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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 |
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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:0048193 | Colorectum | AD | Golgi vesicle transport | 109/3918 | 296/18723 | 1.80e-10 | 1.68e-08 | 109 |
GO:0051656 | Colorectum | AD | establishment of organelle localization | 131/3918 | 390/18723 | 3.00e-09 | 2.06e-07 | 131 |
GO:0006892 | Colorectum | AD | post-Golgi vesicle-mediated transport | 45/3918 | 104/18723 | 2.22e-07 | 9.26e-06 | 45 |
GO:0007034 | Colorectum | AD | vacuolar transport | 60/3918 | 157/18723 | 4.97e-07 | 1.85e-05 | 60 |
GO:0051650 | Colorectum | AD | establishment of vesicle localization | 57/3918 | 161/18723 | 1.47e-05 | 3.15e-04 | 57 |
GO:0051648 | Colorectum | AD | vesicle localization | 59/3918 | 177/18723 | 7.83e-05 | 1.25e-03 | 59 |
GO:0030705 | Colorectum | AD | cytoskeleton-dependent intracellular transport | 60/3918 | 195/18723 | 7.56e-04 | 7.59e-03 | 60 |
GO:0072384 | Colorectum | AD | organelle transport along microtubule | 28/3918 | 85/18723 | 6.55e-03 | 4.07e-02 | 28 |
GO:00516561 | Colorectum | SER | establishment of organelle localization | 100/2897 | 390/18723 | 1.11e-07 | 6.79e-06 | 100 |
GO:00481931 | Colorectum | SER | Golgi vesicle transport | 79/2897 | 296/18723 | 4.20e-07 | 2.15e-05 | 79 |
GO:00070341 | Colorectum | SER | vacuolar transport | 43/2897 | 157/18723 | 8.92e-05 | 1.93e-03 | 43 |
GO:00068921 | Colorectum | SER | post-Golgi vesicle-mediated transport | 31/2897 | 104/18723 | 1.59e-04 | 3.08e-03 | 31 |
GO:00516501 | Colorectum | SER | establishment of vesicle localization | 42/2897 | 161/18723 | 3.38e-04 | 5.35e-03 | 42 |
GO:00516481 | Colorectum | SER | vesicle localization | 43/2897 | 177/18723 | 1.41e-03 | 1.53e-02 | 43 |
GO:00307051 | Colorectum | SER | cytoskeleton-dependent intracellular transport | 44/2897 | 195/18723 | 5.53e-03 | 4.09e-02 | 44 |
GO:004819318 | Esophagus | ESCC | Golgi vesicle transport | 231/8552 | 296/18723 | 1.82e-30 | 9.63e-28 | 231 |
GO:005165617 | Esophagus | ESCC | establishment of organelle localization | 273/8552 | 390/18723 | 9.13e-23 | 1.81e-20 | 273 |
GO:000703417 | Esophagus | ESCC | vacuolar transport | 119/8552 | 157/18723 | 1.16e-14 | 6.30e-13 | 119 |
GO:000689215 | Esophagus | ESCC | post-Golgi vesicle-mediated transport | 82/8552 | 104/18723 | 4.00e-12 | 1.55e-10 | 82 |
GO:005165016 | Esophagus | ESCC | establishment of vesicle localization | 114/8552 | 161/18723 | 8.20e-11 | 2.53e-09 | 114 |
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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 |
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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 |
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 |
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