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Gene: APOLD1 |
Gene summary for APOLD1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | APOLD1 | Gene ID | 81575 |
| Gene name | apolipoprotein L domain containing 1 | |
| Gene Alias | VERGE | |
| Cytomap | 12p13.1 | |
| Gene Type | protein-coding | GO ID | GO:0001525 | UniProtAcc | Q96LR9 |
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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 |
| 81575 | APOLD1 | HTA11_2951_2000001011 | Human | Colorectum | AD | 1.50e-02 | 6.13e-01 | 0.0216 |
| 81575 | APOLD1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.54e-02 | 4.90e-01 | -0.059 |
| 81575 | APOLD1 | HTA11_866_3004761011 | Human | Colorectum | AD | 5.03e-18 | 7.96e-01 | 0.096 |
| 81575 | APOLD1 | HTA11_7663_2000001011 | Human | Colorectum | SER | 2.60e-08 | 1.22e+00 | 0.0131 |
| 81575 | APOLD1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 2.61e-12 | 8.42e-01 | 0.0338 |
| 81575 | APOLD1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.64e-24 | 9.07e-01 | 0.0674 |
| 81575 | APOLD1 | HTA11_6818_2000001011 | Human | Colorectum | AD | 3.14e-11 | 1.07e+00 | 0.0112 |
| 81575 | APOLD1 | HTA11_11156_2000001011 | Human | Colorectum | AD | 4.16e-02 | 1.07e+00 | 0.0397 |
| 81575 | APOLD1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 2.37e-21 | 1.10e+00 | 0.0588 |
| 81575 | APOLD1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.13e-04 | 6.20e-01 | 0.2585 |
| 81575 | APOLD1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.33e-05 | 4.36e-01 | 0.3005 |
| 81575 | APOLD1 | A002-C-010 | Human | Colorectum | FAP | 6.49e-10 | 5.82e-01 | 0.242 |
| 81575 | APOLD1 | A001-C-119 | Human | Colorectum | FAP | 1.01e-03 | 5.52e-01 | -0.1557 |
| 81575 | APOLD1 | A002-C-021 | Human | Colorectum | FAP | 1.73e-20 | 7.62e-01 | 0.1171 |
| 81575 | APOLD1 | A001-C-104 | Human | Colorectum | FAP | 2.61e-03 | 4.58e-01 | 0.0184 |
| 81575 | APOLD1 | A002-C-116 | Human | Colorectum | FAP | 1.71e-03 | 2.13e-01 | -0.0452 |
| 81575 | APOLD1 | A008-E-015 | Human | Colorectum | FAP | 1.80e-02 | 2.96e-01 | 0.0177 |
| 81575 | APOLD1 | F034 | Human | Colorectum | FAP | 3.74e-04 | 3.60e-01 | -0.0665 |
| 81575 | APOLD1 | CRC-1-8810 | Human | Colorectum | CRC | 1.25e-04 | 4.27e-01 | 0.6257 |
| 81575 | APOLD1 | CRC-3-11773 | Human | Colorectum | CRC | 2.64e-14 | 7.03e-01 | 0.2564 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:0070482 | Colorectum | AD | response to oxygen levels | 99/3918 | 347/18723 | 4.29e-04 | 4.82e-03 | 99 |
| GO:0003158 | Colorectum | AD | endothelium development | 44/3918 | 136/18723 | 1.20e-03 | 1.07e-02 | 44 |
| GO:0045446 | Colorectum | AD | endothelial cell differentiation | 39/3918 | 118/18723 | 1.42e-03 | 1.22e-02 | 39 |
| 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:0001666 | Colorectum | AD | response to hypoxia | 86/3918 | 307/18723 | 1.77e-03 | 1.46e-02 | 86 |
| GO:0036293 | Colorectum | AD | response to decreased oxygen levels | 88/3918 | 322/18723 | 3.42e-03 | 2.49e-02 | 88 |
| GO:00704821 | Colorectum | SER | response to oxygen levels | 79/2897 | 347/18723 | 1.99e-04 | 3.64e-03 | 79 |
| GO:00016661 | Colorectum | SER | response to hypoxia | 69/2897 | 307/18723 | 7.07e-04 | 9.39e-03 | 69 |
| GO:00362931 | Colorectum | SER | response to decreased oxygen levels | 71/2897 | 322/18723 | 1.04e-03 | 1.22e-02 | 71 |
| GO:00704822 | Colorectum | MSS | response to oxygen levels | 85/3467 | 347/18723 | 3.08e-03 | 2.34e-02 | 85 |
| GO:00031581 | Colorectum | MSS | endothelium development | 38/3467 | 136/18723 | 4.53e-03 | 3.19e-02 | 38 |
| GO:00016662 | Colorectum | MSS | response to hypoxia | 75/3467 | 307/18723 | 5.56e-03 | 3.78e-02 | 75 |
| GO:00108761 | Colorectum | MSS | lipid localization | 104/3467 | 448/18723 | 6.76e-03 | 4.38e-02 | 104 |
| GO:00454461 | Colorectum | MSS | endothelial cell differentiation | 33/3467 | 118/18723 | 7.66e-03 | 4.81e-02 | 33 |
| GO:00704823 | Colorectum | FAP | response to oxygen levels | 77/2622 | 347/18723 | 2.08e-05 | 5.05e-04 | 77 |
| GO:00016663 | Colorectum | FAP | response to hypoxia | 68/2622 | 307/18723 | 6.53e-05 | 1.25e-03 | 68 |
| GO:00362932 | Colorectum | FAP | response to decreased oxygen levels | 70/2622 | 322/18723 | 9.49e-05 | 1.61e-03 | 70 |
| GO:00068691 | Colorectum | FAP | lipid transport | 81/2622 | 398/18723 | 2.84e-04 | 3.76e-03 | 81 |
| GO:0030856 | Colorectum | FAP | regulation of epithelial cell differentiation | 36/2622 | 154/18723 | 1.16e-03 | 1.11e-02 | 36 |
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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. |
| 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 |
| APOLD1 | SNV | Missense_Mutation | novel | c.619N>G | p.Arg207Gly | p.R207G | Q96LR9 | protein_coding | deleterious(0) | benign(0.206) | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| APOLD1 | SNV | Missense_Mutation | c.703N>A | p.Glu235Lys | p.E235K | Q96LR9 | protein_coding | tolerated(0.06) | benign(0.079) | TCGA-D8-A13Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| APOLD1 | insertion | Frame_Shift_Ins | novel | c.609_610insCATCTGGTCTGGTCTGCAGCAAGTCCACAGAAGCTACA | p.Phe204HisfsTer36 | p.F204Hfs*36 | Q96LR9 | protein_coding | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| APOLD1 | insertion | Frame_Shift_Ins | novel | c.617_618insGGCCAGGTGCTGCGCCTGCGCG | p.Arg207AlafsTer23 | p.R207Afs*23 | Q96LR9 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| APOLD1 | SNV | Missense_Mutation | c.509N>G | p.Glu170Gly | p.E170G | Q96LR9 | protein_coding | deleterious(0.01) | benign(0.061) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| APOLD1 | SNV | Missense_Mutation | novel | c.520N>T | p.Arg174Cys | p.R174C | Q96LR9 | protein_coding | deleterious(0.02) | possibly_damaging(0.841) | TCGA-AA-3968-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| APOLD1 | SNV | Missense_Mutation | c.609N>A | p.Phe203Leu | p.F203L | Q96LR9 | protein_coding | tolerated(0.14) | benign(0.089) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| APOLD1 | SNV | Missense_Mutation | c.516N>A | p.Phe172Leu | p.F172L | Q96LR9 | protein_coding | tolerated(0.76) | benign(0.098) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| APOLD1 | SNV | Missense_Mutation | c.671N>T | p.Ala224Val | p.A224V | Q96LR9 | protein_coding | tolerated(0.09) | benign(0.055) | TCGA-BG-A0W1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| APOLD1 | SNV | Missense_Mutation | c.609C>A | p.Phe203Leu | p.F203L | Q96LR9 | protein_coding | tolerated(0.14) | benign(0.089) | TCGA-BS-A0UV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <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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