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Gene: PNKD |
Gene summary for PNKD |
Gene summary. |
Gene information | Species | Human | Gene symbol | PNKD | Gene ID | 25953 |
Gene name | PNKD metallo-beta-lactamase domain containing | |
Gene Alias | BRP17 | |
Cytomap | 2q35 | |
Gene Type | protein-coding | GO ID | GO:0001505 | UniProtAcc | Q8N490 |
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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 |
25953 | PNKD | GSM4909281 | Human | Breast | IDC | 2.29e-12 | 5.15e-01 | 0.21 |
25953 | PNKD | GSM4909296 | Human | Breast | IDC | 1.26e-11 | 1.39e-01 | 0.1524 |
25953 | PNKD | GSM4909297 | Human | Breast | IDC | 1.37e-10 | 9.84e-02 | 0.1517 |
25953 | PNKD | GSM4909301 | Human | Breast | IDC | 2.73e-06 | 3.55e-01 | 0.1577 |
25953 | PNKD | GSM4909306 | Human | Breast | IDC | 2.03e-02 | 3.47e-01 | 0.1564 |
25953 | PNKD | GSM4909311 | Human | Breast | IDC | 1.77e-29 | -2.22e-01 | 0.1534 |
25953 | PNKD | GSM4909312 | Human | Breast | IDC | 7.69e-08 | -6.01e-02 | 0.1552 |
25953 | PNKD | GSM4909315 | Human | Breast | IDC | 1.34e-03 | 3.76e-01 | 0.21 |
25953 | PNKD | GSM4909316 | Human | Breast | IDC | 2.87e-06 | 4.45e-01 | 0.21 |
25953 | PNKD | GSM4909318 | Human | Breast | IDC | 2.29e-05 | 5.32e-01 | 0.2031 |
25953 | PNKD | GSM4909319 | Human | Breast | IDC | 1.51e-37 | -4.10e-02 | 0.1563 |
25953 | PNKD | GSM4909321 | Human | Breast | IDC | 5.43e-14 | -1.51e-01 | 0.1559 |
25953 | PNKD | NCCBC14 | Human | Breast | DCIS | 2.89e-05 | 6.52e-02 | 0.2021 |
25953 | PNKD | NCCBC5 | Human | Breast | DCIS | 1.35e-07 | -3.41e-02 | 0.2046 |
25953 | PNKD | P1 | Human | Breast | IDC | 2.22e-16 | -2.22e-01 | 0.1527 |
25953 | PNKD | DCIS2 | Human | Breast | DCIS | 5.73e-58 | 6.20e-02 | 0.0085 |
25953 | PNKD | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.55e-08 | 5.99e-01 | -0.1808 |
25953 | PNKD | HTA11_347_2000001011 | Human | Colorectum | AD | 5.00e-17 | 5.47e-01 | -0.1954 |
25953 | PNKD | HTA11_411_2000001011 | Human | Colorectum | SER | 1.28e-03 | 9.00e-01 | -0.2602 |
25953 | PNKD | HTA11_696_2000001011 | Human | Colorectum | AD | 4.66e-06 | 4.28e-01 | -0.1464 |
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Transcriptomic changes along malignancy continuum. |
∗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:00065762 | Thyroid | HT | cellular biogenic amine metabolic process | 14/1272 | 101/18723 | 8.27e-03 | 4.78e-02 | 14 |
GO:00510518 | Thyroid | PTC | negative regulation of transport | 176/5968 | 470/18723 | 5.44e-03 | 2.49e-02 | 176 |
GO:005105114 | Thyroid | ATC | negative regulation of transport | 183/6293 | 470/18723 | 8.12e-03 | 3.13e-02 | 183 |
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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 |
PNKD | SNV | Missense_Mutation | novel | c.1070N>C | p.Gly357Ala | p.G357A | Q8N490 | protein_coding | tolerated(0.61) | benign(0.003) | TCGA-A2-A3Y0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
PNKD | SNV | Missense_Mutation | novel | c.449N>T | p.Asp150Val | p.D150V | Q8N490 | protein_coding | tolerated(0.09) | probably_damaging(0.99) | TCGA-AQ-A7U7-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Targeted Molecular therapy | rituximab | CR |
PNKD | insertion | Frame_Shift_Ins | novel | c.116_117insTCCT | p.Ala40ProfsTer16 | p.A40Pfs*16 | Q8N490 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
PNKD | insertion | Frame_Shift_Ins | novel | c.117_118insCCTCAACCTCCCGAGGAGCTGGGACTACAGGC | p.Ala40ProfsTer44 | p.A40Pfs*44 | Q8N490 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
PNKD | insertion | In_Frame_Ins | novel | c.815_816insTGGCCCCCTTCA | p.Leu272_Ser273insGlyProLeuGln | p.L272_S273insGPLQ | Q8N490 | protein_coding | TCGA-BH-A0BR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
PNKD | SNV | Missense_Mutation | novel | c.341G>C | p.Arg114Pro | p.R114P | Q8N490 | protein_coding | tolerated(0.2) | benign(0.371) | TCGA-C5-A902-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
PNKD | SNV | Missense_Mutation | rs148141539 | c.1130N>A | p.Arg377Gln | p.R377Q | Q8N490 | protein_coding | tolerated(0.24) | benign(0) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
PNKD | SNV | Missense_Mutation | c.505N>A | p.Leu169Met | p.L169M | Q8N490 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
PNKD | SNV | Missense_Mutation | novel | c.899N>G | p.Phe300Cys | p.F300C | Q8N490 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
PNKD | SNV | Missense_Mutation | c.505N>A | p.Leu169Met | p.L169M | Q8N490 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AP-A056-01 | 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 |
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