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Gene: NPTX2 |
Gene summary for NPTX2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | NPTX2 | Gene ID | 4885 |
Gene name | neuronal pentraxin 2 | |
Gene Alias | NARP | |
Cytomap | 7q22.1 | |
Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | P47972 |
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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 |
4885 | NPTX2 | P2T-E | Human | Esophagus | ESCC | 4.79e-93 | 2.49e+00 | 0.1177 |
4885 | NPTX2 | P5T-E | Human | Esophagus | ESCC | 1.78e-03 | 1.38e-01 | 0.1327 |
4885 | NPTX2 | P11T-E | Human | Esophagus | ESCC | 2.94e-14 | 5.83e-01 | 0.1426 |
4885 | NPTX2 | P16T-E | Human | Esophagus | ESCC | 4.26e-95 | 2.13e+00 | 0.1153 |
4885 | NPTX2 | P19T-E | Human | Esophagus | ESCC | 4.64e-06 | 6.95e-01 | 0.1662 |
4885 | NPTX2 | P22T-E | Human | Esophagus | ESCC | 3.97e-04 | 1.26e-01 | 0.1236 |
4885 | NPTX2 | P24T-E | Human | Esophagus | ESCC | 2.06e-08 | 2.49e-01 | 0.1287 |
4885 | NPTX2 | P27T-E | Human | Esophagus | ESCC | 9.56e-08 | 3.58e-01 | 0.1055 |
4885 | NPTX2 | P31T-E | Human | Esophagus | ESCC | 1.66e-02 | 1.28e-01 | 0.1251 |
4885 | NPTX2 | P36T-E | Human | Esophagus | ESCC | 2.82e-02 | 5.56e-01 | 0.1187 |
4885 | NPTX2 | P44T-E | Human | Esophagus | ESCC | 6.93e-04 | 1.71e-01 | 0.1096 |
4885 | NPTX2 | P56T-E | Human | Esophagus | ESCC | 1.11e-24 | 4.90e+00 | 0.1613 |
4885 | NPTX2 | P61T-E | Human | Esophagus | ESCC | 5.46e-11 | 2.79e-01 | 0.099 |
4885 | NPTX2 | P65T-E | Human | Esophagus | ESCC | 2.06e-03 | 1.68e-01 | 0.0978 |
4885 | NPTX2 | P107T-E | Human | Esophagus | ESCC | 5.65e-12 | 3.88e-01 | 0.171 |
4885 | NPTX2 | ATC13 | Human | Thyroid | ATC | 2.71e-09 | 1.71e-01 | 0.34 |
4885 | NPTX2 | ATC2 | Human | Thyroid | ATC | 3.34e-11 | 1.29e+00 | 0.34 |
4885 | NPTX2 | ATC5 | Human | Thyroid | ATC | 5.71e-10 | 2.01e-01 | 0.34 |
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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 |
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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 |
NPTX2 | SNV | Missense_Mutation | novel | c.986N>A | p.Gly329Glu | p.G329E | P47972 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CV-7422-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
NPTX2 | SNV | Missense_Mutation | novel | c.1159G>A | p.Glu387Lys | p.E387K | P47972 | protein_coding | deleterious(0) | possibly_damaging(0.579) | TCGA-D6-6516-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
NPTX2 | SNV | Missense_Mutation | novel | c.679G>C | p.Val227Leu | p.V227L | P47972 | protein_coding | tolerated(0.95) | benign(0.017) | TCGA-D6-6824-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
NPTX2 | SNV | Missense_Mutation | c.956G>T | p.Arg319Leu | p.R319L | P47972 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-G9-6377-01 | Prostate | prostate adenocarcinoma | Male | <65 | 7 | Unknown | Unknown | SD | |
NPTX2 | SNV | Missense_Mutation | novel | c.1003G>T | p.Gly335Trp | p.G335W | P47972 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BR-7716-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NPTX2 | SNV | Missense_Mutation | rs769298573 | c.1151N>A | p.Arg384His | p.R384H | P47972 | protein_coding | tolerated(0.06) | possibly_damaging(0.708) | TCGA-BR-8080-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
NPTX2 | SNV | Missense_Mutation | rs756274665 | c.695N>A | p.Arg232His | p.R232H | P47972 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-BR-8372-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | etoposide | CR |
NPTX2 | SNV | Missense_Mutation | c.910G>A | p.Val304Ile | p.V304I | P47972 | protein_coding | tolerated(0.98) | benign(0.015) | TCGA-CD-A4MJ-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | CR | |
NPTX2 | SNV | Missense_Mutation | rs766600008 | c.1240N>A | p.Gly414Arg | p.G414R | P47972 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-D7-A74A-01 | Stomach | stomach adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
NPTX2 | SNV | Missense_Mutation | rs565519639 | c.523N>T | p.Arg175Cys | p.R175C | P47972 | protein_coding | deleterious(0) | benign(0.328) | TCGA-HU-A4GN-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | mitomycin | PD |
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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 |
4885 | NPTX2 | DRUGGABLE GENOME | PRM-151 | PRM-151 |
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