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Gene: SYNM |
Gene summary for SYNM |
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Gene information | Species | Human | Gene symbol | SYNM | Gene ID | 23336 |
Gene name | synemin | |
Gene Alias | DMN | |
Cytomap | 15q26.3 | |
Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | A0A075B7B1 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
23336 | SYNM | GSM4909281 | Human | Breast | IDC | 4.87e-28 | 6.41e-01 | 0.21 |
23336 | SYNM | GSM4909297 | Human | Breast | IDC | 1.57e-03 | -1.57e-01 | 0.1517 |
23336 | SYNM | GSM4909299 | Human | Breast | IDC | 1.59e-44 | 9.29e-01 | 0.035 |
23336 | SYNM | GSM4909301 | Human | Breast | IDC | 3.51e-04 | -1.58e-01 | 0.1577 |
23336 | SYNM | GSM4909304 | Human | Breast | IDC | 3.66e-05 | -1.61e-01 | 0.1636 |
23336 | SYNM | GSM4909309 | Human | Breast | IDC | 1.31e-05 | 4.18e-01 | 0.0483 |
23336 | SYNM | GSM4909311 | Human | Breast | IDC | 4.94e-03 | -1.37e-01 | 0.1534 |
23336 | SYNM | GSM4909312 | Human | Breast | IDC | 1.65e-04 | -1.61e-01 | 0.1552 |
23336 | SYNM | GSM4909313 | Human | Breast | IDC | 4.16e-17 | 6.54e-01 | 0.0391 |
23336 | SYNM | GSM4909319 | Human | Breast | IDC | 7.43e-04 | -1.61e-01 | 0.1563 |
23336 | SYNM | brca10 | Human | Breast | Precancer | 1.36e-04 | -1.61e-01 | -0.0029 |
23336 | SYNM | M1 | Human | Breast | IDC | 3.22e-02 | -1.61e-01 | 0.1577 |
23336 | SYNM | NCCBC14 | Human | Breast | DCIS | 1.58e-04 | -1.16e-01 | 0.2021 |
23336 | SYNM | NCCBC3 | Human | Breast | DCIS | 1.94e-12 | 5.45e-01 | 0.1198 |
23336 | SYNM | P1 | Human | Breast | IDC | 8.63e-03 | -1.27e-01 | 0.1527 |
23336 | SYNM | P2 | Human | Breast | IDC | 4.28e-02 | -1.61e-01 | 0.21 |
23336 | SYNM | DCIS2 | Human | Breast | DCIS | 5.62e-122 | 1.55e+00 | 0.0085 |
23336 | SYNM | P2T-E | Human | Esophagus | ESCC | 3.07e-07 | 1.74e-01 | 0.1177 |
23336 | SYNM | P4T-E | Human | Esophagus | ESCC | 2.90e-03 | 1.05e-01 | 0.1323 |
23336 | SYNM | P5T-E | Human | Esophagus | ESCC | 1.44e-03 | 7.01e-02 | 0.1327 |
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∗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 |
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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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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0045104 | Breast | Precancer | intermediate filament cytoskeleton organization | 11/1080 | 51/18723 | 1.26e-04 | 2.22e-03 | 11 |
GO:0045103 | Breast | Precancer | intermediate filament-based process | 11/1080 | 52/18723 | 1.52e-04 | 2.60e-03 | 11 |
GO:00451041 | Breast | IDC | intermediate filament cytoskeleton organization | 11/1434 | 51/18723 | 1.40e-03 | 1.44e-02 | 11 |
GO:00451031 | Breast | IDC | intermediate filament-based process | 11/1434 | 52/18723 | 1.66e-03 | 1.63e-02 | 11 |
GO:00030125 | Breast | IDC | muscle system process | 50/1434 | 452/18723 | 5.52e-03 | 4.05e-02 | 50 |
GO:00451042 | Breast | DCIS | intermediate filament cytoskeleton organization | 11/1390 | 51/18723 | 1.09e-03 | 1.18e-02 | 11 |
GO:00451032 | Breast | DCIS | intermediate filament-based process | 11/1390 | 52/18723 | 1.29e-03 | 1.35e-02 | 11 |
GO:000301212 | Breast | DCIS | muscle system process | 50/1390 | 452/18723 | 3.02e-03 | 2.57e-02 | 50 |
GO:00451035 | Esophagus | ESCC | intermediate filament-based process | 32/8552 | 52/18723 | 1.55e-02 | 4.97e-02 | 32 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
SYNM | SNV | Missense_Mutation | c.2336N>A | p.Gly779Asp | p.G779D | O15061 | protein_coding | tolerated(0.13) | benign(0.149) | TCGA-BR-8363-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SYNM | SNV | Missense_Mutation | c.4040N>A | p.Gly1347Asp | p.G1347D | O15061 | protein_coding | tolerated(0.09) | benign(0.024) | TCGA-CG-4465-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | cisplatin | SD | |
SYNM | SNV | Missense_Mutation | rs530141940 | c.4460N>A | p.Arg1487His | p.R1487H | O15061 | protein_coding | tolerated(0.38) | benign(0.001) | TCGA-D7-A6EY-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
SYNM | SNV | Missense_Mutation | novel | c.1457N>C | p.Ser486Thr | p.S486T | O15061 | protein_coding | tolerated(0.07) | benign(0.012) | TCGA-HU-8238-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | didox | SD |
SYNM | SNV | Missense_Mutation | novel | c.1626N>T | p.Leu542Phe | p.L542F | O15061 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-IN-A6RL-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
SYNM | SNV | Missense_Mutation | rs376246829 | c.2755N>A | p.Glu919Lys | p.E919K | O15061 | protein_coding | deleterious(0.04) | benign(0.259) | TCGA-VQ-A8E0-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unspecific | Fluorouracil | PD |
SYNM | SNV | Missense_Mutation | novel | c.38N>G | p.Ala13Gly | p.A13G | O15061 | protein_coding | deleterious(0.05) | probably_damaging(0.999) | TCGA-VQ-A91D-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | PD |
SYNM | SNV | Missense_Mutation | novel | c.3340N>C | p.Ser1114Pro | p.S1114P | O15061 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-VQ-A91E-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | fluorouracil | CR |
SYNM | insertion | Frame_Shift_Ins | novel | c.1811_1812insCTTTCTC | p.Gly605PhefsTer7 | p.G605Ffs*7 | O15061 | protein_coding | TCGA-FY-A4B0-01 | Thyroid | thyroid carcinoma | Male | >=65 | I/II | Hormone Therapy | synthroid | SD | ||
SYNM | insertion | In_Frame_Ins | novel | c.2330_2331insCTATCATCT | p.Ser777_Pro778insTyrHisLeu | p.S777_P778insYHL | O15061 | protein_coding | TCGA-FY-A4B0-01 | Thyroid | thyroid carcinoma | Male | >=65 | I/II | Hormone Therapy | synthroid | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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