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Gene: SCAMP1 |
Gene summary for SCAMP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SCAMP1 | Gene ID | 9522 |
| Gene name | secretory carrier membrane protein 1 | |
| Gene Alias | SCAMP | |
| Cytomap | 5q14.1 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | A0A087WXB0 |
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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 |
| 9522 | SCAMP1 | LZE2T | Human | Esophagus | ESCC | 2.00e-05 | 6.08e-01 | 0.082 |
| 9522 | SCAMP1 | LZE4T | Human | Esophagus | ESCC | 6.79e-18 | 5.16e-01 | 0.0811 |
| 9522 | SCAMP1 | LZE5T | Human | Esophagus | ESCC | 6.12e-03 | 2.07e-01 | 0.0514 |
| 9522 | SCAMP1 | LZE8T | Human | Esophagus | ESCC | 2.08e-05 | 1.04e-01 | 0.067 |
| 9522 | SCAMP1 | LZE22D1 | Human | Esophagus | HGIN | 3.64e-02 | 7.17e-02 | 0.0595 |
| 9522 | SCAMP1 | LZE24T | Human | Esophagus | ESCC | 3.00e-24 | 6.82e-01 | 0.0596 |
| 9522 | SCAMP1 | LZE6T | Human | Esophagus | ESCC | 1.20e-03 | 7.50e-02 | 0.0845 |
| 9522 | SCAMP1 | P2T-E | Human | Esophagus | ESCC | 3.70e-35 | 6.41e-01 | 0.1177 |
| 9522 | SCAMP1 | P4T-E | Human | Esophagus | ESCC | 3.89e-25 | 3.36e-01 | 0.1323 |
| 9522 | SCAMP1 | P5T-E | Human | Esophagus | ESCC | 1.49e-13 | 2.63e-01 | 0.1327 |
| 9522 | SCAMP1 | P8T-E | Human | Esophagus | ESCC | 2.15e-18 | 2.63e-01 | 0.0889 |
| 9522 | SCAMP1 | P9T-E | Human | Esophagus | ESCC | 2.07e-17 | 4.38e-01 | 0.1131 |
| 9522 | SCAMP1 | P10T-E | Human | Esophagus | ESCC | 6.27e-32 | 4.79e-01 | 0.116 |
| 9522 | SCAMP1 | P11T-E | Human | Esophagus | ESCC | 1.10e-11 | 3.37e-01 | 0.1426 |
| 9522 | SCAMP1 | P12T-E | Human | Esophagus | ESCC | 5.92e-23 | 5.74e-01 | 0.1122 |
| 9522 | SCAMP1 | P15T-E | Human | Esophagus | ESCC | 7.90e-43 | 8.68e-01 | 0.1149 |
| 9522 | SCAMP1 | P16T-E | Human | Esophagus | ESCC | 1.20e-24 | 3.26e-01 | 0.1153 |
| 9522 | SCAMP1 | P17T-E | Human | Esophagus | ESCC | 1.43e-05 | 4.18e-01 | 0.1278 |
| 9522 | SCAMP1 | P19T-E | Human | Esophagus | ESCC | 1.20e-06 | 4.94e-01 | 0.1662 |
| 9522 | SCAMP1 | P20T-E | Human | Esophagus | ESCC | 5.28e-26 | 4.70e-01 | 0.1124 |
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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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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. |
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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: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:004819310 | Prostate | BPH | Golgi vesicle transport | 102/3107 | 296/18723 | 3.90e-14 | 4.56e-12 | 102 |
| GO:00068928 | Prostate | BPH | post-Golgi vesicle-mediated transport | 34/3107 | 104/18723 | 4.14e-05 | 4.43e-04 | 34 |
| GO:004819314 | Prostate | Tumor | Golgi vesicle transport | 105/3246 | 296/18723 | 3.55e-14 | 4.33e-12 | 105 |
| GO:000689213 | Prostate | Tumor | post-Golgi vesicle-mediated transport | 35/3246 | 104/18723 | 4.14e-05 | 4.70e-04 | 35 |
| 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 |
| GO:004819320 | Thyroid | PTC | Golgi vesicle transport | 186/5968 | 296/18723 | 3.09e-28 | 1.22e-25 | 186 |
| GO:000689218 | Thyroid | PTC | post-Golgi vesicle-mediated transport | 66/5968 | 104/18723 | 3.36e-11 | 1.24e-09 | 66 |
| GO:0048193111 | Thyroid | ATC | Golgi vesicle transport | 189/6293 | 296/18723 | 9.58e-27 | 5.05e-24 | 189 |
| GO:000689219 | Thyroid | ATC | post-Golgi vesicle-mediated transport | 68/6293 | 104/18723 | 3.30e-11 | 1.10e-09 | 68 |
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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 |
| SCAMP1 | SNV | Missense_Mutation | novel | c.399N>G | p.Phe133Leu | p.F133L | O15126 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SCAMP1 | SNV | Missense_Mutation | novel | c.509N>A | p.Cys170Tyr | p.C170Y | O15126 | protein_coding | deleterious(0) | probably_damaging(0.981) | TCGA-D8-A1XJ-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD |
| SCAMP1 | insertion | Nonsense_Mutation | novel | c.990_991insGGGCTAGGAGAATTGTAGGTTGTTGGTATTGGAAGATGA | p.Gln330_Asn331insGlyLeuGlyGluLeuTerValValGlyIleGlyArgTer | p.Q330_N331insGLGEL*VVGIGR* | O15126 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | ||
| SCAMP1 | SNV | Missense_Mutation | rs763582841 | c.269G>A | p.Arg90His | p.R90H | O15126 | protein_coding | deleterious(0) | probably_damaging(0.919) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD |
| SCAMP1 | SNV | Missense_Mutation | novel | c.233N>C | p.Lys78Thr | p.K78T | O15126 | protein_coding | tolerated(0.29) | benign(0.001) | TCGA-AM-5821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SCAMP1 | SNV | Missense_Mutation | novel | c.381N>G | p.Phe127Leu | p.F127L | O15126 | protein_coding | tolerated(0.22) | benign(0.225) | TCGA-CK-4950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | folfox | SD |
| SCAMP1 | insertion | Frame_Shift_Ins | novel | c.326_327insTGTTCCT | p.Gln109HisfsTer10 | p.Q109Hfs*10 | O15126 | protein_coding | TCGA-AM-5821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| SCAMP1 | SNV | Missense_Mutation | novel | c.815N>T | p.Thr272Ile | p.T272I | O15126 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-AJ-A23O-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SCAMP1 | SNV | Missense_Mutation | novel | c.728G>A | p.Gly243Asp | p.G243D | O15126 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| SCAMP1 | SNV | Missense_Mutation | novel | c.83G>T | p.Arg28Ile | p.R28I | O15126 | protein_coding | tolerated(0.18) | benign(0.01) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | 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 |
| Page: 1 |
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