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Gene: NIPAL3 |
Gene summary for NIPAL3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | NIPAL3 | Gene ID | 57185 |
Gene name | NIPA like domain containing 3 | |
Gene Alias | DJ462O23.2 | |
Cytomap | 1p36.11 | |
Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q6P499 |
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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 |
57185 | NIPAL3 | P23T-E | Human | Esophagus | ESCC | 2.74e-17 | 4.61e-01 | 0.108 |
57185 | NIPAL3 | P24T-E | Human | Esophagus | ESCC | 3.39e-04 | 5.42e-02 | 0.1287 |
57185 | NIPAL3 | P26T-E | Human | Esophagus | ESCC | 4.45e-20 | 3.00e-01 | 0.1276 |
57185 | NIPAL3 | P27T-E | Human | Esophagus | ESCC | 6.79e-19 | 3.17e-01 | 0.1055 |
57185 | NIPAL3 | P28T-E | Human | Esophagus | ESCC | 1.49e-15 | 2.03e-01 | 0.1149 |
57185 | NIPAL3 | P30T-E | Human | Esophagus | ESCC | 5.32e-15 | 4.98e-01 | 0.137 |
57185 | NIPAL3 | P31T-E | Human | Esophagus | ESCC | 3.64e-13 | 1.41e-01 | 0.1251 |
57185 | NIPAL3 | P32T-E | Human | Esophagus | ESCC | 8.90e-10 | 1.83e-01 | 0.1666 |
57185 | NIPAL3 | P36T-E | Human | Esophagus | ESCC | 4.07e-04 | 1.36e-01 | 0.1187 |
57185 | NIPAL3 | P37T-E | Human | Esophagus | ESCC | 1.43e-17 | 1.41e-01 | 0.1371 |
57185 | NIPAL3 | P39T-E | Human | Esophagus | ESCC | 2.70e-11 | 2.53e-01 | 0.0894 |
57185 | NIPAL3 | P40T-E | Human | Esophagus | ESCC | 1.72e-13 | 2.26e-01 | 0.109 |
57185 | NIPAL3 | P42T-E | Human | Esophagus | ESCC | 1.09e-11 | 2.38e-01 | 0.1175 |
57185 | NIPAL3 | P44T-E | Human | Esophagus | ESCC | 7.28e-05 | 1.08e-01 | 0.1096 |
57185 | NIPAL3 | P47T-E | Human | Esophagus | ESCC | 9.72e-08 | 8.13e-02 | 0.1067 |
57185 | NIPAL3 | P48T-E | Human | Esophagus | ESCC | 1.66e-16 | 2.26e-01 | 0.0959 |
57185 | NIPAL3 | P49T-E | Human | Esophagus | ESCC | 9.51e-09 | 4.09e-01 | 0.1768 |
57185 | NIPAL3 | P52T-E | Human | Esophagus | ESCC | 1.53e-13 | 2.44e-01 | 0.1555 |
57185 | NIPAL3 | P54T-E | Human | Esophagus | ESCC | 3.41e-20 | 3.41e-01 | 0.0975 |
57185 | NIPAL3 | P57T-E | Human | Esophagus | ESCC | 1.29e-14 | 2.49e-01 | 0.0926 |
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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:1903830 | Colorectum | FAP | magnesium ion transmembrane transport | 7/2622 | 17/18723 | 5.62e-03 | 3.61e-02 | 7 |
GO:0015693 | Colorectum | FAP | magnesium ion transport | 7/2622 | 18/18723 | 8.10e-03 | 4.77e-02 | 7 |
GO:19038301 | Colorectum | CRC | magnesium ion transmembrane transport | 7/2078 | 17/18723 | 1.46e-03 | 1.57e-02 | 7 |
GO:00156931 | Colorectum | CRC | magnesium ion transport | 7/2078 | 18/18723 | 2.16e-03 | 2.11e-02 | 7 |
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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 |
NIPAL3 | SNV | Missense_Mutation | rs150713534 | c.290N>T | p.Ala97Val | p.A97V | Q6P499 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-D8-A1JD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
NIPAL3 | SNV | Missense_Mutation | c.793C>A | p.Gln265Lys | p.Q265K | Q6P499 | protein_coding | tolerated(1) | benign(0.056) | TCGA-E9-A1NC-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR | |
NIPAL3 | SNV | Missense_Mutation | novel | c.680T>C | p.Leu227Pro | p.L227P | Q6P499 | protein_coding | deleterious(0.03) | benign(0.012) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
NIPAL3 | SNV | Missense_Mutation | novel | c.1117G>A | p.Glu373Lys | p.E373K | Q6P499 | protein_coding | tolerated(0.6) | probably_damaging(0.971) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
NIPAL3 | SNV | Missense_Mutation | rs141630558 | c.773N>T | p.Ala258Val | p.A258V | Q6P499 | protein_coding | deleterious(0.01) | benign(0.063) | TCGA-A6-5660-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Ancillary | leucovorin | SD |
NIPAL3 | SNV | Missense_Mutation | c.190N>G | p.Ser64Ala | p.S64A | Q6P499 | protein_coding | tolerated(0.56) | benign(0.003) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
NIPAL3 | SNV | Missense_Mutation | rs200419498 | c.109N>A | p.Ala37Thr | p.A37T | Q6P499 | protein_coding | tolerated(0.6) | benign(0.023) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
NIPAL3 | SNV | Missense_Mutation | c.799N>A | p.Tyr267Asn | p.Y267N | Q6P499 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
NIPAL3 | SNV | Missense_Mutation | novel | c.599N>G | p.Asn200Ser | p.N200S | Q6P499 | protein_coding | tolerated(0.06) | benign(0.01) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NIPAL3 | SNV | Missense_Mutation | c.491N>A | p.Gly164Asp | p.G164D | Q6P499 | protein_coding | deleterious(0) | possibly_damaging(0.812) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | 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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