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Gene: CLK4 |
Gene summary for CLK4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CLK4 | Gene ID | 57396 |
| Gene name | CDC like kinase 4 | |
| Gene Alias | CLK4 | |
| Cytomap | 5q35.3 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q9HAZ1 |
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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 |
| 57396 | CLK4 | LZE7T | Human | Esophagus | ESCC | 4.47e-07 | 2.19e-01 | 0.0667 |
| 57396 | CLK4 | LZE8T | Human | Esophagus | ESCC | 3.11e-05 | 1.50e-01 | 0.067 |
| 57396 | CLK4 | LZE24T | Human | Esophagus | ESCC | 7.02e-11 | 2.82e-01 | 0.0596 |
| 57396 | CLK4 | LZE6T | Human | Esophagus | ESCC | 3.62e-03 | 1.51e-01 | 0.0845 |
| 57396 | CLK4 | P1T-E | Human | Esophagus | ESCC | 2.07e-02 | 1.62e-01 | 0.0875 |
| 57396 | CLK4 | P2T-E | Human | Esophagus | ESCC | 1.81e-31 | 6.63e-01 | 0.1177 |
| 57396 | CLK4 | P4T-E | Human | Esophagus | ESCC | 1.43e-10 | 2.00e-01 | 0.1323 |
| 57396 | CLK4 | P5T-E | Human | Esophagus | ESCC | 1.14e-13 | 1.78e-01 | 0.1327 |
| 57396 | CLK4 | P8T-E | Human | Esophagus | ESCC | 8.94e-19 | 1.82e-01 | 0.0889 |
| 57396 | CLK4 | P9T-E | Human | Esophagus | ESCC | 1.59e-04 | 1.12e-01 | 0.1131 |
| 57396 | CLK4 | P10T-E | Human | Esophagus | ESCC | 1.97e-12 | 1.20e-01 | 0.116 |
| 57396 | CLK4 | P11T-E | Human | Esophagus | ESCC | 3.69e-12 | 4.81e-01 | 0.1426 |
| 57396 | CLK4 | P12T-E | Human | Esophagus | ESCC | 7.78e-20 | 3.79e-01 | 0.1122 |
| 57396 | CLK4 | P15T-E | Human | Esophagus | ESCC | 9.28e-10 | 1.04e-01 | 0.1149 |
| 57396 | CLK4 | P16T-E | Human | Esophagus | ESCC | 6.38e-25 | 3.90e-01 | 0.1153 |
| 57396 | CLK4 | P17T-E | Human | Esophagus | ESCC | 1.35e-02 | 1.38e-01 | 0.1278 |
| 57396 | CLK4 | P20T-E | Human | Esophagus | ESCC | 7.66e-14 | 3.01e-01 | 0.1124 |
| 57396 | CLK4 | P21T-E | Human | Esophagus | ESCC | 1.42e-06 | 5.29e-02 | 0.1617 |
| 57396 | CLK4 | P22T-E | Human | Esophagus | ESCC | 1.14e-18 | 2.95e-01 | 0.1236 |
| 57396 | CLK4 | P23T-E | Human | Esophagus | ESCC | 2.72e-12 | 1.95e-01 | 0.108 |
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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 |
| ∗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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0008380111 | Esophagus | ESCC | RNA splicing | 336/8552 | 434/18723 | 1.74e-42 | 3.67e-39 | 336 |
| GO:0043484111 | Esophagus | ESCC | regulation of RNA splicing | 116/8552 | 148/18723 | 3.18e-16 | 2.38e-14 | 116 |
| GO:004677710 | Esophagus | ESCC | protein autophosphorylation | 138/8552 | 227/18723 | 2.98e-06 | 3.38e-05 | 138 |
| GO:00182124 | Esophagus | ESCC | peptidyl-tyrosine modification | 202/8552 | 378/18723 | 1.34e-03 | 6.39e-03 | 202 |
| GO:00181084 | Esophagus | ESCC | peptidyl-tyrosine phosphorylation | 200/8552 | 375/18723 | 1.60e-03 | 7.45e-03 | 200 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0513428 | Esophagus | ESCC | Legionellosis | 42/4205 | 57/8465 | 1.83e-04 | 6.90e-04 | 3.53e-04 | 42 |
| hsa0513436 | Esophagus | ESCC | Legionellosis | 42/4205 | 57/8465 | 1.83e-04 | 6.90e-04 | 3.53e-04 | 42 |
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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. |
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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 |
| CLK4 | SNV | Missense_Mutation | c.115G>C | p.Glu39Gln | p.E39Q | Q9HAZ1 | protein_coding | deleterious_low_confidence(0.01) | benign(0.202) | TCGA-A8-A06Q-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| CLK4 | SNV | Missense_Mutation | novel | c.761N>T | p.Ser254Ile | p.S254I | Q9HAZ1 | protein_coding | deleterious(0.01) | possibly_damaging(0.828) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CLK4 | SNV | Missense_Mutation | novel | c.1172N>A | p.Arg391Gln | p.R391Q | Q9HAZ1 | protein_coding | deleterious(0.03) | possibly_damaging(0.722) | TCGA-AR-A2LH-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD |
| CLK4 | SNV | Missense_Mutation | c.1324N>A | p.Asp442Asn | p.D442N | Q9HAZ1 | protein_coding | tolerated(0.2) | benign(0.036) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| CLK4 | SNV | Missense_Mutation | rs372852819 | c.383N>T | p.Ser128Leu | p.S128L | Q9HAZ1 | protein_coding | tolerated(0.14) | benign(0.017) | TCGA-VS-A8EC-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | carboplatin | CR |
| CLK4 | SNV | Missense_Mutation | novel | c.1361N>A | p.Arg454Lys | p.R454K | Q9HAZ1 | protein_coding | tolerated(1) | benign(0.001) | TCGA-VS-A9UV-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | PD |
| CLK4 | SNV | Missense_Mutation | novel | c.454G>A | p.Gly152Arg | p.G152R | Q9HAZ1 | protein_coding | deleterious(0.02) | possibly_damaging(0.672) | TCGA-AY-4070-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | 5-fu | PD |
| CLK4 | SNV | Missense_Mutation | c.785A>G | p.His262Arg | p.H262R | Q9HAZ1 | protein_coding | deleterious(0) | benign(0.353) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CLK4 | SNV | Missense_Mutation | novel | c.761N>A | p.Ser254Asn | p.S254N | Q9HAZ1 | protein_coding | tolerated(1) | benign(0.026) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| CLK4 | SNV | Missense_Mutation | novel | c.1224G>C | p.Lys408Asn | p.K408N | Q9HAZ1 | protein_coding | deleterious(0.01) | possibly_damaging(0.576) | TCGA-DM-A1D9-01 | Colorectum | colon adenocarcinoma | 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 |
| 57396 | CLK4 | SERINE THREONINE KINASE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, ENZYME | TAE-684 | TAE-684 | ||
| 57396 | CLK4 | SERINE THREONINE KINASE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, ENZYME | BMS-387032 | BMS-387032 | ||
| 57396 | CLK4 | SERINE THREONINE KINASE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, ENZYME | FASUDIL | FASUDIL | ||
| 57396 | CLK4 | SERINE THREONINE KINASE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, ENZYME | IMATINIB | IMATINIB | ||
| 57396 | CLK4 | SERINE THREONINE KINASE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, ENZYME | SB-202190 | SB-202190 | ||
| 57396 | CLK4 | SERINE THREONINE KINASE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, ENZYME | ERLOTINIB | ERLOTINIB | ||
| 57396 | CLK4 | SERINE THREONINE KINASE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, ENZYME | LEUCETTAMINE B | LEUCETTAMINE B | 22998443 | |
| 57396 | CLK4 | SERINE THREONINE KINASE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, ENZYME | GNF-PF-3023 | CHEMBL535331 | ||
| 57396 | CLK4 | SERINE THREONINE KINASE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, ENZYME | LY-2090314 | LY-2090314 | ||
| 57396 | CLK4 | SERINE THREONINE KINASE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, ENZYME | TCMDC-125758 | CHEMBL546797 |
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