 32/2311 | 148/18723 | 1.02e-03 | 8.51e-03 | 32 |
| GO:00311134 | Cervix | CC | regulation of microtubule polymerization | 15/2311 | 55/18723 | 2.14e-03 | 1.54e-02 | 15 |
| 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 |
| 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 |
| CDK5RAP2 | SNV | Missense_Mutation | c.1209N>C | p.Lys403Asn | p.K403N | Q96SN8 | protein_coding | deleterious(0.01) | possibly_damaging(0.601) | TCGA-A2-A04W-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| CDK5RAP2 | SNV | Missense_Mutation | rs746903524 | c.2836C>T | p.Arg946Trp | p.R946W | Q96SN8 | protein_coding | deleterious(0.02) | benign(0.23) | TCGA-A2-A0YI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Femara | SD |
| CDK5RAP2 | SNV | Missense_Mutation | rs151280101 | c.1488C>A | p.Phe496Leu | p.F496L | Q96SN8 | protein_coding | tolerated(1) | benign(0) | TCGA-A2-A0YM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CDK5RAP2 | SNV | Missense_Mutation | novel | c.4591N>A | p.Gln1531Lys | p.Q1531K | Q96SN8 | protein_coding | tolerated(0.17) | benign(0.007) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD |
| CDK5RAP2 | SNV | Missense_Mutation | c.4539C>A | p.Ser1513Arg | p.S1513R | Q96SN8 | protein_coding | tolerated(0.19) | benign(0.003) | TCGA-A7-A4SD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR | |
| CDK5RAP2 | SNV | Missense_Mutation | novel | c.920N>A | p.Ala307Asp | p.A307D | Q96SN8 | protein_coding | deleterious(0.01) | possibly_damaging(0.532) | TCGA-A7-A6VV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | CR |
| CDK5RAP2 | SNV | Missense_Mutation | c.1201A>C | p.Ile401Leu | p.I401L | Q96SN8 | protein_coding | tolerated(0.19) | benign(0.006) | TCGA-AN-A0AR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| CDK5RAP2 | SNV | Missense_Mutation | c.1894T>G | p.Tyr632Asp | p.Y632D | Q96SN8 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-B6-A0I9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| CDK5RAP2 | SNV | Missense_Mutation | novel | c.314N>G | p.Glu105Gly | p.E105G | Q96SN8 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BH-A0BV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | SD |
| CDK5RAP2 | SNV | Missense_Mutation | c.5248N>A | p.Glu1750Lys | p.E1750K | Q96SN8 | protein_coding | tolerated(0.15) | benign(0.033) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 |
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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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