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Gene: SCAMP3 |
Gene summary for SCAMP3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SCAMP3 | Gene ID | 10067 |
| Gene name | secretory carrier membrane protein 3 | |
| Gene Alias | C1orf3 | |
| Cytomap | 1q22 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | O14828 |
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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 |
| 10067 | SCAMP3 | LZE2T | Human | Esophagus | ESCC | 5.82e-04 | 9.14e-01 | 0.082 |
| 10067 | SCAMP3 | LZE4T | Human | Esophagus | ESCC | 8.61e-11 | 4.76e-01 | 0.0811 |
| 10067 | SCAMP3 | LZE5T | Human | Esophagus | ESCC | 3.28e-02 | 2.35e-01 | 0.0514 |
| 10067 | SCAMP3 | LZE7T | Human | Esophagus | ESCC | 6.01e-10 | 9.67e-01 | 0.0667 |
| 10067 | SCAMP3 | LZE8T | Human | Esophagus | ESCC | 2.22e-04 | 3.08e-01 | 0.067 |
| 10067 | SCAMP3 | LZE20T | Human | Esophagus | ESCC | 4.90e-12 | 3.37e-01 | 0.0662 |
| 10067 | SCAMP3 | LZE22D1 | Human | Esophagus | HGIN | 1.37e-02 | 6.57e-02 | 0.0595 |
| 10067 | SCAMP3 | LZE22T | Human | Esophagus | ESCC | 7.82e-03 | 6.64e-01 | 0.068 |
| 10067 | SCAMP3 | LZE24T | Human | Esophagus | ESCC | 4.01e-25 | 7.86e-01 | 0.0596 |
| 10067 | SCAMP3 | LZE6T | Human | Esophagus | ESCC | 5.03e-06 | 6.30e-01 | 0.0845 |
| 10067 | SCAMP3 | P1T-E | Human | Esophagus | ESCC | 2.33e-08 | 6.97e-01 | 0.0875 |
| 10067 | SCAMP3 | P2T-E | Human | Esophagus | ESCC | 5.86e-46 | 9.04e-01 | 0.1177 |
| 10067 | SCAMP3 | P4T-E | Human | Esophagus | ESCC | 5.39e-35 | 9.12e-01 | 0.1323 |
| 10067 | SCAMP3 | P5T-E | Human | Esophagus | ESCC | 3.82e-37 | 8.87e-01 | 0.1327 |
| 10067 | SCAMP3 | P8T-E | Human | Esophagus | ESCC | 1.99e-25 | 6.66e-01 | 0.0889 |
| 10067 | SCAMP3 | P9T-E | Human | Esophagus | ESCC | 9.67e-36 | 9.95e-01 | 0.1131 |
| 10067 | SCAMP3 | P10T-E | Human | Esophagus | ESCC | 8.49e-40 | 7.13e-01 | 0.116 |
| 10067 | SCAMP3 | P11T-E | Human | Esophagus | ESCC | 3.44e-29 | 1.14e+00 | 0.1426 |
| 10067 | SCAMP3 | P12T-E | Human | Esophagus | ESCC | 2.69e-24 | 4.57e-01 | 0.1122 |
| 10067 | SCAMP3 | P15T-E | Human | Esophagus | ESCC | 2.04e-29 | 7.47e-01 | 0.1149 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:004819317 | Esophagus | HGIN | Golgi vesicle transport | 83/2587 | 296/18723 | 8.59e-11 | 8.89e-09 | 83 |
| GO:000689210 | Esophagus | HGIN | post-Golgi vesicle-mediated transport | 26/2587 | 104/18723 | 1.63e-03 | 1.81e-02 | 26 |
| GO:004819318 | Esophagus | ESCC | Golgi vesicle transport | 231/8552 | 296/18723 | 1.82e-30 | 9.63e-28 | 231 |
| GO:000689215 | Esophagus | ESCC | post-Golgi vesicle-mediated transport | 82/8552 | 104/18723 | 4.00e-12 | 1.55e-10 | 82 |
| GO:004819311 | Liver | Cirrhotic | Golgi vesicle transport | 153/4634 | 296/18723 | 1.02e-23 | 6.43e-21 | 153 |
| GO:000689211 | Liver | Cirrhotic | post-Golgi vesicle-mediated transport | 51/4634 | 104/18723 | 7.12e-08 | 2.15e-06 | 51 |
| GO:004819321 | Liver | HCC | Golgi vesicle transport | 217/7958 | 296/18723 | 2.58e-27 | 1.02e-24 | 217 |
| GO:000689221 | Liver | HCC | post-Golgi vesicle-mediated transport | 77/7958 | 104/18723 | 6.14e-11 | 2.24e-09 | 77 |
| GO:004819315 | Oral cavity | OSCC | Golgi vesicle transport | 209/7305 | 296/18723 | 1.39e-28 | 6.30e-26 | 209 |
| GO:00068929 | Oral cavity | OSCC | post-Golgi vesicle-mediated transport | 71/7305 | 104/18723 | 1.37e-09 | 3.33e-08 | 71 |
| GO:004819316 | Oral cavity | LP | Golgi vesicle transport | 141/4623 | 296/18723 | 6.11e-18 | 1.06e-15 | 141 |
| GO:000689214 | Oral cavity | LP | post-Golgi vesicle-mediated transport | 44/4623 | 104/18723 | 5.90e-05 | 8.05e-04 | 44 |
| GO:0048193110 | Skin | cSCC | Golgi vesicle transport | 153/4864 | 296/18723 | 1.85e-21 | 3.41e-19 | 153 |
| GO:000689217 | Skin | cSCC | post-Golgi vesicle-mediated transport | 49/4864 | 104/18723 | 2.71e-06 | 4.30e-05 | 49 |
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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 |
| SCAMP3 | SNV | Missense_Mutation | c.412C>G | p.Leu138Val | p.L138V | O14828 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-BH-A0DX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR | |
| SCAMP3 | SNV | Missense_Mutation | c.37N>A | p.Glu13Lys | p.E13K | O14828 | protein_coding | deleterious(0.03) | benign(0.015) | TCGA-C8-A12Q-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| SCAMP3 | SNV | Missense_Mutation | novel | c.280G>C | p.Ala94Pro | p.A94P | O14828 | protein_coding | tolerated(0.09) | possibly_damaging(0.889) | TCGA-C5-A1BE-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| SCAMP3 | SNV | Missense_Mutation | c.115N>C | p.Asp39His | p.D39H | O14828 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-EK-A2RC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| SCAMP3 | SNV | Missense_Mutation | c.334N>C | p.Glu112Gln | p.E112Q | O14828 | protein_coding | deleterious(0) | benign(0.335) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| SCAMP3 | SNV | Missense_Mutation | c.331N>C | p.Glu111Gln | p.E111Q | O14828 | protein_coding | tolerated(0.09) | benign(0.014) | TCGA-LP-A4AV-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| SCAMP3 | SNV | Missense_Mutation | novel | c.81N>G | p.Ile27Met | p.I27M | O14828 | protein_coding | tolerated(0.06) | benign(0.233) | TCGA-VS-A9V1-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| SCAMP3 | SNV | Missense_Mutation | novel | c.65N>G | p.Gln22Arg | p.Q22R | O14828 | protein_coding | tolerated(0.05) | benign(0.003) | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SCAMP3 | SNV | Missense_Mutation | c.74N>T | p.Ala25Val | p.A25V | O14828 | protein_coding | deleterious(0) | possibly_damaging(0.612) | TCGA-AY-4070-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | 5-fu | PD | |
| SCAMP3 | SNV | Missense_Mutation | novel | c.223N>T | p.Leu75Phe | p.L75F | O14828 | protein_coding | tolerated(0.05) | possibly_damaging(0.454) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | 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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