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Gene: NPHP3 |
Gene summary for NPHP3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NPHP3 | Gene ID | 27031 |
| Gene name | nephrocystin 3 | |
| Gene Alias | CFAP31 | |
| Cytomap | 3q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0001655 | UniProtAcc | Q7Z494 |
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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 |
| 27031 | NPHP3 | S029 | Human | Liver | HCC | 4.57e-02 | 1.03e-01 | 0.2581 |
| 27031 | NPHP3 | HTA12-25-1 | Human | Pancreas | PDAC | 7.76e-06 | 5.97e-01 | 0.313 |
| 27031 | NPHP3 | HTA12-26-1 | Human | Pancreas | PDAC | 2.03e-06 | 5.13e-01 | 0.3728 |
| 27031 | NPHP3 | HTA12-29-1 | Human | Pancreas | PDAC | 6.31e-20 | 5.26e-01 | 0.3722 |
| 27031 | NPHP3 | male-WTA | Human | Thyroid | PTC | 6.71e-12 | 1.33e-01 | 0.1037 |
| 27031 | NPHP3 | PTC01 | Human | Thyroid | PTC | 3.98e-12 | 2.49e-01 | 0.1899 |
| 27031 | NPHP3 | PTC04 | Human | Thyroid | PTC | 4.39e-17 | 2.84e-01 | 0.1927 |
| 27031 | NPHP3 | PTC05 | Human | Thyroid | PTC | 9.68e-17 | 5.60e-01 | 0.2065 |
| 27031 | NPHP3 | PTC06 | Human | Thyroid | PTC | 1.30e-19 | 5.17e-01 | 0.2057 |
| 27031 | NPHP3 | PTC07 | Human | Thyroid | PTC | 5.08e-15 | 3.18e-01 | 0.2044 |
| 27031 | NPHP3 | ATC09 | Human | Thyroid | ATC | 9.61e-08 | 2.09e-01 | 0.2871 |
| 27031 | NPHP3 | ATC11 | Human | Thyroid | ATC | 3.32e-04 | 5.33e-01 | 0.3386 |
| 27031 | NPHP3 | ATC12 | Human | Thyroid | ATC | 9.57e-11 | 2.06e-01 | 0.34 |
| 27031 | NPHP3 | ATC13 | Human | Thyroid | ATC | 1.67e-27 | 4.30e-01 | 0.34 |
| 27031 | NPHP3 | ATC1 | Human | Thyroid | ATC | 6.06e-08 | 2.42e-01 | 0.2878 |
| 27031 | NPHP3 | ATC2 | Human | Thyroid | ATC | 3.77e-09 | 5.63e-01 | 0.34 |
| 27031 | NPHP3 | ATC3 | Human | Thyroid | ATC | 1.62e-09 | 6.72e-01 | 0.338 |
| 27031 | NPHP3 | ATC4 | Human | Thyroid | ATC | 1.58e-12 | 2.87e-01 | 0.34 |
| 27031 | NPHP3 | ATC5 | Human | Thyroid | ATC | 6.45e-28 | 4.66e-01 | 0.34 |
| Page: 1 2 3 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:0048732 | Colorectum | AD | gland development | 149/3918 | 436/18723 | 6.07e-11 | 6.33e-09 | 149 |
| GO:0061008 | Colorectum | AD | hepaticobiliary system development | 55/3918 | 150/18723 | 6.34e-06 | 1.59e-04 | 55 |
| GO:0001889 | Colorectum | AD | liver development | 54/3918 | 147/18723 | 7.20e-06 | 1.77e-04 | 54 |
| GO:0030111 | Colorectum | AD | regulation of Wnt signaling pathway | 102/3918 | 328/18723 | 8.51e-06 | 2.03e-04 | 102 |
| GO:0016055 | Colorectum | AD | Wnt signaling pathway | 130/3918 | 444/18723 | 1.60e-05 | 3.37e-04 | 130 |
| GO:0198738 | Colorectum | AD | cell-cell signaling by wnt | 130/3918 | 446/18723 | 2.02e-05 | 4.10e-04 | 130 |
| GO:0060249 | Colorectum | AD | anatomical structure homeostasis | 94/3918 | 314/18723 | 9.37e-05 | 1.42e-03 | 94 |
| GO:0060070 | Colorectum | AD | canonical Wnt signaling pathway | 90/3918 | 303/18723 | 1.76e-04 | 2.38e-03 | 90 |
| GO:0001894 | Colorectum | AD | tissue homeostasis | 81/3918 | 268/18723 | 1.96e-04 | 2.62e-03 | 81 |
| GO:0060828 | Colorectum | AD | regulation of canonical Wnt signaling pathway | 77/3918 | 253/18723 | 2.19e-04 | 2.87e-03 | 77 |
| GO:0060562 | Colorectum | AD | epithelial tube morphogenesis | 93/3918 | 325/18723 | 5.65e-04 | 6.00e-03 | 93 |
| GO:0014020 | Colorectum | AD | primary neural tube formation | 33/3918 | 94/18723 | 1.02e-03 | 9.50e-03 | 33 |
| GO:0001841 | Colorectum | AD | neural tube formation | 35/3918 | 102/18723 | 1.16e-03 | 1.05e-02 | 35 |
| GO:0045995 | Colorectum | AD | regulation of embryonic development | 24/3918 | 64/18723 | 1.72e-03 | 1.43e-02 | 24 |
| GO:0001843 | Colorectum | AD | neural tube closure | 30/3918 | 88/18723 | 2.83e-03 | 2.12e-02 | 30 |
| GO:0060606 | Colorectum | AD | tube closure | 30/3918 | 89/18723 | 3.42e-03 | 2.49e-02 | 30 |
| GO:0035148 | Colorectum | AD | tube formation | 45/3918 | 148/18723 | 4.13e-03 | 2.87e-02 | 45 |
| GO:0001738 | Colorectum | AD | morphogenesis of a polarized epithelium | 31/3918 | 94/18723 | 4.30e-03 | 2.95e-02 | 31 |
| GO:0001838 | Colorectum | AD | embryonic epithelial tube formation | 38/3918 | 121/18723 | 4.40e-03 | 3.01e-02 | 38 |
| GO:0048568 | Colorectum | AD | embryonic organ development | 112/3918 | 427/18723 | 4.60e-03 | 3.14e-02 | 112 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 |
| 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 |
| NPHP3 | SNV | Missense_Mutation | novel | c.1655N>A | p.Pro552His | p.P552H | Q7Z494 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A7-A0DB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| NPHP3 | SNV | Missense_Mutation | rs758498695 | c.988N>A | p.Glu330Lys | p.E330K | Q7Z494 | protein_coding | deleterious(0.03) | probably_damaging(0.969) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| NPHP3 | SNV | Missense_Mutation | c.790N>C | p.Asp264His | p.D264H | Q7Z494 | protein_coding | deleterious(0) | probably_damaging(0.937) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| NPHP3 | SNV | Missense_Mutation | c.688N>C | p.Glu230Gln | p.E230Q | Q7Z494 | protein_coding | tolerated(0.05) | benign(0.177) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| NPHP3 | insertion | Frame_Shift_Ins | novel | c.1752_1753insATATATGTGT | p.His585IlefsTer17 | p.H585Ifs*17 | Q7Z494 | protein_coding | TCGA-A8-A0A4-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | CR | ||
| NPHP3 | SNV | Missense_Mutation | c.2800N>A | p.Glu934Lys | p.E934K | Q7Z494 | protein_coding | tolerated(0.34) | benign(0.078) | TCGA-EK-A2PG-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NPHP3 | SNV | Missense_Mutation | rs150867534 | c.2986N>A | p.Val996Met | p.V996M | Q7Z494 | protein_coding | tolerated(0.18) | benign(0.059) | TCGA-A6-6654-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | oxaliplatin | SD |
| NPHP3 | SNV | Missense_Mutation | c.982N>C | p.Met328Leu | p.M328L | Q7Z494 | protein_coding | tolerated(0.85) | benign(0) | TCGA-AA-3982-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| NPHP3 | SNV | Missense_Mutation | novel | c.2383T>G | p.Ser795Ala | p.S795A | Q7Z494 | protein_coding | tolerated(0.14) | benign(0.005) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
| NPHP3 | SNV | Missense_Mutation | c.1432N>A | p.Gly478Ser | p.G478S | Q7Z494 | protein_coding | tolerated(0.09) | possibly_damaging(0.833) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 |
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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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