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Gene: ABCA3 |
Gene summary for ABCA3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | ABCA3 | Gene ID | 21 |
Gene name | ATP binding cassette subfamily A member 3 | |
Gene Alias | ABC-C | |
Cytomap | 16p13.3 | |
Gene Type | protein-coding | GO ID | GO:0001894 | UniProtAcc | Q4LE27 |
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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 |
21 | ABCA3 | HCC2 | Human | Liver | HCC | 6.01e-05 | 2.88e+00 | 0.5341 |
21 | ABCA3 | S014 | Human | Liver | HCC | 5.03e-13 | 4.34e-01 | 0.2254 |
21 | ABCA3 | S015 | Human | Liver | HCC | 4.36e-06 | 2.86e-01 | 0.2375 |
21 | ABCA3 | S016 | Human | Liver | HCC | 5.69e-13 | 3.98e-01 | 0.2243 |
21 | ABCA3 | S027 | Human | Liver | HCC | 3.48e-08 | 5.20e-01 | 0.2446 |
21 | ABCA3 | S028 | Human | Liver | HCC | 2.19e-15 | 5.11e-01 | 0.2503 |
21 | ABCA3 | S029 | Human | Liver | HCC | 9.53e-10 | 2.85e-01 | 0.2581 |
21 | ABCA3 | TD9 | Human | Lung | IAC | 3.53e-05 | -1.37e-01 | 0.088 |
21 | ABCA3 | RNA-P10T2-P10T2-1 | Human | Lung | AAH | 1.33e-03 | 2.85e-02 | -0.1271 |
21 | ABCA3 | RNA-P10T2-P10T2-2 | Human | Lung | AAH | 1.18e-08 | 3.08e-02 | -0.1406 |
21 | ABCA3 | RNA-P10T2-P10T2-3 | Human | Lung | AAH | 1.09e-03 | -1.37e-01 | -0.1408 |
21 | ABCA3 | RNA-P10T2-P10T2-4 | Human | Lung | AAH | 9.91e-08 | 2.80e-01 | -0.138 |
21 | ABCA3 | RNA-P17T-P17T-6 | Human | Lung | IAC | 8.59e-04 | -6.42e-01 | 0.3385 |
21 | ABCA3 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 1.01e-11 | 1.33e-01 | -0.2116 |
21 | ABCA3 | RNA-P25T1-P25T1-2 | Human | Lung | AIS | 2.91e-06 | 1.40e-02 | -0.1941 |
21 | ABCA3 | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 1.34e-03 | -2.12e-02 | -0.2107 |
21 | ABCA3 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 1.93e-11 | 1.28e-01 | -0.2119 |
21 | ABCA3 | RNA-P3T-P3T-1 | Human | Lung | IAC | 1.49e-02 | -8.37e-01 | 0.1829 |
21 | ABCA3 | RNA-P3T-P3T-4 | Human | Lung | IAC | 1.32e-03 | -7.56e-01 | 0.1859 |
21 | ABCA3 | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 1.08e-11 | -1.77e-01 | -0.0166 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:004325422 | Liver | HCC | regulation of protein-containing complex assembly | 264/7958 | 428/18723 | 5.47e-16 | 4.39e-14 | 264 |
GO:004854522 | Liver | HCC | response to steroid hormone | 206/7958 | 339/18723 | 6.81e-12 | 2.92e-10 | 206 |
GO:003133412 | Liver | HCC | positive regulation of protein-containing complex assembly | 150/7958 | 237/18723 | 7.35e-11 | 2.63e-09 | 150 |
GO:00066444 | Liver | HCC | phospholipid metabolic process | 214/7958 | 383/18723 | 7.25e-08 | 1.48e-06 | 214 |
GO:00550882 | Liver | HCC | lipid homeostasis | 103/7958 | 167/18723 | 4.27e-07 | 7.18e-06 | 103 |
GO:004648611 | Liver | HCC | glycerolipid metabolic process | 215/7958 | 392/18723 | 4.54e-07 | 7.49e-06 | 215 |
GO:000941022 | Liver | HCC | response to xenobiotic stimulus | 248/7958 | 462/18723 | 6.47e-07 | 1.02e-05 | 248 |
GO:00192162 | Liver | HCC | regulation of lipid metabolic process | 181/7958 | 331/18723 | 4.58e-06 | 5.79e-05 | 181 |
GO:005138421 | Liver | HCC | response to glucocorticoid | 90/7958 | 148/18723 | 5.18e-06 | 6.47e-05 | 90 |
GO:00066504 | Liver | HCC | glycerophospholipid metabolic process | 168/7958 | 306/18723 | 7.27e-06 | 8.62e-05 | 168 |
GO:003196021 | Liver | HCC | response to corticosteroid | 98/7958 | 167/18723 | 1.73e-05 | 1.87e-04 | 98 |
GO:001087621 | Liver | HCC | lipid localization | 228/7958 | 448/18723 | 1.80e-04 | 1.41e-03 | 228 |
GO:01200092 | Liver | HCC | intermembrane lipid transfer | 33/7958 | 48/18723 | 2.12e-04 | 1.63e-03 | 33 |
GO:00468902 | Liver | HCC | regulation of lipid biosynthetic process | 96/7958 | 171/18723 | 2.14e-04 | 1.63e-03 | 96 |
GO:000686921 | Liver | HCC | lipid transport | 198/7958 | 398/18723 | 1.92e-03 | 9.78e-03 | 198 |
GO:00303012 | Liver | HCC | cholesterol transport | 65/7958 | 117/18723 | 2.95e-03 | 1.38e-02 | 65 |
GO:00159182 | Liver | HCC | sterol transport | 71/7958 | 130/18723 | 3.49e-03 | 1.58e-02 | 71 |
GO:003032311 | Liver | HCC | respiratory tube development | 95/7958 | 181/18723 | 4.15e-03 | 1.81e-02 | 95 |
GO:003032411 | Liver | HCC | lung development | 91/7958 | 177/18723 | 1.01e-02 | 3.80e-02 | 91 |
GO:0048875 | Lung | IAC | chemical homeostasis within a tissue | 11/2061 | 14/18723 | 7.44e-09 | 1.05e-06 | 11 |
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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. |
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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 |
ABCA3 | SNV | Missense_Mutation | rs148823458 | c.4964G>A | p.Arg1655His | p.R1655H | Q99758 | protein_coding | tolerated(0.18) | benign(0) | TCGA-QF-A5YS-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
ABCA3 | SNV | Missense_Mutation | rs773021659 | c.2512C>T | p.Arg838Trp | p.R838W | Q99758 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-SL-A6JA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
ABCA3 | insertion | In_Frame_Ins | novel | c.518_519insAAAACGAAGATACAATACAATGCA | p.Lys174_Glu175insArgArgTyrAsnThrMetGlnLys | p.K174_E175insRRYNTMQK | Q99758 | protein_coding | TCGA-EC-A1NJ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
ABCA3 | SNV | Missense_Mutation | rs368905104 | c.4886N>T | p.Ala1629Val | p.A1629V | Q99758 | protein_coding | tolerated(0.27) | benign(0.147) | TCGA-DD-A4NA-01 | Liver | liver hepatocellular carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
ABCA3 | SNV | Missense_Mutation | novel | c.1864N>G | p.Thr622Ala | p.T622A | Q99758 | protein_coding | deleterious(0) | probably_damaging(0.984) | TCGA-DD-AACI-01 | Liver | liver hepatocellular carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
ABCA3 | SNV | Missense_Mutation | rs565777051 | c.3242G>A | p.Arg1081Gln | p.R1081Q | Q99758 | protein_coding | tolerated(0.47) | benign(0.017) | TCGA-DD-AACS-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
ABCA3 | SNV | Missense_Mutation | novel | c.2624G>T | p.Cys875Phe | p.C875F | Q99758 | protein_coding | tolerated(0.05) | benign(0.072) | TCGA-DD-AAD8-01 | Liver | liver hepatocellular carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
ABCA3 | SNV | Missense_Mutation | c.3681G>A | p.Met1227Ile | p.M1227I | Q99758 | protein_coding | tolerated(0.87) | benign(0) | TCGA-44-7670-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | |
ABCA3 | SNV | Missense_Mutation | rs150902383 | c.265G>T | p.Ala89Ser | p.A89S | Q99758 | protein_coding | tolerated(0.06) | possibly_damaging(0.564) | TCGA-49-4505-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
ABCA3 | SNV | Missense_Mutation | novel | c.4474G>T | p.Gly1492Trp | p.G1492W | Q99758 | protein_coding | deleterious(0.01) | possibly_damaging(0.856) | TCGA-53-7626-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unspecific | Cisplatin | PD |
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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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