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Gene: NPC1L1 |
Gene summary for NPC1L1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NPC1L1 | Gene ID | 29881 |
| Gene name | NPC1 like intracellular cholesterol transporter 1 | |
| Gene Alias | LDLCQ7 | |
| Cytomap | 7p13 | |
| Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | A0A0C4DFX6 |
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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 |
| 29881 | NPC1L1 | S43 | Human | Liver | Cirrhotic | 3.36e-03 | 3.14e-02 | -0.0187 |
| 29881 | NPC1L1 | HCC1_Meng | Human | Liver | HCC | 4.51e-35 | 5.22e-02 | 0.0246 |
| 29881 | NPC1L1 | HCC2_Meng | Human | Liver | HCC | 1.04e-15 | 1.44e-01 | 0.0107 |
| 29881 | NPC1L1 | Pt13.a | Human | Liver | HCC | 9.68e-04 | -8.95e-02 | 0.021 |
| 29881 | NPC1L1 | Pt14.d | Human | Liver | HCC | 4.57e-04 | -8.53e-02 | 0.0143 |
| 29881 | NPC1L1 | S027 | Human | Liver | HCC | 2.63e-10 | 1.03e+00 | 0.2446 |
| 29881 | NPC1L1 | S028 | Human | Liver | HCC | 1.56e-20 | 8.42e-01 | 0.2503 |
| 29881 | NPC1L1 | S029 | Human | Liver | HCC | 1.26e-23 | 1.12e+00 | 0.2581 |
| 29881 | NPC1L1 | Pat01-B | Human | Stomach | GC | 9.51e-22 | 4.54e-01 | 0.5754 |
| 29881 | NPC1L1 | Pat02-B | Human | Stomach | GC | 3.76e-03 | 7.78e-02 | 0.0368 |
| 29881 | NPC1L1 | Pat03-B | Human | Stomach | GC | 2.33e-09 | 2.33e-01 | 0.3693 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:000820211 | Liver | Cirrhotic | steroid metabolic process | 143/4634 | 319/18723 | 2.79e-15 | 3.18e-13 | 143 |
| GO:19026521 | Liver | Cirrhotic | secondary alcohol metabolic process | 75/4634 | 147/18723 | 5.62e-12 | 3.91e-10 | 75 |
| GO:00082031 | Liver | Cirrhotic | cholesterol metabolic process | 70/4634 | 137/18723 | 2.59e-11 | 1.55e-09 | 70 |
| GO:00161251 | Liver | Cirrhotic | sterol metabolic process | 75/4634 | 152/18723 | 4.54e-11 | 2.61e-09 | 75 |
| GO:000606612 | Liver | Cirrhotic | alcohol metabolic process | 141/4634 | 353/18723 | 1.57e-10 | 8.03e-09 | 141 |
| GO:00066941 | Liver | Cirrhotic | steroid biosynthetic process | 77/4634 | 173/18723 | 1.02e-08 | 3.91e-07 | 77 |
| GO:0016126 | Liver | Cirrhotic | sterol biosynthetic process | 37/4634 | 64/18723 | 1.74e-08 | 6.32e-07 | 37 |
| GO:0006695 | Liver | Cirrhotic | cholesterol biosynthetic process | 34/4634 | 57/18723 | 2.22e-08 | 7.77e-07 | 34 |
| GO:1902653 | Liver | Cirrhotic | secondary alcohol biosynthetic process | 34/4634 | 57/18723 | 2.22e-08 | 7.77e-07 | 34 |
| GO:001087611 | Liver | Cirrhotic | lipid localization | 147/4634 | 448/18723 | 6.24e-05 | 7.12e-04 | 147 |
| GO:0046165 | Liver | Cirrhotic | alcohol biosynthetic process | 55/4634 | 140/18723 | 9.74e-05 | 1.03e-03 | 55 |
| GO:0042157 | Liver | Cirrhotic | lipoprotein metabolic process | 53/4634 | 135/18723 | 1.32e-04 | 1.29e-03 | 53 |
| GO:000686911 | Liver | Cirrhotic | lipid transport | 128/4634 | 398/18723 | 4.54e-04 | 3.69e-03 | 128 |
| GO:19016171 | Liver | Cirrhotic | organic hydroxy compound biosynthetic process | 81/4634 | 237/18723 | 6.73e-04 | 5.06e-03 | 81 |
| GO:001591811 | Liver | Cirrhotic | sterol transport | 48/4634 | 130/18723 | 1.32e-03 | 8.83e-03 | 48 |
| GO:003030111 | Liver | Cirrhotic | cholesterol transport | 44/4634 | 117/18723 | 1.34e-03 | 8.98e-03 | 44 |
| GO:00715013 | Liver | Cirrhotic | cellular response to sterol depletion | 10/4634 | 16/18723 | 1.51e-03 | 9.91e-03 | 10 |
| GO:00069912 | Liver | Cirrhotic | response to sterol depletion | 10/4634 | 18/18723 | 5.00e-03 | 2.59e-02 | 10 |
| GO:000606621 | Liver | HCC | alcohol metabolic process | 208/7958 | 353/18723 | 2.80e-10 | 9.50e-09 | 208 |
| GO:19026522 | Liver | HCC | secondary alcohol metabolic process | 100/7958 | 147/18723 | 3.26e-10 | 1.09e-08 | 100 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04975 | Stomach | GC | Fat digestion and absorption | 14/708 | 43/8465 | 5.71e-06 | 8.30e-05 | 5.84e-05 | 14 |
| hsa049751 | Stomach | GC | Fat digestion and absorption | 14/708 | 43/8465 | 5.71e-06 | 8.30e-05 | 5.84e-05 | 14 |
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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 |
| NPC1L1 | SNV | Missense_Mutation | c.3412N>A | p.Glu1138Lys | p.E1138K | Q9UHC9 | protein_coding | deleterious(0.01) | probably_damaging(0.96) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD | |
| NPC1L1 | SNV | Missense_Mutation | rs139110095 | c.422N>A | p.Arg141His | p.R141H | Q9UHC9 | protein_coding | deleterious(0.05) | possibly_damaging(0.884) | TCGA-A7-A13G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | PD |
| NPC1L1 | SNV | Missense_Mutation | rs372455452 | c.79N>G | p.Ile27Val | p.I27V | Q9UHC9 | protein_coding | tolerated(0.26) | benign(0) | TCGA-A7-A6VW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
| NPC1L1 | SNV | Missense_Mutation | novel | c.3622T>C | p.Phe1208Leu | p.F1208L | Q9UHC9 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A8-A09Q-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | SD |
| NPC1L1 | SNV | Missense_Mutation | c.2233N>T | p.Pro745Ser | p.P745S | Q9UHC9 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NPC1L1 | SNV | Missense_Mutation | c.3988N>C | p.Asp1330His | p.D1330H | Q9UHC9 | protein_coding | tolerated_low_confidence(0.1) | benign(0.06) | TCGA-C8-A274-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| NPC1L1 | SNV | Missense_Mutation | c.2620G>C | p.Glu874Gln | p.E874Q | Q9UHC9 | protein_coding | tolerated(0.1) | benign(0.028) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
| NPC1L1 | insertion | In_Frame_Ins | novel | c.2571_2572insTCAACCCTTAGGCCCCTGGGATTTGGGGAG | p.Phe857_Gly858insSerThrLeuArgProLeuGlyPheGlyGlu | p.F857_G858insSTLRPLGFGE | Q9UHC9 | protein_coding | TCGA-AO-A03R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
| NPC1L1 | insertion | Frame_Shift_Ins | novel | c.2320_2321insAAAACTCTTTCCTTTTTGCAAAATTGAAA | p.Leu774GlnfsTer11 | p.L774Qfs*11 | Q9UHC9 | protein_coding | TCGA-AO-A03T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | ||
| NPC1L1 | insertion | Frame_Shift_Ins | novel | c.3221_3222insAGGCCAGGGCAGTGGGTGGAAATGT | p.Arg1075GlyfsTer40 | p.R1075Gfs*40 | Q9UHC9 | protein_coding | TCGA-BH-A0HX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adrimycin | 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 |
| 29881 | NPC1L1 | DRUGGABLE GENOME, TRANSPORTER | EZETIMIBE | EZETIMIBE | ||
| 29881 | NPC1L1 | DRUGGABLE GENOME, TRANSPORTER | pravastatin | PRAVASTATIN | 19752398 | |
| 29881 | NPC1L1 | DRUGGABLE GENOME, TRANSPORTER | EMZETIBE | |||
| 29881 | NPC1L1 | DRUGGABLE GENOME, TRANSPORTER | antagonist | 178103422 | EZETIMIBE | |
| 29881 | NPC1L1 | DRUGGABLE GENOME, TRANSPORTER | Ezetimibe | EZETIMIBE | ||
| 29881 | NPC1L1 | DRUGGABLE GENOME, TRANSPORTER | inhibitor | CHEMBL1138 | EZETIMIBE | |
| 29881 | NPC1L1 | DRUGGABLE GENOME, TRANSPORTER | EZETIMIBE | EZETIMIBE |
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