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Gene: ABCB4 |
Gene summary for ABCB4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ABCB4 | Gene ID | 5244 |
| Gene name | ATP binding cassette subfamily B member 4 | |
| Gene Alias | ABC21 | |
| Cytomap | 7q21.12 | |
| Gene Type | protein-coding | GO ID | GO:0006629 | UniProtAcc | P21439 |
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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 |
| 5244 | ABCB4 | NAFLD1 | Human | Liver | NAFLD | 1.32e-16 | 1.26e+00 | -0.04 |
| 5244 | ABCB4 | S43 | Human | Liver | Cirrhotic | 8.67e-05 | -1.67e-01 | -0.0187 |
| 5244 | ABCB4 | HCC1_Meng | Human | Liver | HCC | 6.85e-51 | -2.50e-01 | 0.0246 |
| 5244 | ABCB4 | HCC2_Meng | Human | Liver | HCC | 4.41e-09 | -3.44e-01 | 0.0107 |
| 5244 | ABCB4 | cirrhotic1 | Human | Liver | Cirrhotic | 3.70e-09 | -3.42e-01 | 0.0202 |
| 5244 | ABCB4 | cirrhotic2 | Human | Liver | Cirrhotic | 1.33e-08 | -3.38e-01 | 0.0201 |
| 5244 | ABCB4 | cirrhotic3 | Human | Liver | Cirrhotic | 5.63e-03 | -3.41e-01 | 0.0215 |
| 5244 | ABCB4 | HCC5 | Human | Liver | HCC | 1.61e-08 | 2.56e+00 | 0.4932 |
| 5244 | ABCB4 | Pt13.a | Human | Liver | HCC | 3.00e-05 | -2.63e-01 | 0.021 |
| 5244 | ABCB4 | Pt13.b | Human | Liver | HCC | 4.04e-03 | -2.97e-01 | 0.0251 |
| 5244 | ABCB4 | Pt14.a | Human | Liver | HCC | 3.92e-02 | -8.34e-03 | 0.0169 |
| 5244 | ABCB4 | Pt14.b | Human | Liver | HCC | 1.41e-04 | -3.05e-05 | 0.018 |
| 5244 | ABCB4 | Pt14.d | Human | Liver | HCC | 2.02e-04 | -1.50e-01 | 0.0143 |
| 5244 | ABCB4 | S014 | Human | Liver | HCC | 5.36e-05 | -9.33e-02 | 0.2254 |
| 5244 | ABCB4 | S016 | Human | Liver | HCC | 9.20e-07 | -8.23e-02 | 0.2243 |
| 5244 | ABCB4 | S028 | Human | Liver | HCC | 5.06e-05 | -7.30e-03 | 0.2503 |
| 5244 | ABCB4 | S029 | Human | Liver | HCC | 2.47e-03 | 1.12e-01 | 0.2581 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:00550883 | Liver | NAFLD | lipid homeostasis | 44/1882 | 167/18723 | 1.48e-09 | 2.54e-07 | 44 |
| GO:00108765 | Liver | NAFLD | lipid localization | 79/1882 | 448/18723 | 4.75e-07 | 2.92e-05 | 79 |
| GO:00303013 | Liver | NAFLD | cholesterol transport | 30/1882 | 117/18723 | 1.08e-06 | 5.40e-05 | 30 |
| GO:00068694 | Liver | NAFLD | lipid transport | 71/1882 | 398/18723 | 1.16e-06 | 5.59e-05 | 71 |
| GO:00159183 | Liver | NAFLD | sterol transport | 32/1882 | 130/18723 | 1.27e-06 | 6.01e-05 | 32 |
| GO:0032373 | Liver | NAFLD | positive regulation of sterol transport | 15/1882 | 38/18723 | 1.68e-06 | 7.43e-05 | 15 |
| GO:0032376 | Liver | NAFLD | positive regulation of cholesterol transport | 15/1882 | 38/18723 | 1.68e-06 | 7.43e-05 | 15 |
| GO:0015850 | Liver | NAFLD | organic hydroxy compound transport | 50/1882 | 284/18723 | 6.01e-05 | 1.32e-03 | 50 |
| GO:0032371 | Liver | NAFLD | regulation of sterol transport | 20/1882 | 78/18723 | 6.46e-05 | 1.39e-03 | 20 |
| GO:0032374 | Liver | NAFLD | regulation of cholesterol transport | 20/1882 | 78/18723 | 6.46e-05 | 1.39e-03 | 20 |
| GO:1905952 | Liver | NAFLD | regulation of lipid localization | 34/1882 | 181/18723 | 2.51e-04 | 4.12e-03 | 34 |
| GO:1905954 | Liver | NAFLD | positive regulation of lipid localization | 23/1882 | 110/18723 | 5.16e-04 | 7.15e-03 | 23 |
| GO:0032368 | Liver | NAFLD | regulation of lipid transport | 28/1882 | 149/18723 | 8.39e-04 | 1.03e-02 | 28 |
| GO:19016547 | Liver | NAFLD | response to ketone | 34/1882 | 194/18723 | 9.22e-04 | 1.10e-02 | 34 |
| GO:0032370 | Liver | NAFLD | positive regulation of lipid transport | 18/1882 | 84/18723 | 1.49e-03 | 1.64e-02 | 18 |
| GO:0045472 | Liver | NAFLD | response to ether | 6/1882 | 14/18723 | 1.51e-03 | 1.64e-02 | 6 |
| GO:190165412 | Liver | Cirrhotic | response to ketone | 86/4634 | 194/18723 | 1.82e-09 | 7.73e-08 | 86 |
| GO:005508811 | Liver | Cirrhotic | lipid homeostasis | 74/4634 | 167/18723 | 2.46e-08 | 8.51e-07 | 74 |
| GO:001087611 | Liver | Cirrhotic | lipid localization | 147/4634 | 448/18723 | 6.24e-05 | 7.12e-04 | 147 |
| GO:000686911 | Liver | Cirrhotic | lipid transport | 128/4634 | 398/18723 | 4.54e-04 | 3.69e-03 | 128 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa02010 | Liver | NAFLD | ABC transporters | 16/1043 | 45/8465 | 4.97e-05 | 1.16e-03 | 9.37e-04 | 16 |
| hsa049762 | Liver | NAFLD | Bile secretion | 20/1043 | 89/8465 | 5.08e-03 | 4.43e-02 | 3.57e-02 | 20 |
| hsa020101 | Liver | NAFLD | ABC transporters | 16/1043 | 45/8465 | 4.97e-05 | 1.16e-03 | 9.37e-04 | 16 |
| hsa0497611 | Liver | NAFLD | Bile secretion | 20/1043 | 89/8465 | 5.08e-03 | 4.43e-02 | 3.57e-02 | 20 |
| hsa020102 | Liver | HCC | ABC transporters | 29/4020 | 45/8465 | 1.62e-02 | 3.88e-02 | 2.16e-02 | 29 |
| hsa020103 | Liver | HCC | ABC transporters | 29/4020 | 45/8465 | 1.62e-02 | 3.88e-02 | 2.16e-02 | 29 |
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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 |
| ABCB4 | SNV | Missense_Mutation | c.296N>T | p.Ser99Phe | p.S99F | P21439 | protein_coding | deleterious(0.02) | benign(0.006) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD | |
| ABCB4 | SNV | Missense_Mutation | c.2230N>A | p.Asp744Asn | p.D744N | P21439 | protein_coding | tolerated(0.38) | benign(0.048) | TCGA-BH-A0AW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD | |
| ABCB4 | SNV | Missense_Mutation | c.1537N>C | p.Glu513Gln | p.E513Q | P21439 | protein_coding | deleterious(0) | benign(0.219) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| ABCB4 | SNV | Missense_Mutation | c.2249N>G | p.Lys750Arg | p.K750R | P21439 | protein_coding | tolerated(0.36) | benign(0.02) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ABCB4 | SNV | Missense_Mutation | c.2354N>A | p.Arg785Lys | p.R785K | P21439 | protein_coding | tolerated(1) | benign(0) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| ABCB4 | SNV | Missense_Mutation | c.1537N>C | p.Glu513Gln | p.E513Q | P21439 | protein_coding | deleterious(0) | benign(0.219) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| ABCB4 | SNV | Missense_Mutation | c.3262N>A | p.Pro1088Thr | p.P1088T | P21439 | protein_coding | deleterious(0.03) | possibly_damaging(0.768) | TCGA-D8-A27M-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | methotrexate+5 | SD | |
| ABCB4 | SNV | Missense_Mutation | c.1577T>G | p.Val526Gly | p.V526G | P21439 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-EW-A1PB-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| ABCB4 | SNV | Missense_Mutation | c.3461N>T | p.Ala1154Val | p.A1154V | P21439 | protein_coding | tolerated(0.13) | possibly_damaging(0.483) | TCGA-GM-A2DO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | CR | |
| ABCB4 | insertion | Frame_Shift_Ins | novel | c.436_437insCTCCCAG | p.Ile146ThrfsTer7 | p.I146Tfs*7 | P21439 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 |
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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 |
| 5244 | ABCB4 | TRANSPORTER, DRUGGABLE GENOME, ENZYME, ABC TRANSPORTER | VINBLASTINE | VINBLASTINE | 7918493 | |
| 5244 | ABCB4 | TRANSPORTER, DRUGGABLE GENOME, ENZYME, ABC TRANSPORTER | Ortataxel | ORTATAXEL | ||
| 5244 | ABCB4 | TRANSPORTER, DRUGGABLE GENOME, ENZYME, ABC TRANSPORTER | VINCRISTINE | VINCRISTINE | 1673638 | |
| 5244 | ABCB4 | TRANSPORTER, DRUGGABLE GENOME, ENZYME, ABC TRANSPORTER | CYCLOSPORINE | CYCLOSPORINE | 1972761 | |
| 5244 | ABCB4 | TRANSPORTER, DRUGGABLE GENOME, ENZYME, ABC TRANSPORTER | MITOMYCIN-C | 11167651 | ||
| 5244 | ABCB4 | TRANSPORTER, DRUGGABLE GENOME, ENZYME, ABC TRANSPORTER | anthracyclines and related substances | 23441093,21900104 | ||
| 5244 | ABCB4 | TRANSPORTER, DRUGGABLE GENOME, ENZYME, ABC TRANSPORTER | Benzquinamide | BENZQUINAMIDE | ||
| 5244 | ABCB4 | TRANSPORTER, DRUGGABLE GENOME, ENZYME, ABC TRANSPORTER | imatinib | IMATINIB | 30237583 | |
| 5244 | ABCB4 | TRANSPORTER, DRUGGABLE GENOME, ENZYME, ABC TRANSPORTER | Curcumin | CURCUMIN |
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