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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 | HTA11_3410_2000001011 | Human | Colorectum | AD | 5.90e-11 | 2.46e-01 | 0.0155 |
| 27031 | NPHP3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 6.13e-19 | 4.62e-01 | -0.1808 |
| 27031 | NPHP3 | HTA11_2951_2000001011 | Human | Colorectum | AD | 3.22e-05 | 3.36e-01 | 0.0216 |
| 27031 | NPHP3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 4.60e-24 | 6.33e-01 | -0.0811 |
| 27031 | NPHP3 | HTA11_78_2000001011 | Human | Colorectum | AD | 7.85e-13 | 3.92e-01 | -0.1088 |
| 27031 | NPHP3 | HTA11_347_2000001011 | Human | Colorectum | AD | 5.98e-43 | 7.58e-01 | -0.1954 |
| 27031 | NPHP3 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.86e-06 | 3.68e-01 | -0.2602 |
| 27031 | NPHP3 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.71e-03 | 3.67e-01 | -0.2196 |
| 27031 | NPHP3 | HTA11_3361_2000001011 | Human | Colorectum | AD | 9.32e-14 | 3.99e-01 | -0.1207 |
| 27031 | NPHP3 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.45e-18 | 4.88e-01 | -0.1526 |
| 27031 | NPHP3 | HTA11_696_2000001011 | Human | Colorectum | AD | 9.02e-22 | 3.75e-01 | -0.1464 |
| 27031 | NPHP3 | HTA11_866_2000001011 | Human | Colorectum | AD | 3.10e-42 | 6.75e-01 | -0.1001 |
| 27031 | NPHP3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 5.12e-18 | 4.15e-01 | -0.059 |
| 27031 | NPHP3 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.72e-05 | 3.33e-01 | -0.1706 |
| 27031 | NPHP3 | HTA11_5216_2000001011 | Human | Colorectum | SER | 2.49e-08 | 4.15e-01 | -0.1462 |
| 27031 | NPHP3 | HTA11_546_2000001011 | Human | Colorectum | AD | 4.31e-15 | 5.06e-01 | -0.0842 |
| 27031 | NPHP3 | HTA11_9341_2000001011 | Human | Colorectum | SER | 1.35e-12 | 6.00e-01 | -0.00410000000000005 |
| 27031 | NPHP3 | HTA11_7862_2000001011 | Human | Colorectum | AD | 4.04e-16 | 6.27e-01 | -0.0179 |
| 27031 | NPHP3 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.22e-19 | 3.85e-01 | 0.096 |
| 27031 | NPHP3 | HTA11_4255_2000001011 | Human | Colorectum | SER | 1.84e-10 | 5.85e-01 | 0.0446 |
| 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:003032311 | Liver | HCC | respiratory tube development | 95/7958 | 181/18723 | 4.15e-03 | 1.81e-02 | 95 |
| GO:00018384 | Liver | HCC | embryonic epithelial tube formation | 66/7958 | 121/18723 | 4.94e-03 | 2.07e-02 | 66 |
| GO:00721754 | Liver | HCC | epithelial tube formation | 70/7958 | 132/18723 | 9.29e-03 | 3.57e-02 | 70 |
| GO:003032411 | Liver | HCC | lung development | 91/7958 | 177/18723 | 1.01e-02 | 3.80e-02 | 91 |
| GO:00351484 | Liver | HCC | tube formation | 77/7958 | 148/18723 | 1.20e-02 | 4.39e-02 | 77 |
| GO:0016055110 | Thyroid | PTC | Wnt signaling pathway | 217/5968 | 444/18723 | 3.71e-14 | 2.30e-12 | 217 |
| GO:0198738110 | Thyroid | PTC | cell-cell signaling by wnt | 217/5968 | 446/18723 | 6.68e-14 | 3.73e-12 | 217 |
| GO:0030111110 | Thyroid | PTC | regulation of Wnt signaling pathway | 163/5968 | 328/18723 | 1.05e-11 | 4.29e-10 | 163 |
| GO:0060828110 | Thyroid | PTC | regulation of canonical Wnt signaling pathway | 123/5968 | 253/18723 | 1.83e-08 | 4.26e-07 | 123 |
| GO:0048732113 | Thyroid | PTC | gland development | 193/5968 | 436/18723 | 2.88e-08 | 6.42e-07 | 193 |
| GO:0001889112 | Thyroid | PTC | liver development | 79/5968 | 147/18723 | 3.08e-08 | 6.82e-07 | 79 |
| GO:0061008112 | Thyroid | PTC | hepaticobiliary system development | 80/5968 | 150/18723 | 3.94e-08 | 8.55e-07 | 80 |
| GO:0060070110 | Thyroid | PTC | canonical Wnt signaling pathway | 141/5968 | 303/18723 | 5.71e-08 | 1.21e-06 | 141 |
| GO:000184118 | Thyroid | PTC | neural tube formation | 58/5968 | 102/18723 | 1.59e-07 | 3.03e-06 | 58 |
| GO:000182215 | Thyroid | PTC | kidney development | 133/5968 | 293/18723 | 7.57e-07 | 1.18e-05 | 133 |
| GO:000183817 | Thyroid | PTC | embryonic epithelial tube formation | 64/5968 | 121/18723 | 1.27e-06 | 1.83e-05 | 64 |
| GO:000165517 | Thyroid | PTC | urogenital system development | 149/5968 | 338/18723 | 1.41e-06 | 2.01e-05 | 149 |
| GO:007200114 | Thyroid | PTC | renal system development | 135/5968 | 302/18723 | 1.76e-06 | 2.43e-05 | 135 |
| GO:001402016 | Thyroid | PTC | primary neural tube formation | 52/5968 | 94/18723 | 2.14e-06 | 2.89e-05 | 52 |
| GO:002191514 | Thyroid | PTC | neural tube development | 76/5968 | 152/18723 | 2.40e-06 | 3.17e-05 | 76 |
| 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 |
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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 |
| 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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