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Gene: NPHP1 |
Gene summary for NPHP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NPHP1 | Gene ID | 4867 |
| Gene name | nephrocystin 1 | |
| Gene Alias | JBTS4 | |
| Cytomap | 2q13 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | O15259 |
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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 |
| 4867 | NPHP1 | P2T-E | Human | Esophagus | ESCC | 7.17e-07 | 1.65e-01 | 0.1177 |
| 4867 | NPHP1 | P4T-E | Human | Esophagus | ESCC | 1.94e-05 | 7.52e-02 | 0.1323 |
| 4867 | NPHP1 | P5T-E | Human | Esophagus | ESCC | 3.40e-03 | 8.76e-02 | 0.1327 |
| 4867 | NPHP1 | P8T-E | Human | Esophagus | ESCC | 6.87e-04 | 7.53e-02 | 0.0889 |
| 4867 | NPHP1 | P9T-E | Human | Esophagus | ESCC | 2.49e-04 | 6.77e-02 | 0.1131 |
| 4867 | NPHP1 | P10T-E | Human | Esophagus | ESCC | 1.02e-09 | 2.47e-01 | 0.116 |
| 4867 | NPHP1 | P11T-E | Human | Esophagus | ESCC | 4.72e-06 | 2.61e-01 | 0.1426 |
| 4867 | NPHP1 | P15T-E | Human | Esophagus | ESCC | 7.69e-05 | 8.58e-02 | 0.1149 |
| 4867 | NPHP1 | P16T-E | Human | Esophagus | ESCC | 7.48e-08 | 1.82e-01 | 0.1153 |
| 4867 | NPHP1 | P20T-E | Human | Esophagus | ESCC | 1.44e-02 | 6.90e-02 | 0.1124 |
| 4867 | NPHP1 | P21T-E | Human | Esophagus | ESCC | 2.19e-14 | 3.37e-01 | 0.1617 |
| 4867 | NPHP1 | P23T-E | Human | Esophagus | ESCC | 1.58e-02 | 5.30e-02 | 0.108 |
| 4867 | NPHP1 | P24T-E | Human | Esophagus | ESCC | 4.49e-06 | 1.07e-01 | 0.1287 |
| 4867 | NPHP1 | P26T-E | Human | Esophagus | ESCC | 1.00e-06 | 1.94e-01 | 0.1276 |
| 4867 | NPHP1 | P27T-E | Human | Esophagus | ESCC | 1.46e-02 | 9.12e-02 | 0.1055 |
| 4867 | NPHP1 | P32T-E | Human | Esophagus | ESCC | 2.13e-06 | 1.77e-01 | 0.1666 |
| 4867 | NPHP1 | P42T-E | Human | Esophagus | ESCC | 1.85e-02 | 6.31e-02 | 0.1175 |
| 4867 | NPHP1 | P48T-E | Human | Esophagus | ESCC | 1.65e-03 | 9.36e-02 | 0.0959 |
| 4867 | NPHP1 | P49T-E | Human | Esophagus | ESCC | 1.05e-02 | 1.97e-01 | 0.1768 |
| 4867 | NPHP1 | P54T-E | Human | Esophagus | ESCC | 1.09e-04 | 9.67e-02 | 0.0975 |
| Page: 1 2 |
| 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 |
| ∗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:000931419 | Esophagus | ESCC | response to radiation | 277/8552 | 456/18723 | 4.42e-11 | 1.43e-09 | 277 |
| GO:000941611 | Esophagus | ESCC | response to light stimulus | 183/8552 | 320/18723 | 2.03e-05 | 1.76e-04 | 183 |
| GO:00017387 | Esophagus | ESCC | morphogenesis of a polarized epithelium | 63/8552 | 94/18723 | 2.34e-05 | 2.00e-04 | 63 |
| GO:003432918 | Esophagus | ESCC | cell junction assembly | 227/8552 | 420/18723 | 3.06e-04 | 1.83e-03 | 227 |
| GO:004521620 | Esophagus | ESCC | cell-cell junction organization | 114/8552 | 200/18723 | 8.04e-04 | 4.16e-03 | 114 |
| GO:00017361 | Esophagus | ESCC | establishment of planar polarity | 45/8552 | 72/18723 | 2.97e-03 | 1.24e-02 | 45 |
| GO:00071641 | Esophagus | ESCC | establishment of tissue polarity | 45/8552 | 72/18723 | 2.97e-03 | 1.24e-02 | 45 |
| GO:004329718 | Esophagus | ESCC | apical junction assembly | 48/8552 | 78/18723 | 3.45e-03 | 1.41e-02 | 48 |
| GO:190188810 | Esophagus | ESCC | regulation of cell junction assembly | 109/8552 | 204/18723 | 1.53e-02 | 4.96e-02 | 109 |
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| 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 |
| NPHP1 | SNV | Missense_Mutation | c.1887N>A | p.Ser629Arg | p.S629R | O15259 | protein_coding | deleterious(0) | possibly_damaging(0.865) | TCGA-A8-A09A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| NPHP1 | SNV | Missense_Mutation | c.1382N>T | p.Ser461Phe | p.S461F | O15259 | protein_coding | deleterious(0.02) | probably_damaging(0.994) | TCGA-A8-A0A7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NPHP1 | SNV | Missense_Mutation | c.1432N>T | p.Arg478Cys | p.R478C | O15259 | protein_coding | deleterious(0.04) | benign(0.03) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NPHP1 | SNV | Missense_Mutation | rs753700300 | c.1225N>T | p.Arg409Cys | p.R409C | O15259 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-B6-A0IK-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| NPHP1 | SNV | Missense_Mutation | c.247N>C | p.Glu83Gln | p.E83Q | O15259 | protein_coding | tolerated(0.23) | possibly_damaging(0.56) | TCGA-B6-A0IK-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| NPHP1 | SNV | Missense_Mutation | rs756812918 | c.1733C>T | p.Ser578Phe | p.S578F | O15259 | protein_coding | tolerated(0.65) | benign(0.15) | TCGA-C8-A3M7-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| NPHP1 | deletion | Frame_Shift_Del | rs766524637,rs886042650 | c.555delN | p.Lys185AsnfsTer7 | p.K185Nfs*7 | O15259 | protein_coding | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | ||
| NPHP1 | SNV | Missense_Mutation | novel | c.1940A>G | p.Glu647Gly | p.E647G | O15259 | protein_coding | deleterious(0.04) | probably_damaging(0.999) | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| NPHP1 | SNV | Missense_Mutation | novel | c.1939G>A | p.Glu647Lys | p.E647K | O15259 | protein_coding | tolerated(0.05) | probably_damaging(0.997) | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| NPHP1 | SNV | Missense_Mutation | rs753700300 | c.1225N>T | p.Arg409Cys | p.R409C | O15259 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | 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 |
| Page: 1 |
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