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Gene: SYAP1 |
Gene summary for SYAP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SYAP1 | Gene ID | 94056 |
| Gene name | synapse associated protein 1 | |
| Gene Alias | BSTA | |
| Cytomap | Xp22.2 | |
| Gene Type | protein-coding | GO ID | GO:0001932 | UniProtAcc | Q96A49 |
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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 |
| 94056 | SYAP1 | GSM4909281 | Human | Breast | IDC | 1.82e-06 | 3.34e-01 | 0.21 |
| 94056 | SYAP1 | GSM4909293 | Human | Breast | IDC | 1.60e-03 | 1.91e-01 | 0.1581 |
| 94056 | SYAP1 | GSM4909294 | Human | Breast | IDC | 1.74e-03 | 1.57e-01 | 0.2022 |
| 94056 | SYAP1 | GSM4909296 | Human | Breast | IDC | 5.18e-07 | 1.55e-01 | 0.1524 |
| 94056 | SYAP1 | GSM4909297 | Human | Breast | IDC | 6.68e-08 | -1.27e-01 | 0.1517 |
| 94056 | SYAP1 | GSM4909298 | Human | Breast | IDC | 1.14e-08 | 3.42e-01 | 0.1551 |
| 94056 | SYAP1 | GSM4909301 | Human | Breast | IDC | 2.97e-08 | 3.23e-01 | 0.1577 |
| 94056 | SYAP1 | GSM4909304 | Human | Breast | IDC | 1.58e-13 | 4.41e-01 | 0.1636 |
| 94056 | SYAP1 | GSM4909306 | Human | Breast | IDC | 2.29e-05 | 3.21e-01 | 0.1564 |
| 94056 | SYAP1 | GSM4909308 | Human | Breast | IDC | 6.30e-08 | 3.78e-01 | 0.158 |
| 94056 | SYAP1 | GSM4909311 | Human | Breast | IDC | 3.57e-20 | -1.16e-01 | 0.1534 |
| 94056 | SYAP1 | GSM4909312 | Human | Breast | IDC | 2.68e-07 | 1.72e-01 | 0.1552 |
| 94056 | SYAP1 | GSM4909313 | Human | Breast | IDC | 4.74e-03 | 1.66e-01 | 0.0391 |
| 94056 | SYAP1 | GSM4909319 | Human | Breast | IDC | 6.32e-29 | -1.27e-01 | 0.1563 |
| 94056 | SYAP1 | GSM4909320 | Human | Breast | IDC | 2.13e-07 | 3.64e-01 | 0.1575 |
| 94056 | SYAP1 | GSM4909321 | Human | Breast | IDC | 4.42e-09 | -4.53e-02 | 0.1559 |
| 94056 | SYAP1 | brca2 | Human | Breast | Precancer | 3.87e-05 | 2.02e-01 | -0.024 |
| 94056 | SYAP1 | M1 | Human | Breast | IDC | 8.77e-10 | 5.48e-01 | 0.1577 |
| 94056 | SYAP1 | NCCBC14 | Human | Breast | DCIS | 1.00e-07 | 2.67e-01 | 0.2021 |
| 94056 | SYAP1 | NCCBC5 | Human | Breast | DCIS | 1.81e-06 | 9.31e-02 | 0.2046 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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:007137516 | Esophagus | ESCC | cellular response to peptide hormone stimulus | 166/8552 | 290/18723 | 4.48e-05 | 3.55e-04 | 166 |
| GO:00456007 | Esophagus | ESCC | positive regulation of fat cell differentiation | 46/8552 | 66/18723 | 6.72e-05 | 5.11e-04 | 46 |
| GO:00319294 | Esophagus | ESCC | TOR signaling | 79/8552 | 126/18723 | 8.57e-05 | 6.21e-04 | 79 |
| GO:00455984 | Esophagus | ESCC | regulation of fat cell differentiation | 79/8552 | 139/18723 | 5.23e-03 | 1.97e-02 | 79 |
| GO:004343412 | Liver | Cirrhotic | response to peptide hormone | 149/4634 | 414/18723 | 1.70e-07 | 4.49e-06 | 149 |
| GO:007137511 | Liver | Cirrhotic | cellular response to peptide hormone stimulus | 110/4634 | 290/18723 | 3.73e-07 | 8.82e-06 | 110 |
| GO:190165311 | Liver | Cirrhotic | cellular response to peptide | 129/4634 | 359/18723 | 1.23e-06 | 2.49e-05 | 129 |
| GO:003286911 | Liver | Cirrhotic | cellular response to insulin stimulus | 80/4634 | 203/18723 | 2.55e-06 | 4.63e-05 | 80 |
| GO:003286811 | Liver | Cirrhotic | response to insulin | 95/4634 | 264/18723 | 2.77e-05 | 3.54e-04 | 95 |
| GO:00708495 | Liver | Cirrhotic | response to epidermal growth factor | 25/4634 | 49/18723 | 6.57e-05 | 7.47e-04 | 25 |
| GO:00713645 | Liver | Cirrhotic | cellular response to epidermal growth factor stimulus | 22/4634 | 45/18723 | 3.90e-04 | 3.23e-03 | 22 |
| GO:007190011 | Liver | Cirrhotic | regulation of protein serine/threonine kinase activity | 110/4634 | 359/18723 | 6.19e-03 | 3.08e-02 | 110 |
| GO:00319292 | Liver | Cirrhotic | TOR signaling | 44/4634 | 126/18723 | 6.69e-03 | 3.30e-02 | 44 |
| GO:004586011 | Liver | Cirrhotic | positive regulation of protein kinase activity | 117/4634 | 386/18723 | 7.07e-03 | 3.41e-02 | 117 |
| GO:00454442 | Liver | Cirrhotic | fat cell differentiation | 73/4634 | 229/18723 | 8.57e-03 | 3.97e-02 | 73 |
| GO:003286821 | Liver | HCC | response to insulin | 172/7958 | 264/18723 | 7.14e-14 | 4.23e-12 | 172 |
| GO:003286921 | Liver | HCC | cellular response to insulin stimulus | 137/7958 | 203/18723 | 4.69e-13 | 2.44e-11 | 137 |
| GO:004343422 | Liver | HCC | response to peptide hormone | 247/7958 | 414/18723 | 9.55e-13 | 4.77e-11 | 247 |
| GO:007137521 | Liver | HCC | cellular response to peptide hormone stimulus | 179/7958 | 290/18723 | 2.54e-11 | 9.88e-10 | 179 |
| GO:190165321 | Liver | HCC | cellular response to peptide | 211/7958 | 359/18723 | 2.86e-10 | 9.63e-09 | 211 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| 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 |
| SYAP1 | SNV | Missense_Mutation | c.910N>C | p.Glu304Gln | p.E304Q | Q96A49 | protein_coding | tolerated(0.11) | benign(0.003) | TCGA-AN-A0FV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SYAP1 | SNV | Missense_Mutation | novel | c.371N>C | p.Val124Ala | p.V124A | Q96A49 | protein_coding | deleterious(0) | benign(0.342) | TCGA-C5-A8ZZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unspecific | Cisplatin | SD |
| SYAP1 | SNV | Missense_Mutation | novel | c.701G>C | p.Arg234Thr | p.R234T | Q96A49 | protein_coding | tolerated(0.63) | benign(0.024) | TCGA-C5-A902-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| SYAP1 | SNV | Missense_Mutation | c.912N>T | p.Glu304Asp | p.E304D | Q96A49 | protein_coding | tolerated(0.24) | benign(0) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| SYAP1 | SNV | Missense_Mutation | rs140529370 | c.454N>T | p.Arg152Cys | p.R152C | Q96A49 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-CM-6162-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | oxaliplatin | SD |
| SYAP1 | SNV | Missense_Mutation | c.920N>T | p.Ala307Val | p.A307V | Q96A49 | protein_coding | tolerated(0.27) | benign(0) | TCGA-G4-6309-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | xeloda | PD | |
| SYAP1 | SNV | Missense_Mutation | novel | c.257C>T | p.Ser86Phe | p.S86F | Q96A49 | protein_coding | deleterious(0) | benign(0.326) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SYAP1 | SNV | Missense_Mutation | c.565N>A | p.Val189Ile | p.V189I | Q96A49 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| SYAP1 | SNV | Missense_Mutation | rs140529370 | c.454N>T | p.Arg152Cys | p.R152C | Q96A49 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SYAP1 | SNV | Missense_Mutation | c.1056N>G | p.Asn352Lys | p.N352K | Q96A49 | protein_coding | deleterious(0.01) | possibly_damaging(0.63) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
| Page: 1 2 3 4 |
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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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