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Gene: NEK4 |
Gene summary for NEK4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NEK4 | Gene ID | 6787 |
| Gene name | NIMA related kinase 4 | |
| Gene Alias | NRK2 | |
| Cytomap | 3p21.1 | |
| Gene Type | protein-coding | GO ID | GO:0000278 | UniProtAcc | P51957 |
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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 |
| 6787 | NEK4 | NAFLD1 | Human | Liver | NAFLD | 3.88e-03 | 2.74e-01 | -0.04 |
| 6787 | NEK4 | HCC1_Meng | Human | Liver | HCC | 1.59e-11 | -8.64e-02 | 0.0246 |
| 6787 | NEK4 | HCC1 | Human | Liver | HCC | 5.74e-04 | 2.93e+00 | 0.5336 |
| 6787 | NEK4 | HCC2 | Human | Liver | HCC | 1.10e-09 | 3.10e+00 | 0.5341 |
| 6787 | NEK4 | S014 | Human | Liver | HCC | 2.07e-04 | 2.89e-01 | 0.2254 |
| 6787 | NEK4 | S015 | Human | Liver | HCC | 4.22e-02 | 2.78e-01 | 0.2375 |
| 6787 | NEK4 | S016 | Human | Liver | HCC | 1.59e-03 | 2.42e-01 | 0.2243 |
| 6787 | NEK4 | S027 | Human | Liver | HCC | 5.21e-03 | 5.06e-01 | 0.2446 |
| 6787 | NEK4 | S028 | Human | Liver | HCC | 2.38e-14 | 6.82e-01 | 0.2503 |
| 6787 | NEK4 | S029 | Human | Liver | HCC | 7.26e-09 | 5.85e-01 | 0.2581 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:00075687 | Liver | NAFLD | aging | 53/1882 | 339/18723 | 7.78e-04 | 9.77e-03 | 53 |
| GO:20010206 | Liver | NAFLD | regulation of response to DNA damage stimulus | 36/1882 | 219/18723 | 2.14e-03 | 2.08e-02 | 36 |
| GO:00075692 | Liver | NAFLD | cell aging | 23/1882 | 132/18723 | 6.18e-03 | 4.62e-02 | 23 |
| GO:200102021 | Liver | HCC | regulation of response to DNA damage stimulus | 128/7958 | 219/18723 | 1.31e-06 | 1.90e-05 | 128 |
| GO:000756822 | Liver | HCC | aging | 185/7958 | 339/18723 | 4.28e-06 | 5.50e-05 | 185 |
| GO:00075691 | Liver | HCC | cell aging | 73/7958 | 132/18723 | 2.00e-03 | 1.01e-02 | 73 |
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| 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. |
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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 |
| NEK4 | SNV | Missense_Mutation | novel | c.151G>A | p.Glu51Lys | p.E51K | P51957 | protein_coding | deleterious(0) | possibly_damaging(0.809) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| NEK4 | SNV | Missense_Mutation | rs763564376 | c.2496N>C | p.Leu832Phe | p.L832F | P51957 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NEK4 | insertion | Nonsense_Mutation | novel | c.96_97insAATTGATATGCCCAGTGATTTCATCTGTCAGTCTGCTGGGGTACA | p.Tyr32_Val33insAsnTerTyrAlaGlnTerPheHisLeuSerValCysTrpGlyThr | p.Y32_V33insN*YAQ*FHLSVCWGT | P51957 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| NEK4 | SNV | Missense_Mutation | c.403N>G | p.Gln135Glu | p.Q135E | P51957 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-C5-A3HE-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD | |
| NEK4 | SNV | Missense_Mutation | c.1344N>G | p.Ile448Met | p.I448M | P51957 | protein_coding | tolerated(0.19) | benign(0.127) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| NEK4 | SNV | Missense_Mutation | c.592N>A | p.Glu198Lys | p.E198K | P51957 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-EK-A2RJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| NEK4 | SNV | Missense_Mutation | c.2035N>A | p.Asp679Asn | p.D679N | P51957 | protein_coding | deleterious(0) | possibly_damaging(0.884) | TCGA-IR-A3LH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| NEK4 | SNV | Missense_Mutation | novel | c.618N>G | p.Phe206Leu | p.F206L | P51957 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| NEK4 | SNV | Missense_Mutation | c.2519A>T | p.Asn840Ile | p.N840I | P51957 | protein_coding | deleterious(0.01) | possibly_damaging(0.736) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| NEK4 | SNV | Missense_Mutation | rs771909270 | c.1897N>T | p.Pro633Ser | p.P633S | P51957 | protein_coding | tolerated(0.13) | possibly_damaging(0.719) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
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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 |
| 6787 | NEK4 | KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME | TAMATINIB | R-406 | ||
| 6787 | NEK4 | KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME | DOVITINIB | DOVITINIB | ||
| 6787 | NEK4 | KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME | BAY-613606 | CHEMBL541400 | ||
| 6787 | NEK4 | KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME | GW441756X | GW441756X | ||
| 6787 | NEK4 | KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME | TAE-684 | TAE-684 | ||
| 6787 | NEK4 | KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME | SNS-314 | SNS-314 | ||
| 6787 | NEK4 | KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME | CENISERTIB | CENISERTIB | ||
| 6787 | NEK4 | KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME | CYC-116 | CYC-116 | ||
| 6787 | NEK4 | KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME | PHA-767491 | CHEMBL225519 | ||
| 6787 | NEK4 | KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME | SP-600125 | SP-600125 |
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