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Gene: NEK2 |
Gene summary for NEK2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NEK2 | Gene ID | 4751 |
| Gene name | NIMA related kinase 2 | |
| Gene Alias | HsPK21 | |
| Cytomap | 1q32.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | F6U4U2 |
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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 |
| 4751 | NEK2 | LZE2T | Human | Esophagus | ESCC | 3.16e-03 | 7.32e-01 | 0.082 |
| 4751 | NEK2 | P2T-E | Human | Esophagus | ESCC | 9.56e-08 | 3.38e-01 | 0.1177 |
| 4751 | NEK2 | P4T-E | Human | Esophagus | ESCC | 8.76e-05 | 3.53e-01 | 0.1323 |
| 4751 | NEK2 | P5T-E | Human | Esophagus | ESCC | 4.12e-11 | 2.45e-01 | 0.1327 |
| 4751 | NEK2 | P21T-E | Human | Esophagus | ESCC | 8.40e-04 | 1.69e-01 | 0.1617 |
| 4751 | NEK2 | P24T-E | Human | Esophagus | ESCC | 2.05e-07 | 3.04e-01 | 0.1287 |
| 4751 | NEK2 | P28T-E | Human | Esophagus | ESCC | 1.78e-03 | 9.94e-02 | 0.1149 |
| 4751 | NEK2 | P32T-E | Human | Esophagus | ESCC | 9.44e-07 | 2.53e-01 | 0.1666 |
| 4751 | NEK2 | P52T-E | Human | Esophagus | ESCC | 9.20e-06 | 2.37e-01 | 0.1555 |
| 4751 | NEK2 | P74T-E | Human | Esophagus | ESCC | 5.09e-08 | 5.73e-01 | 0.1479 |
| 4751 | NEK2 | P75T-E | Human | Esophagus | ESCC | 7.90e-03 | 1.73e-01 | 0.1125 |
| 4751 | NEK2 | P76T-E | Human | Esophagus | ESCC | 8.84e-05 | 3.39e-01 | 0.1207 |
| 4751 | NEK2 | P79T-E | Human | Esophagus | ESCC | 1.66e-02 | 1.32e-01 | 0.1154 |
| 4751 | NEK2 | P83T-E | Human | Esophagus | ESCC | 1.26e-07 | 3.80e-01 | 0.1738 |
| 4751 | NEK2 | P91T-E | Human | Esophagus | ESCC | 2.72e-02 | 9.43e-01 | 0.1828 |
| 4751 | NEK2 | P107T-E | Human | Esophagus | ESCC | 2.60e-09 | 3.12e-01 | 0.171 |
| 4751 | NEK2 | P130T-E | Human | Esophagus | ESCC | 4.24e-18 | 8.39e-01 | 0.1676 |
| 4751 | NEK2 | P2_cSCC | Human | Skin | cSCC | 2.98e-04 | 2.28e-01 | -0.024 |
| 4751 | NEK2 | P4_cSCC | Human | Skin | cSCC | 4.65e-08 | 2.53e-01 | -0.00290000000000005 |
| 4751 | NEK2 | P10_cSCC | Human | Skin | cSCC | 1.79e-08 | 2.89e-01 | 0.1017 |
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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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:014001414 | Esophagus | ESCC | mitotic nuclear division | 218/8552 | 287/18723 | 6.17e-26 | 1.78e-23 | 218 |
| GO:000007011 | Esophagus | ESCC | mitotic sister chromatid segregation | 138/8552 | 168/18723 | 1.37e-22 | 2.63e-20 | 138 |
| GO:00008194 | Esophagus | ESCC | sister chromatid segregation | 157/8552 | 202/18723 | 8.41e-21 | 1.33e-18 | 157 |
| GO:0051098111 | Esophagus | ESCC | regulation of binding | 251/8552 | 363/18723 | 6.73e-20 | 8.46e-18 | 251 |
| GO:003304416 | Esophagus | ESCC | regulation of chromosome organization | 145/8552 | 187/18723 | 3.80e-19 | 4.31e-17 | 145 |
| GO:000705911 | Esophagus | ESCC | chromosome segregation | 238/8552 | 346/18723 | 1.72e-18 | 1.82e-16 | 238 |
| GO:190285015 | Esophagus | ESCC | microtubule cytoskeleton organization involved in mitosis | 116/8552 | 147/18723 | 1.25e-16 | 9.91e-15 | 116 |
| GO:000734615 | Esophagus | ESCC | regulation of mitotic cell cycle | 293/8552 | 457/18723 | 8.00e-16 | 5.64e-14 | 293 |
| GO:000170119 | Esophagus | ESCC | in utero embryonic development | 243/8552 | 367/18723 | 1.00e-15 | 6.86e-14 | 243 |
| GO:000705214 | Esophagus | ESCC | mitotic spindle organization | 97/8552 | 120/18723 | 2.17e-15 | 1.33e-13 | 97 |
| GO:000705114 | Esophagus | ESCC | spindle organization | 134/8552 | 184/18723 | 5.70e-14 | 2.87e-12 | 134 |
| GO:005105215 | Esophagus | ESCC | regulation of DNA metabolic process | 232/8552 | 359/18723 | 2.40e-13 | 1.13e-11 | 232 |
| GO:00482853 | Esophagus | ESCC | organelle fission | 301/8552 | 488/18723 | 4.64e-13 | 2.12e-11 | 301 |
| GO:00988133 | Esophagus | ESCC | nuclear chromosome segregation | 187/8552 | 281/18723 | 1.00e-12 | 4.36e-11 | 187 |
| GO:000072319 | Esophagus | ESCC | telomere maintenance | 99/8552 | 131/18723 | 2.68e-12 | 1.08e-10 | 99 |
| GO:007189716 | Esophagus | ESCC | DNA biosynthetic process | 127/8552 | 180/18723 | 1.04e-11 | 3.85e-10 | 127 |
| GO:00002802 | Esophagus | ESCC | nuclear division | 270/8552 | 439/18723 | 1.17e-11 | 4.24e-10 | 270 |
| GO:005105417 | Esophagus | ESCC | positive regulation of DNA metabolic process | 139/8552 | 201/18723 | 1.20e-11 | 4.33e-10 | 139 |
| GO:200057319 | Esophagus | ESCC | positive regulation of DNA biosynthetic process | 56/8552 | 66/18723 | 4.51e-11 | 1.45e-09 | 56 |
| GO:003220417 | Esophagus | ESCC | regulation of telomere maintenance | 65/8552 | 80/18723 | 6.02e-11 | 1.90e-09 | 65 |
| Page: 1 2 3 4 5 6 |
| 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 |
| NEK2 | SNV | Missense_Mutation | c.463N>A | p.Val155Ile | p.V155I | P51955 | protein_coding | tolerated(0.12) | possibly_damaging(0.742) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| NEK2 | SNV | Missense_Mutation | c.112N>C | p.Glu38Gln | p.E38Q | P51955 | protein_coding | deleterious(0.03) | possibly_damaging(0.806) | TCGA-EK-A2PM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NEK2 | SNV | Missense_Mutation | c.887N>T | p.Ser296Leu | p.S296L | P51955 | protein_coding | tolerated(0.71) | benign(0) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NEK2 | SNV | Missense_Mutation | c.908T>C | p.Leu303Ser | p.L303S | P51955 | protein_coding | tolerated(0.43) | benign(0) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| NEK2 | SNV | Missense_Mutation | novel | c.433N>A | p.Ala145Thr | p.A145T | P51955 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NEK2 | SNV | Missense_Mutation | c.554C>T | p.Pro185Leu | p.P185L | P51955 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| NEK2 | SNV | Missense_Mutation | c.527T>G | p.Phe176Cys | p.F176C | P51955 | protein_coding | deleterious(0.03) | probably_damaging(0.988) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| NEK2 | SNV | Missense_Mutation | c.1268N>A | p.Arg423Gln | p.R423Q | P51955 | protein_coding | deleterious_low_confidence(0.04) | possibly_damaging(0.685) | TCGA-AG-A015-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| NEK2 | SNV | Missense_Mutation | rs763584429 | c.1010N>A | p.Arg337His | p.R337H | P51955 | protein_coding | deleterious(0.01) | probably_damaging(0.96) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NEK2 | SNV | Missense_Mutation | c.1327N>T | p.Gly443Cys | p.G443C | P51955 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.995) | TCGA-A5-A0VP-01 | Endometrium | uterine corpus endometrioid carcinoma | 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 |
| 4751 | NEK2 | ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE | AZD-1775 | ADAVOSERTIB | ||
| 4751 | NEK2 | ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE | DNDI1417467 | CHEMBL1997335 | ||
| 4751 | NEK2 | ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE | inhibitor | HESPERADIN | HESPERADIN | 19035792 |
| 4751 | NEK2 | ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE | GW441756X | GW441756X | ||
| 4751 | NEK2 | ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE | TAMATINIB | R-406 | ||
| 4751 | NEK2 | ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE | TAE-684 | TAE-684 | ||
| 4751 | NEK2 | ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE | DACTOLISIB | DACTOLISIB | ||
| 4751 | NEK2 | ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE | CENISERTIB | CENISERTIB | ||
| 4751 | NEK2 | ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE | inhibitor | 249565829 | ||
| 4751 | NEK2 | ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE | PAZOPANIB | PAZOPANIB |
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