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Gene: NKX3-1 |
Gene summary for NKX3-1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NKX3-1 | Gene ID | 4824 |
| Gene name | NK3 homeobox 1 | |
| Gene Alias | BAPX2 | |
| Cytomap | 8p21.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q99801 |
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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 |
| 4824 | NKX3-1 | M5 | Human | Breast | IDC | 7.60e-20 | 1.09e+00 | 0.1598 |
| 4824 | NKX3-1 | DCIS2 | Human | Breast | DCIS | 8.16e-16 | 8.40e-02 | 0.0085 |
| 4824 | NKX3-1 | GSM5252128_BPH327PrGF_Via | Human | Prostate | BPH | 4.24e-11 | 6.90e-01 | -0.1688 |
| 4824 | NKX3-1 | GSM5252132_BPH389PrGF | Human | Prostate | BPH | 5.00e-03 | 6.25e-01 | -0.2247 |
| 4824 | NKX3-1 | GSM5252136_BPH556PrGA1_Fcol | Human | Prostate | BPH | 4.59e-13 | 7.69e-01 | -0.23 |
| 4824 | NKX3-1 | GSM5252137_BPH556PrGA2_Fcol | Human | Prostate | BPH | 3.27e-06 | 6.72e-01 | -0.23 |
| 4824 | NKX3-1 | 047563_1562-all-cells | Human | Prostate | BPH | 4.70e-03 | -5.99e-02 | 0.0791 |
| 4824 | NKX3-1 | 048752_1579-all-cells | Human | Prostate | BPH | 3.81e-02 | 1.24e-01 | 0.1008 |
| 4824 | NKX3-1 | Dong_P1 | Human | Prostate | Tumor | 4.22e-19 | 3.16e-01 | 0.035 |
| 4824 | NKX3-1 | Dong_P3 | Human | Prostate | Tumor | 3.26e-11 | 2.43e-01 | 0.0278 |
| 4824 | NKX3-1 | Dong_P5 | Human | Prostate | Tumor | 2.33e-09 | -1.83e-01 | 0.053 |
| 4824 | NKX3-1 | GSM5353215_PA_AUG_PB_1B_S2 | Human | Prostate | Tumor | 3.42e-10 | 8.94e-01 | 0.1557 |
| 4824 | NKX3-1 | GSM5353236_PA_PR5251_T1_S7_L001 | Human | Prostate | Tumor | 3.53e-03 | 5.90e-01 | 0.1608 |
| 4824 | NKX3-1 | GSM5353237_PA_PR5251_T2_S8_L001 | Human | Prostate | Tumor | 2.98e-02 | 7.04e-01 | 0.1622 |
| 4824 | NKX3-1 | GSM5353243_PA_PR5261_T1_S23_L002 | Human | Prostate | Tumor | 6.14e-09 | 2.93e-01 | 0.1545 |
| 4824 | NKX3-1 | GSM5353244_PA_PR5261_T2_S24_L002 | Human | Prostate | Tumor | 7.39e-06 | 3.95e-01 | 0.1569 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| ∗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:200123314 | Breast | IDC | regulation of apoptotic signaling pathway | 82/1434 | 356/18723 | 6.27e-20 | 5.93e-17 | 82 |
| GO:005254714 | Breast | IDC | regulation of peptidase activity | 96/1434 | 461/18723 | 7.58e-20 | 6.15e-17 | 96 |
| GO:009719314 | Breast | IDC | intrinsic apoptotic signaling pathway | 69/1434 | 288/18723 | 6.32e-18 | 2.99e-15 | 69 |
| GO:005254814 | Breast | IDC | regulation of endopeptidase activity | 88/1434 | 432/18723 | 1.20e-17 | 4.85e-15 | 88 |
| GO:200124214 | Breast | IDC | regulation of intrinsic apoptotic signaling pathway | 47/1434 | 164/18723 | 8.25e-16 | 2.93e-13 | 47 |
| GO:004854514 | Breast | IDC | response to steroid hormone | 70/1434 | 339/18723 | 1.34e-14 | 4.23e-12 | 70 |
| GO:200011614 | Breast | IDC | regulation of cysteine-type endopeptidase activity | 55/1434 | 235/18723 | 4.25e-14 | 1.21e-11 | 55 |
| GO:004328114 | Breast | IDC | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 50/1434 | 209/18723 | 2.49e-13 | 6.14e-11 | 50 |
| GO:007048214 | Breast | IDC | response to oxygen levels | 64/1434 | 347/18723 | 3.45e-11 | 5.57e-09 | 64 |
| GO:003629314 | Breast | IDC | response to decreased oxygen levels | 60/1434 | 322/18723 | 9.26e-11 | 1.25e-08 | 60 |
| GO:004586214 | Breast | IDC | positive regulation of proteolysis | 66/1434 | 372/18723 | 9.76e-11 | 1.29e-08 | 66 |
| GO:000166614 | Breast | IDC | response to hypoxia | 58/1434 | 307/18723 | 1.09e-10 | 1.38e-08 | 58 |
| GO:200123514 | Breast | IDC | positive regulation of apoptotic signaling pathway | 31/1434 | 126/18723 | 4.13e-09 | 3.35e-07 | 31 |
| GO:001095214 | Breast | IDC | positive regulation of peptidase activity | 40/1434 | 197/18723 | 1.04e-08 | 7.67e-07 | 40 |
| GO:003629413 | Breast | IDC | cellular response to decreased oxygen levels | 34/1434 | 161/18723 | 4.73e-08 | 3.02e-06 | 34 |
| GO:007145613 | Breast | IDC | cellular response to hypoxia | 32/1434 | 151/18723 | 1.07e-07 | 6.26e-06 | 32 |
| GO:004328013 | Breast | IDC | positive regulation of cysteine-type endopeptidase activity involved in apoptotic process | 29/1434 | 129/18723 | 1.10e-07 | 6.35e-06 | 29 |
| GO:007145313 | Breast | IDC | cellular response to oxygen levels | 35/1434 | 177/18723 | 1.68e-07 | 9.10e-06 | 35 |
| GO:200124412 | Breast | IDC | positive regulation of intrinsic apoptotic signaling pathway | 18/1434 | 58/18723 | 1.73e-07 | 9.17e-06 | 18 |
| GO:200105613 | Breast | IDC | positive regulation of cysteine-type endopeptidase activity | 31/1434 | 148/18723 | 2.22e-07 | 1.17e-05 | 31 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa052159 | Prostate | BPH | Prostate cancer | 48/1718 | 97/8465 | 1.08e-10 | 1.87e-09 | 1.16e-09 | 48 |
| hsa0521514 | Prostate | BPH | Prostate cancer | 48/1718 | 97/8465 | 1.08e-10 | 1.87e-09 | 1.16e-09 | 48 |
| hsa0521523 | Prostate | Tumor | Prostate cancer | 48/1791 | 97/8465 | 4.86e-10 | 8.93e-09 | 5.54e-09 | 48 |
| hsa0521533 | Prostate | Tumor | Prostate cancer | 48/1791 | 97/8465 | 4.86e-10 | 8.93e-09 | 5.54e-09 | 48 |
| 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 |
| NKX3-1 | SEC | Liver | HCC | RP11-242D8.1,PIGA,HSPA1B, etc. | 1.89e-01 |  |
| NKX3-1 | LUM | Prostate | Healthy | NPDC1,SPDEF,STEAP2, etc. | 2.72e-01 |  |
| NKX3-1 | pDC | Prostate | ADJ | RDH11,STEAP2,KLK2, etc. | 2.24e-01 |  |
| NKX3-1 | pDC | Prostate | Tumor | RDH11,STEAP2,KLK2, etc. | 2.16e-01 |  |
| NKX3-1 | FIB | Prostate | Tumor | PMEPA1,SLC45A3,PPP3CA, etc. | 5.17e-01 | |
| ∗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 |
| NKX3-1 | SNV | Missense_Mutation | novel | c.464C>A | p.Ala155Asp | p.A155D | Q99801 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD |
| NKX3-1 | SNV | Missense_Mutation | c.538N>G | p.Lys180Glu | p.K180E | Q99801 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NKX3-1 | SNV | Missense_Mutation | c.591N>C | p.Leu197Phe | p.L197F | Q99801 | protein_coding | tolerated(0.05) | benign(0.352) | TCGA-BH-A0BZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | CR | |
| NKX3-1 | insertion | Nonsense_Mutation | novel | c.319_320insTAAAAGAGAGGGGCAAATA | p.Glu107ValfsTer7 | p.E107Vfs*7 | Q99801 | protein_coding | TCGA-B6-A0IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
| NKX3-1 | SNV | Missense_Mutation | c.526N>T | p.Arg176Cys | p.R176C | Q99801 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-A02O-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| NKX3-1 | SNV | Missense_Mutation | rs759016206 | c.340N>T | p.Pro114Ser | p.P114S | Q99801 | protein_coding | tolerated(0.1) | benign(0.009) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| NKX3-1 | SNV | Missense_Mutation | c.550N>A | p.Leu184Ile | p.L184I | Q99801 | protein_coding | tolerated(0.1) | benign(0.341) | TCGA-DY-A0XA-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Chemotherapy | mayo | CR | |
| NKX3-1 | SNV | Missense_Mutation | novel | c.334N>A | p.Ala112Thr | p.A112T | Q99801 | protein_coding | tolerated(0.37) | benign(0.001) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NKX3-1 | SNV | Missense_Mutation | c.542G>A | p.Arg181Gln | p.R181Q | Q99801 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AJ-A5DW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NKX3-1 | SNV | Missense_Mutation | c.511N>G | p.Trp171Gly | p.W171G | Q99801 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| Page: 1 2 3 |
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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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