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Gene: NDRG1 |
Gene summary for NDRG1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | NDRG1 | Gene ID | 10397 |
Gene name | N-myc downstream regulated 1 | |
Gene Alias | CAP43 | |
Cytomap | 8q24.22 | |
Gene Type | protein-coding | GO ID | GO:0001666 | UniProtAcc | Q92597 |
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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 |
10397 | NDRG1 | P62T-E | Human | Esophagus | ESCC | 1.67e-60 | 2.22e+00 | 0.1302 |
10397 | NDRG1 | P65T-E | Human | Esophagus | ESCC | 3.78e-06 | -1.13e-01 | 0.0978 |
10397 | NDRG1 | P74T-E | Human | Esophagus | ESCC | 6.23e-15 | 1.25e+00 | 0.1479 |
10397 | NDRG1 | P75T-E | Human | Esophagus | ESCC | 3.82e-21 | 9.08e-01 | 0.1125 |
10397 | NDRG1 | P80T-E | Human | Esophagus | ESCC | 2.51e-32 | 2.19e+00 | 0.155 |
10397 | NDRG1 | P82T-E | Human | Esophagus | ESCC | 1.06e-07 | 1.49e+00 | 0.1072 |
10397 | NDRG1 | P83T-E | Human | Esophagus | ESCC | 3.18e-44 | 2.96e+00 | 0.1738 |
10397 | NDRG1 | P84T-E | Human | Esophagus | ESCC | 1.22e-08 | 1.74e+00 | 0.0933 |
10397 | NDRG1 | P89T-E | Human | Esophagus | ESCC | 1.34e-26 | 4.63e+00 | 0.1752 |
10397 | NDRG1 | P91T-E | Human | Esophagus | ESCC | 2.46e-20 | 4.32e+00 | 0.1828 |
10397 | NDRG1 | P107T-E | Human | Esophagus | ESCC | 6.70e-46 | 3.50e+00 | 0.171 |
10397 | NDRG1 | P126T-E | Human | Esophagus | ESCC | 1.20e-12 | 2.36e+00 | 0.1125 |
10397 | NDRG1 | P127T-E | Human | Esophagus | ESCC | 4.36e-11 | 4.48e-01 | 0.0826 |
10397 | NDRG1 | P128T-E | Human | Esophagus | ESCC | 5.90e-31 | 2.95e+00 | 0.1241 |
10397 | NDRG1 | P130T-E | Human | Esophagus | ESCC | 2.95e-33 | 1.93e+00 | 0.1676 |
10397 | NDRG1 | S43 | Human | Liver | Cirrhotic | 7.04e-03 | -1.20e-01 | -0.0187 |
10397 | NDRG1 | HCC1_Meng | Human | Liver | HCC | 6.45e-50 | 2.10e-01 | 0.0246 |
10397 | NDRG1 | HCC2_Meng | Human | Liver | HCC | 3.84e-36 | 3.35e-01 | 0.0107 |
10397 | NDRG1 | cirrhotic2 | Human | Liver | Cirrhotic | 3.67e-04 | 1.39e-01 | 0.0201 |
10397 | NDRG1 | cirrhotic3 | Human | Liver | Cirrhotic | 1.28e-02 | 5.59e-02 | 0.0215 |
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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:00362939 | Breast | Precancer | response to decreased oxygen levels | 53/1080 | 322/18723 | 4.09e-12 | 6.84e-10 | 53 |
GO:00016669 | Breast | Precancer | response to hypoxia | 51/1080 | 307/18723 | 7.33e-12 | 1.11e-09 | 51 |
GO:00704829 | Breast | Precancer | response to oxygen levels | 55/1080 | 347/18723 | 7.47e-12 | 1.11e-09 | 55 |
GO:00362948 | Breast | Precancer | cellular response to decreased oxygen levels | 31/1080 | 161/18723 | 2.61e-09 | 2.11e-07 | 31 |
GO:00714538 | Breast | Precancer | cellular response to oxygen levels | 32/1080 | 177/18723 | 7.32e-09 | 5.52e-07 | 32 |
GO:00714565 | Breast | Precancer | cellular response to hypoxia | 29/1080 | 151/18723 | 8.98e-09 | 6.50e-07 | 29 |
GO:00100389 | Breast | Precancer | response to metal ion | 47/1080 | 373/18723 | 3.88e-07 | 1.79e-05 | 47 |
GO:00723319 | Breast | Precancer | signal transduction by p53 class mediator | 26/1080 | 163/18723 | 2.23e-06 | 7.76e-05 | 26 |
GO:00420633 | Breast | Precancer | gliogenesis | 33/1080 | 301/18723 | 3.06e-04 | 4.40e-03 | 33 |
GO:00100013 | Breast | Precancer | glial cell differentiation | 25/1080 | 225/18723 | 1.29e-03 | 1.37e-02 | 25 |
GO:00303309 | Breast | Precancer | DNA damage response, signal transduction by p53 class mediator | 11/1080 | 72/18723 | 2.65e-03 | 2.36e-02 | 11 |
GO:0021782 | Breast | Precancer | glial cell development | 14/1080 | 116/18723 | 6.92e-03 | 4.67e-02 | 14 |
GO:007048214 | Breast | IDC | response to oxygen levels | 64/1434 | 347/18723 | 3.45e-11 | 5.57e-09 | 64 |
GO:003629314 | Breast | IDC | response to decreased oxygen levels | 60/1434 | 322/18723 | 9.26e-11 | 1.25e-08 | 60 |
GO:000166614 | Breast | IDC | response to hypoxia | 58/1434 | 307/18723 | 1.09e-10 | 1.38e-08 | 58 |
GO:001003814 | Breast | IDC | response to metal ion | 65/1434 | 373/18723 | 2.95e-10 | 3.42e-08 | 65 |
GO:003629413 | Breast | IDC | cellular response to decreased oxygen levels | 34/1434 | 161/18723 | 4.73e-08 | 3.02e-06 | 34 |
GO:007145613 | Breast | IDC | cellular response to hypoxia | 32/1434 | 151/18723 | 1.07e-07 | 6.26e-06 | 32 |
GO:007145313 | Breast | IDC | cellular response to oxygen levels | 35/1434 | 177/18723 | 1.68e-07 | 9.10e-06 | 35 |
GO:007233114 | Breast | IDC | signal transduction by p53 class mediator | 30/1434 | 163/18723 | 5.82e-06 | 1.89e-04 | 30 |
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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 |
NDRG1 | SNV | Missense_Mutation | rs779194865 | c.563C>T | p.Pro188Leu | p.P188L | Q92597 | protein_coding | tolerated(0.16) | probably_damaging(1) | TCGA-C8-A27B-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
NDRG1 | SNV | Missense_Mutation | c.734N>C | p.Gly245Ala | p.G245A | Q92597 | protein_coding | tolerated(0.13) | benign(0.15) | TCGA-D8-A147-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine | SD | |
NDRG1 | SNV | Missense_Mutation | rs780329667 | c.196G>A | p.Gly66Ser | p.G66S | Q92597 | protein_coding | deleterious(0.02) | probably_damaging(1) | TCGA-C5-A3HL-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
NDRG1 | SNV | Missense_Mutation | c.226N>A | p.Leu76Ile | p.L76I | Q92597 | protein_coding | tolerated(0.07) | probably_damaging(0.914) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
NDRG1 | SNV | Missense_Mutation | rs748331213 | c.704N>A | p.Arg235His | p.R235H | Q92597 | protein_coding | deleterious(0.01) | probably_damaging(0.939) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
NDRG1 | SNV | Missense_Mutation | c.506N>T | p.Ala169Val | p.A169V | Q92597 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-DM-A1D4-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
NDRG1 | SNV | Missense_Mutation | c.635G>A | p.Arg212His | p.R212H | Q92597 | protein_coding | deleterious(0.02) | probably_damaging(0.943) | TCGA-G4-6628-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
NDRG1 | SNV | Missense_Mutation | c.979C>T | p.Arg327Cys | p.R327C | Q92597 | protein_coding | deleterious(0) | possibly_damaging(0.863) | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
NDRG1 | SNV | Missense_Mutation | c.112N>A | p.Glu38Lys | p.E38K | Q92597 | protein_coding | deleterious(0) | possibly_damaging(0.81) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
NDRG1 | SNV | Missense_Mutation | novel | c.910N>A | p.Ala304Thr | p.A304T | Q92597 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
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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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