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Gene: ABCA12 |
Gene summary for ABCA12 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ABCA12 | Gene ID | 26154 |
| Gene name | ATP binding cassette subfamily A member 12 | |
| Gene Alias | ARCI4A | |
| Cytomap | 2q35 | |
| Gene Type | protein-coding | GO ID | GO:0001678 | UniProtAcc | B3KVV3 |
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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 |
| 26154 | ABCA12 | RNA-P17T-P17T-2 | Human | Lung | IAC | 2.13e-03 | 6.02e-01 | 0.3371 |
| 26154 | ABCA12 | RNA-P17T-P17T-4 | Human | Lung | IAC | 4.71e-02 | 5.10e-01 | 0.343 |
| 26154 | ABCA12 | RNA-P17T-P17T-6 | Human | Lung | IAC | 1.48e-03 | 5.88e-01 | 0.3385 |
| 26154 | ABCA12 | RNA-P17T-P17T-8 | Human | Lung | IAC | 5.44e-06 | 6.53e-01 | 0.3329 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma |
| ∗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:0048875 | Lung | IAC | chemical homeostasis within a tissue | 11/2061 | 14/18723 | 7.44e-09 | 1.05e-06 | 11 |
| GO:0043129 | Lung | IAC | surfactant homeostasis | 10/2061 | 12/18723 | 1.37e-08 | 1.77e-06 | 10 |
| GO:00020648 | Lung | IAC | epithelial cell development | 52/2061 | 220/18723 | 6.75e-08 | 6.91e-06 | 52 |
| GO:00726598 | Lung | IAC | protein localization to plasma membrane | 60/2061 | 284/18723 | 4.74e-07 | 3.10e-05 | 60 |
| GO:19907787 | Lung | IAC | protein localization to cell periphery | 66/2061 | 333/18723 | 1.44e-06 | 7.22e-05 | 66 |
| GO:00308562 | Lung | IAC | regulation of epithelial cell differentiation | 34/2061 | 154/18723 | 5.40e-05 | 1.21e-03 | 34 |
| GO:00224078 | Lung | IAC | regulation of cell-cell adhesion | 76/2061 | 448/18723 | 8.16e-05 | 1.68e-03 | 76 |
| GO:0045616 | Lung | IAC | regulation of keratinocyte differentiation | 13/2061 | 37/18723 | 9.33e-05 | 1.87e-03 | 13 |
| GO:00323867 | Lung | IAC | regulation of intracellular transport | 60/2061 | 337/18723 | 1.16e-04 | 2.22e-03 | 60 |
| GO:00435882 | Lung | IAC | skin development | 49/2061 | 263/18723 | 1.56e-04 | 2.82e-03 | 49 |
| GO:0045604 | Lung | IAC | regulation of epidermal cell differentiation | 16/2061 | 58/18723 | 3.85e-04 | 5.87e-03 | 16 |
| GO:00097438 | Lung | IAC | response to carbohydrate | 46/2061 | 253/18723 | 4.28e-04 | 6.37e-03 | 46 |
| GO:0045682 | Lung | IAC | regulation of epidermis development | 17/2061 | 65/18723 | 5.07e-04 | 7.33e-03 | 17 |
| GO:00099135 | Lung | IAC | epidermal cell differentiation | 37/2061 | 202/18723 | 1.29e-03 | 1.45e-02 | 37 |
| GO:00323887 | Lung | IAC | positive regulation of intracellular transport | 37/2061 | 202/18723 | 1.29e-03 | 1.45e-02 | 37 |
| GO:00018947 | Lung | IAC | tissue homeostasis | 46/2061 | 268/18723 | 1.50e-03 | 1.60e-02 | 46 |
| GO:0030216 | Lung | IAC | keratinocyte differentiation | 27/2061 | 139/18723 | 2.34e-03 | 2.28e-02 | 27 |
| GO:19038298 | Lung | IAC | positive regulation of cellular protein localization | 46/2061 | 276/18723 | 2.74e-03 | 2.50e-02 | 46 |
| GO:00342848 | Lung | IAC | response to monosaccharide | 39/2061 | 225/18723 | 2.75e-03 | 2.51e-02 | 39 |
| GO:00602497 | Lung | IAC | anatomical structure homeostasis | 51/2061 | 314/18723 | 2.91e-03 | 2.61e-02 | 51 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| ABCA12 | SNV | Missense_Mutation | c.2194N>G | p.Gln732Glu | p.Q732E | Q86UK0 | protein_coding | tolerated(0.35) | benign(0.05) | TCGA-A2-A0CL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD | |
| ABCA12 | SNV | Missense_Mutation | c.5812C>G | p.Pro1938Ala | p.P1938A | Q86UK0 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A8-A06Q-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| ABCA12 | SNV | Missense_Mutation | c.2674N>T | p.Asp892Tyr | p.D892Y | Q86UK0 | protein_coding | deleterious(0) | benign(0.328) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| ABCA12 | SNV | Missense_Mutation | rs866662919 | c.591N>G | p.Phe197Leu | p.F197L | Q86UK0 | protein_coding | tolerated(1) | benign(0) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
| ABCA12 | SNV | Missense_Mutation | novel | c.6605N>T | p.Ser2202Phe | p.S2202F | Q86UK0 | protein_coding | tolerated(0.17) | benign(0) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ABCA12 | SNV | Missense_Mutation | rs767287642 | c.5096N>A | p.Ser1699Tyr | p.S1699Y | Q86UK0 | protein_coding | tolerated(0.06) | possibly_damaging(0.825) | TCGA-B6-A0IJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ABCA12 | SNV | Missense_Mutation | c.7092N>C | p.Lys2364Asn | p.K2364N | Q86UK0 | protein_coding | deleterious(0.01) | benign(0.014) | TCGA-BH-A0B1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | adriamycin | SD | |
| ABCA12 | SNV | Missense_Mutation | c.7402C>G | p.Gln2468Glu | p.Q2468E | Q86UK0 | protein_coding | deleterious(0.01) | possibly_damaging(0.695) | TCGA-BH-A0HA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| ABCA12 | SNV | Missense_Mutation | c.6807G>C | p.Lys2269Asn | p.K2269N | Q86UK0 | protein_coding | tolerated(0.17) | benign(0.003) | TCGA-BH-A18P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| ABCA12 | SNV | Missense_Mutation | rs762358538 | c.6739N>C | p.Gly2247Arg | p.G2247R | Q86UK0 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-BH-A18V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | 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 |
| Page: 1 |
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