Tissue | Expression Dynamics | Abbreviation |
Breast | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Breast/SYNE2_pca_on_diff_genes.png) | IDC: Invasive ductal carcinoma |
DCIS: Ductal carcinoma in situ |
Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers |
Cervix | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Cervix/SYNE2_pca_on_diff_genes.png) | CC: Cervix cancer |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions |
N_HPV: HPV-infected normal cervix |
Colorectum (GSE201348) | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Colorectum/Becker/SYNE2_pca_on_diff_genes.png) | FAP: Familial adenomatous polyposis |
CRC: Colorectal cancer |
Colorectum (HTA11) | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Colorectum/Chen/SYNE2_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal cancer |
Endometrium | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Endometrium/SYNE2_pca_on_diff_genes.png) | AEH: Atypical endometrial hyperplasia |
EEC: Endometrioid Cancer |
Esophagus | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Esophagus/SYNE2_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
GC | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/GC/SYNE2_pca_on_diff_genes.png) | CAG: Chronic atrophic gastritis |
CAG with IM: Chronic atrophic gastritis with intestinal metaplasia |
CSG: Chronic superficial gastritis |
GC: Gastric cancer |
SIM: Severe intestinal metaplasia |
WIM: Wild intestinal metaplasia |
Liver | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Liver/SYNE2_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
Lung | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Lung/SYNE2_pca_on_diff_genes.png) | AAH: Atypical adenomatous hyperplasia |
AIS: Adenocarcinoma in situ |
IAC: Invasive lung adenocarcinoma |
MIA: Minimally invasive adenocarcinoma |
Oral Cavity | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/OralCavity/SYNE2_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
Prostate | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Prostate/SYNE2_pca_on_diff_genes.png) | BPH: Benign Prostatic Hyperplasia |
Skin | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Skin/SYNE2_pca_on_diff_genes.png) | AK: Actinic keratosis |
cSCC: Cutaneous squamous cell carcinoma |
SCCIS:squamous cell carcinoma in situ |
Thyroid | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Thyroid/SYNE2_pca_on_diff_genes.png) | ATC: Anaplastic thyroid cancer |
HT: Hashimoto's thyroiditis |
PTC: Papillary thyroid cancer |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00516567 | Cervix | CC | establishment of organelle localization | 76/2311 | 390/18723 | 3.17e-05 | 5.21e-04 | 76 |
GO:00300487 | Cervix | CC | actin filament-based movement | 29/2311 | 127/18723 | 6.91e-04 | 6.33e-03 | 29 |
GO:00307057 | Cervix | CC | cytoskeleton-dependent intracellular transport | 40/2311 | 195/18723 | 7.92e-04 | 6.99e-03 | 40 |
GO:00618425 | Cervix | CC | microtubule organizing center localization | 11/2311 | 33/18723 | 1.42e-03 | 1.11e-02 | 11 |
GO:00995157 | Cervix | CC | actin filament-based transport | 8/2311 | 21/18723 | 2.44e-03 | 1.71e-02 | 8 |
GO:00516425 | Cervix | CC | centrosome localization | 10/2311 | 32/18723 | 3.96e-03 | 2.48e-02 | 10 |
GO:003004813 | Cervix | HSIL_HPV | actin filament-based movement | 12/737 | 127/18723 | 4.37e-03 | 3.68e-02 | 12 |
GO:006184212 | Cervix | N_HPV | microtubule organizing center localization | 6/534 | 33/18723 | 3.01e-04 | 4.64e-03 | 6 |
GO:005164211 | Cervix | N_HPV | centrosome localization | 5/534 | 32/18723 | 1.97e-03 | 1.93e-02 | 5 |
GO:003070513 | Cervix | N_HPV | cytoskeleton-dependent intracellular transport | 13/534 | 195/18723 | 4.03e-03 | 3.16e-02 | 13 |
GO:0051656 | Colorectum | AD | establishment of organelle localization | 131/3918 | 390/18723 | 3.00e-09 | 2.06e-07 | 131 |
GO:0030048 | Colorectum | AD | actin filament-based movement | 44/3918 | 127/18723 | 2.31e-04 | 2.99e-03 | 44 |
GO:0099515 | Colorectum | AD | actin filament-based transport | 12/3918 | 21/18723 | 3.02e-04 | 3.62e-03 | 12 |
GO:0030705 | Colorectum | AD | cytoskeleton-dependent intracellular transport | 60/3918 | 195/18723 | 7.56e-04 | 7.59e-03 | 60 |
GO:0007097 | Colorectum | AD | nuclear migration | 10/3918 | 20/18723 | 3.67e-03 | 2.60e-02 | 10 |
GO:0051647 | Colorectum | AD | nucleus localization | 11/3918 | 24/18723 | 5.43e-03 | 3.55e-02 | 11 |
GO:00516561 | Colorectum | SER | establishment of organelle localization | 100/2897 | 390/18723 | 1.11e-07 | 6.79e-06 | 100 |
GO:00300481 | Colorectum | SER | actin filament-based movement | 38/2897 | 127/18723 | 2.80e-05 | 7.56e-04 | 38 |
GO:00995151 | Colorectum | SER | actin filament-based transport | 11/2897 | 21/18723 | 9.28e-05 | 1.98e-03 | 11 |
GO:00307051 | Colorectum | SER | cytoskeleton-dependent intracellular transport | 44/2897 | 195/18723 | 5.53e-03 | 4.09e-02 | 44 |
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 |
SYNE2 | SNV | Missense_Mutation | | c.13049C>T | p.Ser4350Leu | p.S4350L | Q8WXH0 | protein_coding | tolerated(0.06) | benign(0.015) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
SYNE2 | SNV | Missense_Mutation | | c.13813G>C | p.Glu4605Gln | p.E4605Q | Q8WXH0 | protein_coding | tolerated(0.23) | benign(0.107) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
SYNE2 | SNV | Missense_Mutation | novel | c.18166G>C | p.Asp6056His | p.D6056H | Q8WXH0 | protein_coding | deleterious(0) | benign(0.364) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
SYNE2 | SNV | Missense_Mutation | | c.5643N>G | p.Phe1881Leu | p.F1881L | Q8WXH0 | protein_coding | deleterious(0.01) | possibly_damaging(0.808) | TCGA-A2-A0CR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
SYNE2 | SNV | Missense_Mutation | | c.3278N>T | p.Ser1093Leu | p.S1093L | Q8WXH0 | protein_coding | deleterious(0.03) | benign(0.027) | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
SYNE2 | SNV | Missense_Mutation | | c.15141N>G | p.Ile5047Met | p.I5047M | Q8WXH0 | protein_coding | deleterious(0) | probably_damaging(0.935) | TCGA-A2-A1FW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD |
SYNE2 | SNV | Missense_Mutation | novel | c.11789G>T | p.Gly3930Val | p.G3930V | Q8WXH0 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-A7-A0DB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
SYNE2 | SNV | Missense_Mutation | | c.12647C>G | p.Ser4216Cys | p.S4216C | Q8WXH0 | protein_coding | tolerated(0.18) | possibly_damaging(0.614) | TCGA-A7-A0DB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
SYNE2 | SNV | Missense_Mutation | novel | c.17066G>T | p.Arg5689Leu | p.R5689L | Q8WXH0 | protein_coding | deleterious(0.03) | benign(0.036) | TCGA-A7-A0DB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
SYNE2 | SNV | Missense_Mutation | novel | c.15958N>A | p.Leu5320Ile | p.L5320I | Q8WXH0 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-A7-A26I-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cytoxan | SD |