|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: AP3S1 |
Gene summary for AP3S1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | AP3S1 | Gene ID | 1176 |
| Gene name | adaptor related protein complex 3 subunit sigma 1 | |
| Gene Alias | CLAPS3 | |
| Cytomap | 5q22.3-q23.1 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q92572 |
Top |
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 |
| 1176 | AP3S1 | AEH-subject1 | Human | Endometrium | AEH | 4.24e-09 | -2.63e-01 | -0.3059 |
| 1176 | AP3S1 | AEH-subject2 | Human | Endometrium | AEH | 4.96e-03 | -2.63e-01 | -0.2525 |
| 1176 | AP3S1 | AEH-subject3 | Human | Endometrium | AEH | 7.59e-11 | -2.86e-01 | -0.2576 |
| 1176 | AP3S1 | AEH-subject5 | Human | Endometrium | AEH | 5.69e-05 | -2.48e-01 | -0.2953 |
| 1176 | AP3S1 | EEC-subject1 | Human | Endometrium | EEC | 1.11e-07 | -2.44e-01 | -0.2682 |
| 1176 | AP3S1 | EEC-subject2 | Human | Endometrium | EEC | 1.94e-16 | -3.35e-01 | -0.2607 |
| 1176 | AP3S1 | EEC-subject3 | Human | Endometrium | EEC | 5.69e-28 | -4.10e-01 | -0.2525 |
| 1176 | AP3S1 | EEC-subject4 | Human | Endometrium | EEC | 2.10e-09 | -2.83e-01 | -0.2571 |
| 1176 | AP3S1 | EEC-subject5 | Human | Endometrium | EEC | 2.34e-06 | -2.65e-01 | -0.249 |
| 1176 | AP3S1 | GSM5276934 | Human | Endometrium | EEC | 3.35e-04 | -2.01e-01 | -0.0913 |
| 1176 | AP3S1 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 1.04e-22 | -1.52e-01 | -0.1869 |
| 1176 | AP3S1 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 3.45e-22 | -1.82e-01 | -0.1875 |
| 1176 | AP3S1 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 4.37e-29 | -1.26e-01 | -0.1883 |
| 1176 | AP3S1 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 1.20e-34 | -2.54e-01 | -0.1934 |
| 1176 | AP3S1 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 1.59e-54 | -8.71e-02 | -0.1917 |
| 1176 | AP3S1 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 1.24e-34 | -1.05e-01 | -0.1916 |
| 1176 | AP3S1 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 1.62e-09 | -1.91e-01 | -0.1269 |
| 1176 | AP3S1 | LZE4T | Human | Esophagus | ESCC | 5.02e-11 | 3.33e-01 | 0.0811 |
| 1176 | AP3S1 | LZE5T | Human | Esophagus | ESCC | 3.63e-05 | 2.87e-01 | 0.0514 |
| 1176 | AP3S1 | LZE7T | Human | Esophagus | ESCC | 4.66e-06 | 1.94e-01 | 0.0667 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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. |
Top |
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:00516568 | Endometrium | AEH | establishment of organelle localization | 77/2100 | 390/18723 | 4.89e-07 | 1.94e-05 | 77 |
| GO:00481939 | Endometrium | AEH | Golgi vesicle transport | 60/2100 | 296/18723 | 3.65e-06 | 9.79e-05 | 60 |
| GO:19016539 | Endometrium | AEH | cellular response to peptide | 64/2100 | 359/18723 | 1.16e-04 | 1.63e-03 | 64 |
| GO:004343410 | Endometrium | AEH | response to peptide hormone | 70/2100 | 414/18723 | 2.93e-04 | 3.35e-03 | 70 |
| GO:00307058 | Endometrium | AEH | cytoskeleton-dependent intracellular transport | 38/2100 | 195/18723 | 4.72e-04 | 4.91e-03 | 38 |
| GO:00516507 | Endometrium | AEH | establishment of vesicle localization | 32/2100 | 161/18723 | 8.99e-04 | 8.24e-03 | 32 |
| GO:00328699 | Endometrium | AEH | cellular response to insulin stimulus | 37/2100 | 203/18723 | 1.97e-03 | 1.54e-02 | 37 |
| GO:00713758 | Endometrium | AEH | cellular response to peptide hormone stimulus | 49/2100 | 290/18723 | 2.24e-03 | 1.72e-02 | 49 |
| GO:00516487 | Endometrium | AEH | vesicle localization | 32/2100 | 177/18723 | 4.33e-03 | 2.86e-02 | 32 |
| GO:00082866 | Endometrium | AEH | insulin receptor signaling pathway | 23/2100 | 116/18723 | 4.58e-03 | 2.95e-02 | 23 |
| GO:00070348 | Endometrium | AEH | vacuolar transport | 29/2100 | 157/18723 | 4.69e-03 | 2.99e-02 | 29 |
| GO:00328689 | Endometrium | AEH | response to insulin | 44/2100 | 264/18723 | 4.70e-03 | 3.00e-02 | 44 |
| GO:00484891 | Endometrium | AEH | synaptic vesicle transport | 11/2100 | 42/18723 | 5.45e-03 | 3.37e-02 | 11 |
| GO:00080887 | Endometrium | AEH | axo-dendritic transport | 16/2100 | 75/18723 | 8.13e-03 | 4.49e-02 | 16 |
| GO:005165613 | Endometrium | EEC | establishment of organelle localization | 75/2168 | 390/18723 | 6.23e-06 | 1.49e-04 | 75 |
| GO:004819313 | Endometrium | EEC | Golgi vesicle transport | 60/2168 | 296/18723 | 9.91e-06 | 2.17e-04 | 60 |
| GO:190165314 | Endometrium | EEC | cellular response to peptide | 68/2168 | 359/18723 | 2.75e-05 | 4.83e-04 | 68 |
| GO:004343416 | Endometrium | EEC | response to peptide hormone | 74/2168 | 414/18723 | 9.11e-05 | 1.28e-03 | 74 |
| GO:003070514 | Endometrium | EEC | cytoskeleton-dependent intracellular transport | 39/2168 | 195/18723 | 4.40e-04 | 4.58e-03 | 39 |
| GO:007137513 | Endometrium | EEC | cellular response to peptide hormone stimulus | 52/2168 | 290/18723 | 8.77e-04 | 8.01e-03 | 52 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| hsa041424 | Liver | Cirrhotic | Lysosome | 68/2530 | 132/8465 | 1.34e-07 | 1.97e-06 | 1.21e-06 | 68 |
| hsa0414211 | Liver | Cirrhotic | Lysosome | 68/2530 | 132/8465 | 1.34e-07 | 1.97e-06 | 1.21e-06 | 68 |
| 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 |
| hsa041425 | Oral cavity | OSCC | Lysosome | 87/3704 | 132/8465 | 1.97e-07 | 1.35e-06 | 6.86e-07 | 87 |
| hsa0414212 | Oral cavity | OSCC | Lysosome | 87/3704 | 132/8465 | 1.97e-07 | 1.35e-06 | 6.86e-07 | 87 |
| hsa0414221 | Oral cavity | LP | Lysosome | 67/2418 | 132/8465 | 5.13e-08 | 7.77e-07 | 5.01e-07 | 67 |
| hsa0414231 | Oral cavity | LP | Lysosome | 67/2418 | 132/8465 | 5.13e-08 | 7.77e-07 | 5.01e-07 | 67 |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| AP3S1 | SNV | Missense_Mutation | c.467N>A | p.Gly156Glu | p.G156E | Q92572 | protein_coding | tolerated(0.26) | benign(0.044) | TCGA-BH-A18P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| AP3S1 | SNV | Missense_Mutation | c.327N>C | p.Leu109Phe | p.L109F | Q92572 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| AP3S1 | SNV | Missense_Mutation | c.572C>A | p.Ser191Tyr | p.S191Y | Q92572 | protein_coding | deleterious_low_confidence(0.01) | benign(0.003) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| AP3S1 | SNV | Missense_Mutation | rs200347946 | c.34G>A | p.Gly12Arg | p.G12R | Q92572 | protein_coding | deleterious(0.03) | possibly_damaging(0.873) | TCGA-CM-5868-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | fluorouracil | SD |
| AP3S1 | SNV | Missense_Mutation | c.125G>T | p.Arg42Ile | p.R42I | Q92572 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| AP3S1 | SNV | Missense_Mutation | novel | c.137N>C | p.Val46Ala | p.V46A | Q92572 | protein_coding | tolerated(0.15) | benign(0.034) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| AP3S1 | SNV | Missense_Mutation | novel | c.115N>A | p.Val39Ile | p.V39I | Q92572 | protein_coding | tolerated(0.18) | possibly_damaging(0.576) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| AP3S1 | SNV | Missense_Mutation | novel | c.208N>C | p.Thr70Pro | p.T70P | Q92572 | protein_coding | deleterious(0) | possibly_damaging(0.651) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| AP3S1 | SNV | Missense_Mutation | novel | c.119N>A | p.Ser40Tyr | p.S40Y | Q92572 | protein_coding | deleterious(0) | probably_damaging(0.958) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| AP3S1 | SNV | Missense_Mutation | c.209N>T | p.Thr70Met | p.T70M | Q92572 | protein_coding | deleterious(0.02) | probably_damaging(0.997) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |