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Gene: NPC2 |
Gene summary for NPC2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NPC2 | Gene ID | 10577 |
| Gene name | NPC intracellular cholesterol transporter 2 | |
| Gene Alias | EDDM1 | |
| Cytomap | 14q24.3 | |
| Gene Type | protein-coding | GO ID | GO:0006066 | UniProtAcc | A0A024R6C0 |
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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 |
| 10577 | NPC2 | GSM4909281 | Human | Breast | IDC | 3.35e-22 | 5.74e-01 | 0.21 |
| 10577 | NPC2 | GSM4909282 | Human | Breast | IDC | 1.70e-14 | 4.75e-01 | -0.0288 |
| 10577 | NPC2 | GSM4909285 | Human | Breast | IDC | 3.76e-20 | 5.79e-01 | 0.21 |
| 10577 | NPC2 | GSM4909288 | Human | Breast | IDC | 2.85e-05 | -5.51e-02 | 0.0988 |
| 10577 | NPC2 | GSM4909289 | Human | Breast | IDC | 1.42e-02 | 3.58e-01 | 0.1064 |
| 10577 | NPC2 | GSM4909293 | Human | Breast | IDC | 2.62e-11 | 4.60e-01 | 0.1581 |
| 10577 | NPC2 | GSM4909294 | Human | Breast | IDC | 7.62e-12 | -3.13e-01 | 0.2022 |
| 10577 | NPC2 | GSM4909296 | Human | Breast | IDC | 1.24e-18 | 3.46e-02 | 0.1524 |
| 10577 | NPC2 | GSM4909297 | Human | Breast | IDC | 2.90e-17 | -2.27e-01 | 0.1517 |
| 10577 | NPC2 | GSM4909299 | Human | Breast | IDC | 1.27e-22 | 6.15e-01 | 0.035 |
| 10577 | NPC2 | GSM4909301 | Human | Breast | IDC | 5.41e-07 | -2.45e-01 | 0.1577 |
| 10577 | NPC2 | GSM4909302 | Human | Breast | IDC | 1.14e-09 | 2.91e-01 | 0.1545 |
| 10577 | NPC2 | GSM4909305 | Human | Breast | IDC | 1.95e-07 | 4.46e-01 | 0.0436 |
| 10577 | NPC2 | GSM4909306 | Human | Breast | IDC | 1.41e-09 | 4.58e-01 | 0.1564 |
| 10577 | NPC2 | GSM4909307 | Human | Breast | IDC | 1.34e-09 | 3.60e-01 | 0.1569 |
| 10577 | NPC2 | GSM4909309 | Human | Breast | IDC | 7.24e-26 | 5.35e-01 | 0.0483 |
| 10577 | NPC2 | GSM4909311 | Human | Breast | IDC | 5.90e-43 | -1.48e-01 | 0.1534 |
| 10577 | NPC2 | GSM4909312 | Human | Breast | IDC | 3.14e-15 | -8.68e-02 | 0.1552 |
| 10577 | NPC2 | GSM4909313 | Human | Breast | IDC | 7.62e-22 | 3.67e-01 | 0.0391 |
| 10577 | NPC2 | GSM4909316 | Human | Breast | IDC | 1.15e-03 | 6.58e-02 | 0.21 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:00192164 | Breast | Precancer | regulation of lipid metabolic process | 34/1080 | 331/18723 | 8.14e-04 | 9.55e-03 | 34 |
| GO:001921612 | Breast | IDC | regulation of lipid metabolic process | 45/1434 | 331/18723 | 1.21e-04 | 2.24e-03 | 45 |
| GO:00096157 | Breast | IDC | response to virus | 47/1434 | 367/18723 | 3.53e-04 | 5.16e-03 | 47 |
| GO:001921621 | Breast | DCIS | regulation of lipid metabolic process | 43/1390 | 331/18723 | 2.37e-04 | 3.71e-03 | 43 |
| GO:000961512 | Breast | DCIS | response to virus | 45/1390 | 367/18723 | 6.16e-04 | 7.82e-03 | 45 |
| GO:00096158 | Cervix | CC | response to virus | 73/2311 | 367/18723 | 2.22e-05 | 3.95e-04 | 73 |
| GO:0006066 | Colorectum | AD | alcohol metabolic process | 106/3918 | 353/18723 | 3.02e-05 | 5.57e-04 | 106 |
| GO:0010876 | Colorectum | AD | lipid localization | 120/3918 | 448/18723 | 1.59e-03 | 1.33e-02 | 120 |
| GO:0006869 | Colorectum | AD | lipid transport | 108/3918 | 398/18723 | 1.67e-03 | 1.39e-02 | 108 |
| GO:0015748 | Colorectum | AD | organophosphate ester transport | 42/3918 | 140/18723 | 7.04e-03 | 4.31e-02 | 42 |
| GO:0008202 | Colorectum | AD | steroid metabolic process | 85/3918 | 319/18723 | 8.07e-03 | 4.75e-02 | 85 |
| GO:00060661 | Colorectum | SER | alcohol metabolic process | 79/2897 | 353/18723 | 3.50e-04 | 5.50e-03 | 79 |
| GO:00060662 | Colorectum | MSS | alcohol metabolic process | 92/3467 | 353/18723 | 2.57e-04 | 3.46e-03 | 92 |
| GO:00108761 | Colorectum | MSS | lipid localization | 104/3467 | 448/18723 | 6.76e-03 | 4.38e-02 | 104 |
| GO:0009615 | Colorectum | MSI-H | response to virus | 40/1319 | 367/18723 | 3.99e-03 | 4.61e-02 | 40 |
| GO:00096159 | Endometrium | AEH | response to virus | 63/2100 | 367/18723 | 3.81e-04 | 4.10e-03 | 63 |
| GO:00192165 | Endometrium | AEH | regulation of lipid metabolic process | 53/2100 | 331/18723 | 4.86e-03 | 3.07e-02 | 53 |
| GO:000961513 | Endometrium | EEC | response to virus | 66/2168 | 367/18723 | 1.78e-04 | 2.20e-03 | 66 |
| GO:001921613 | Endometrium | EEC | regulation of lipid metabolic process | 54/2168 | 331/18723 | 5.82e-03 | 3.49e-02 | 54 |
| GO:000961517 | Esophagus | HGIN | response to virus | 69/2587 | 367/18723 | 4.39e-03 | 3.86e-02 | 69 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04142 | Colorectum | SER | Lysosome | 38/1580 | 132/8465 | 2.87e-03 | 2.03e-02 | 1.47e-02 | 38 |
| hsa041421 | Colorectum | SER | Lysosome | 38/1580 | 132/8465 | 2.87e-03 | 2.03e-02 | 1.47e-02 | 38 |
| hsa041426 | Esophagus | HGIN | Lysosome | 33/1383 | 132/8465 | 6.65e-03 | 4.37e-02 | 3.47e-02 | 33 |
| hsa0414213 | Esophagus | HGIN | Lysosome | 33/1383 | 132/8465 | 6.65e-03 | 4.37e-02 | 3.47e-02 | 33 |
| hsa0414222 | Esophagus | ESCC | Lysosome | 102/4205 | 132/8465 | 5.11e-11 | 7.13e-10 | 3.65e-10 | 102 |
| hsa0414232 | Esophagus | ESCC | Lysosome | 102/4205 | 132/8465 | 5.11e-11 | 7.13e-10 | 3.65e-10 | 102 |
| hsa041424 | Liver | Cirrhotic | Lysosome | 68/2530 | 132/8465 | 1.34e-07 | 1.97e-06 | 1.21e-06 | 68 |
| hsa049792 | Liver | Cirrhotic | Cholesterol metabolism | 30/2530 | 51/8465 | 1.59e-05 | 1.39e-04 | 8.60e-05 | 30 |
| hsa0414211 | Liver | Cirrhotic | Lysosome | 68/2530 | 132/8465 | 1.34e-07 | 1.97e-06 | 1.21e-06 | 68 |
| hsa049793 | Liver | Cirrhotic | Cholesterol metabolism | 30/2530 | 51/8465 | 1.59e-05 | 1.39e-04 | 8.60e-05 | 30 |
| hsa041422 | Liver | HCC | Lysosome | 100/4020 | 132/8465 | 2.32e-11 | 4.31e-10 | 2.40e-10 | 100 |
| hsa049794 | Liver | HCC | Cholesterol metabolism | 41/4020 | 51/8465 | 1.33e-06 | 1.35e-05 | 7.49e-06 | 41 |
| hsa041423 | Liver | HCC | Lysosome | 100/4020 | 132/8465 | 2.32e-11 | 4.31e-10 | 2.40e-10 | 100 |
| hsa049795 | Liver | HCC | Cholesterol metabolism | 41/4020 | 51/8465 | 1.33e-06 | 1.35e-05 | 7.49e-06 | 41 |
| hsa041425 | Oral cavity | OSCC | Lysosome | 87/3704 | 132/8465 | 1.97e-07 | 1.35e-06 | 6.86e-07 | 87 |
| hsa0414212 | Oral cavity | OSCC | Lysosome | 87/3704 | 132/8465 | 1.97e-07 | 1.35e-06 | 6.86e-07 | 87 |
| hsa0414221 | Oral cavity | LP | Lysosome | 67/2418 | 132/8465 | 5.13e-08 | 7.77e-07 | 5.01e-07 | 67 |
| hsa0414231 | Oral cavity | LP | Lysosome | 67/2418 | 132/8465 | 5.13e-08 | 7.77e-07 | 5.01e-07 | 67 |
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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 |
| NPC2 | SNV | Missense_Mutation | c.412C>A | p.Leu138Ile | p.L138I | P61916 | protein_coding | tolerated(0.23) | benign(0.163) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| NPC2 | SNV | Missense_Mutation | c.412N>A | p.Leu138Ile | p.L138I | P61916 | protein_coding | tolerated(0.23) | benign(0.163) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NPC2 | SNV | Missense_Mutation | novel | c.268N>T | p.Pro90Ser | p.P90S | P61916 | protein_coding | tolerated(0.22) | benign(0.124) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NPC2 | SNV | Missense_Mutation | novel | c.310N>T | p.Asp104Tyr | p.D104Y | P61916 | protein_coding | deleterious(0.01) | possibly_damaging(0.747) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
| NPC2 | insertion | Frame_Shift_Ins | novel | c.334_335insCC | p.Lys112ThrfsTer5 | p.K112Tfs*5 | P61916 | protein_coding | TCGA-55-8097-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| NPC2 | SNV | Missense_Mutation | c.4N>T | p.Arg2Cys | p.R2C | P61916 | protein_coding | deleterious(0.03) | benign(0) | TCGA-J4-A6G3-01 | Prostate | prostate adenocarcinoma | Male | <65 | 8 | Hormone Therapy | leuprolide | PD | |
| NPC2 | SNV | Missense_Mutation | c.215N>T | p.Ala72Val | p.A72V | P61916 | protein_coding | deleterious(0) | possibly_damaging(0.565) | TCGA-HU-A4G8-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD |
| Page: 1 |
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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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