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Gene: AP3S2 |
Gene summary for AP3S2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | AP3S2 | Gene ID | 10239 |
| Gene name | adaptor related protein complex 3 subunit sigma 2 | |
| Gene Alias | AP3S3 | |
| Cytomap | 15q26.1 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | A0A024RC62 |
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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 |
| 10239 | AP3S2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.29e-04 | 2.26e-01 | -0.1808 |
| 10239 | AP3S2 | HTA11_78_2000001011 | Human | Colorectum | AD | 3.17e-03 | 1.97e-01 | -0.1088 |
| 10239 | AP3S2 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.76e-09 | 3.01e-01 | -0.1954 |
| 10239 | AP3S2 | HTA11_83_2000001011 | Human | Colorectum | SER | 7.41e-04 | 2.73e-01 | -0.1526 |
| 10239 | AP3S2 | HTA11_696_2000001011 | Human | Colorectum | AD | 7.36e-05 | 1.82e-01 | -0.1464 |
| 10239 | AP3S2 | HTA11_866_2000001011 | Human | Colorectum | AD | 4.47e-04 | 1.20e-01 | -0.1001 |
| 10239 | AP3S2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 8.21e-05 | 2.27e-01 | -0.059 |
| 10239 | AP3S2 | LZE4T | Human | Esophagus | ESCC | 4.27e-05 | 1.84e-01 | 0.0811 |
| 10239 | AP3S2 | LZE5T | Human | Esophagus | ESCC | 2.72e-03 | 2.90e-01 | 0.0514 |
| 10239 | AP3S2 | LZE7T | Human | Esophagus | ESCC | 1.07e-09 | 4.12e-01 | 0.0667 |
| 10239 | AP3S2 | LZE24T | Human | Esophagus | ESCC | 9.00e-08 | 2.00e-01 | 0.0596 |
| 10239 | AP3S2 | P2T-E | Human | Esophagus | ESCC | 2.64e-10 | 2.24e-01 | 0.1177 |
| 10239 | AP3S2 | P4T-E | Human | Esophagus | ESCC | 3.85e-10 | 2.85e-01 | 0.1323 |
| 10239 | AP3S2 | P5T-E | Human | Esophagus | ESCC | 1.04e-07 | 2.22e-01 | 0.1327 |
| 10239 | AP3S2 | P8T-E | Human | Esophagus | ESCC | 5.82e-10 | 2.01e-01 | 0.0889 |
| 10239 | AP3S2 | P9T-E | Human | Esophagus | ESCC | 1.45e-06 | 2.03e-01 | 0.1131 |
| 10239 | AP3S2 | P10T-E | Human | Esophagus | ESCC | 4.61e-15 | 2.89e-01 | 0.116 |
| 10239 | AP3S2 | P11T-E | Human | Esophagus | ESCC | 4.59e-09 | 3.57e-01 | 0.1426 |
| 10239 | AP3S2 | P12T-E | Human | Esophagus | ESCC | 2.48e-10 | 3.05e-01 | 0.1122 |
| 10239 | AP3S2 | P15T-E | Human | Esophagus | ESCC | 3.71e-17 | 4.01e-01 | 0.1149 |
| Page: 1 2 3 4 |
| 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 | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| 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:005164821 | Liver | HCC | vesicle localization | 107/7958 | 177/18723 | 1.05e-06 | 1.57e-05 | 107 |
| GO:00080882 | Liver | HCC | axo-dendritic transport | 52/7958 | 75/18723 | 2.34e-06 | 3.14e-05 | 52 |
| GO:00723843 | Liver | HCC | organelle transport along microtubule | 56/7958 | 85/18723 | 1.13e-05 | 1.29e-04 | 56 |
| GO:003070521 | Liver | HCC | cytoskeleton-dependent intracellular transport | 111/7958 | 195/18723 | 3.25e-05 | 3.28e-04 | 111 |
| GO:0047496 | Liver | HCC | vesicle transport along microtubule | 34/7958 | 47/18723 | 3.27e-05 | 3.29e-04 | 34 |
| GO:0098930 | Liver | HCC | axonal transport | 43/7958 | 64/18723 | 5.73e-05 | 5.31e-04 | 43 |
| GO:00109702 | Liver | HCC | transport along microtubule | 90/7958 | 155/18723 | 6.49e-05 | 5.92e-04 | 90 |
| GO:00995182 | Liver | HCC | vesicle cytoskeletal trafficking | 46/7958 | 73/18723 | 3.23e-04 | 2.28e-03 | 46 |
| GO:0008089 | Liver | HCC | anterograde axonal transport | 32/7958 | 50/18723 | 1.76e-03 | 9.12e-03 | 32 |
| GO:0006896 | Liver | HCC | Golgi to vacuole transport | 15/7958 | 20/18723 | 3.31e-03 | 1.51e-02 | 15 |
| GO:0048489 | Liver | HCC | synaptic vesicle transport | 27/7958 | 42/18723 | 3.60e-03 | 1.60e-02 | 27 |
| GO:0048490 | Liver | HCC | anterograde synaptic vesicle transport | 14/7958 | 19/18723 | 5.94e-03 | 2.44e-02 | 14 |
| GO:0099514 | Liver | HCC | synaptic vesicle cytoskeletal transport | 14/7958 | 19/18723 | 5.94e-03 | 2.44e-02 | 14 |
| GO:0099517 | Liver | HCC | synaptic vesicle transport along microtubule | 14/7958 | 19/18723 | 5.94e-03 | 2.44e-02 | 14 |
| Page: 1 2 3 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04142 | Colorectum | SER | Lysosome | 38/1580 | 132/8465 | 2.87e-03 | 2.03e-02 | 1.47e-02 | 38 |
| hsa041421 | Colorectum | SER | Lysosome | 38/1580 | 132/8465 | 2.87e-03 | 2.03e-02 | 1.47e-02 | 38 |
| hsa0414222 | Esophagus | ESCC | Lysosome | 102/4205 | 132/8465 | 5.11e-11 | 7.13e-10 | 3.65e-10 | 102 |
| hsa0414232 | Esophagus | ESCC | Lysosome | 102/4205 | 132/8465 | 5.11e-11 | 7.13e-10 | 3.65e-10 | 102 |
| hsa041422 | Liver | HCC | Lysosome | 100/4020 | 132/8465 | 2.32e-11 | 4.31e-10 | 2.40e-10 | 100 |
| hsa041423 | Liver | HCC | Lysosome | 100/4020 | 132/8465 | 2.32e-11 | 4.31e-10 | 2.40e-10 | 100 |
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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 |
| AP3S2 | SNV | Missense_Mutation | c.24N>G | p.Phe8Leu | p.F8L | P59780 | protein_coding | deleterious(0.04) | possibly_damaging(0.612) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| AP3S2 | SNV | Missense_Mutation | rs774639100 | c.476N>T | p.Ala159Val | p.A159V | P59780 | protein_coding | deleterious(0.01) | benign(0.014) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| AP3S2 | SNV | Missense_Mutation | novel | c.516N>T | p.Glu172Asp | p.E172D | P59780 | protein_coding | tolerated_low_confidence(0.08) | benign(0.003) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| AP3S2 | SNV | Missense_Mutation | novel | c.444N>T | p.Glu148Asp | p.E148D | P59780 | protein_coding | tolerated(0.11) | benign(0.033) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| AP3S2 | SNV | Missense_Mutation | rs148740750 | c.304G>A | p.Glu102Lys | p.E102K | P59780 | protein_coding | deleterious(0.02) | probably_damaging(0.986) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| AP3S2 | SNV | Missense_Mutation | rs372598574 | c.197G>A | p.Arg66Gln | p.R66Q | P59780 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| AP3S2 | SNV | Missense_Mutation | rs781619946 | c.280G>A | p.Val94Met | p.V94M | P59780 | protein_coding | deleterious(0.02) | probably_damaging(0.981) | TCGA-B5-A11U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| AP3S2 | SNV | Missense_Mutation | rs776607280 | c.478N>T | p.Arg160Trp | p.R160W | P59780 | protein_coding | deleterious(0.01) | possibly_damaging(0.696) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| AP3S2 | SNV | Missense_Mutation | rs538209457 | c.485N>C | p.Val162Ala | p.V162A | P59780 | protein_coding | tolerated(0.2) | benign(0.007) | TCGA-BG-A222-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| AP3S2 | SNV | Missense_Mutation | novel | c.160N>C | p.Ser54Arg | p.S54R | P59780 | protein_coding | tolerated(0.42) | benign(0.043) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid 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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