Tissue | Expression Dynamics | Abbreviation |
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/SHROOM3_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/SHROOM3_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/SHROOM3_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/SHROOM3_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/SHROOM3_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/SHROOM3_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/SHROOM3_pca_on_diff_genes.png) | AAH: Atypical adenomatous hyperplasia |
AIS: Adenocarcinoma in situ |
IAC: Invasive lung adenocarcinoma |
MIA: Minimally invasive adenocarcinoma |
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/SHROOM3_pca_on_diff_genes.png) | BPH: Benign Prostatic Hyperplasia |
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/SHROOM3_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:00018415 | Liver | HCC | neural tube formation | 62/7958 | 102/18723 | 1.47e-04 | 1.18e-03 | 62 |
GO:00018433 | Liver | HCC | neural tube closure | 53/7958 | 88/18723 | 5.95e-04 | 3.75e-03 | 53 |
GO:00140204 | Liver | HCC | primary neural tube formation | 56/7958 | 94/18723 | 6.19e-04 | 3.86e-03 | 56 |
GO:00606063 | Liver | HCC | tube closure | 53/7958 | 89/18723 | 8.67e-04 | 5.14e-03 | 53 |
GO:00219154 | Liver | HCC | neural tube development | 82/7958 | 152/18723 | 2.83e-03 | 1.33e-02 | 82 |
GO:000206422 | Liver | HCC | epithelial cell development | 114/7958 | 220/18723 | 3.19e-03 | 1.47e-02 | 114 |
GO:00018384 | Liver | HCC | embryonic epithelial tube formation | 66/7958 | 121/18723 | 4.94e-03 | 2.07e-02 | 66 |
GO:00721754 | Liver | HCC | epithelial tube formation | 70/7958 | 132/18723 | 9.29e-03 | 3.57e-02 | 70 |
GO:00351484 | Liver | HCC | tube formation | 77/7958 | 148/18723 | 1.20e-02 | 4.39e-02 | 77 |
GO:00226048 | Lung | IAC | regulation of cell morphogenesis | 74/2061 | 309/18723 | 6.31e-11 | 1.70e-08 | 74 |
GO:00070158 | Lung | IAC | actin filament organization | 92/2061 | 442/18723 | 1.01e-09 | 1.93e-07 | 92 |
GO:00020648 | Lung | IAC | epithelial cell development | 52/2061 | 220/18723 | 6.75e-08 | 6.91e-06 | 52 |
GO:00083607 | Lung | IAC | regulation of cell shape | 37/2061 | 154/18723 | 3.35e-06 | 1.42e-04 | 37 |
GO:00605624 | Lung | IAC | epithelial tube morphogenesis | 63/2061 | 325/18723 | 5.28e-06 | 2.07e-04 | 63 |
GO:00018416 | Lung | IAC | neural tube formation | 24/2061 | 102/18723 | 2.35e-04 | 4.04e-03 | 24 |
GO:00140205 | Lung | IAC | primary neural tube formation | 22/2061 | 94/18723 | 4.55e-04 | 6.70e-03 | 22 |
GO:00018434 | Lung | IAC | neural tube closure | 20/2061 | 88/18723 | 1.20e-03 | 1.38e-02 | 20 |
GO:00018385 | Lung | IAC | embryonic epithelial tube formation | 25/2061 | 121/18723 | 1.38e-03 | 1.53e-02 | 25 |
GO:00606064 | Lung | IAC | tube closure | 20/2061 | 89/18723 | 1.39e-03 | 1.53e-02 | 20 |
GO:00351485 | Lung | IAC | tube formation | 29/2061 | 148/18723 | 1.44e-03 | 1.55e-02 | 29 |
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 |
SHROOM3 | SNV | Missense_Mutation | novel | c.2479N>C | p.Glu827Gln | p.E827Q | Q8TF72 | protein_coding | deleterious(0.05) | possibly_damaging(0.462) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
SHROOM3 | SNV | Missense_Mutation | novel | c.1815C>G | p.Cys605Trp | p.C605W | Q8TF72 | protein_coding | tolerated(0.18) | possibly_damaging(0.506) | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
SHROOM3 | SNV | Missense_Mutation | | c.739N>A | p.Asp247Asn | p.D247N | Q8TF72 | protein_coding | deleterious(0) | possibly_damaging(0.902) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
SHROOM3 | SNV | Missense_Mutation | | c.16G>A | p.Glu6Lys | p.E6K | Q8TF72 | protein_coding | deleterious_low_confidence(0.01) | benign(0.326) | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD |
SHROOM3 | SNV | Missense_Mutation | | c.223G>A | p.Glu75Lys | p.E75K | Q8TF72 | protein_coding | deleterious(0) | probably_damaging(0.96) | TCGA-E2-A152-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | trastuzumab | PD |
SHROOM3 | SNV | Missense_Mutation | rs752151821 | c.4702C>T | p.Arg1568Cys | p.R1568C | Q8TF72 | protein_coding | tolerated(0.21) | benign(0) | TCGA-E2-A152-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | trastuzumab | PD |
SHROOM3 | SNV | Missense_Mutation | novel | c.2431N>G | p.Pro811Ala | p.P811A | Q8TF72 | protein_coding | tolerated(0.08) | benign(0.051) | TCGA-LL-A6FP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
SHROOM3 | insertion | Frame_Shift_Ins | novel | c.1347_1348insAAAC | p.His450LysfsTer3 | p.H450Kfs*3 | Q8TF72 | protein_coding | | | TCGA-A7-A0CG-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SHROOM3 | insertion | Nonsense_Mutation | novel | c.1349_1350insATCTCAGTCCTGAATTTATGGATC | p.His450delinsGlnSerGlnSerTerIleTyrGlySer | p.H450delinsQSQS*IYGS | Q8TF72 | protein_coding | | | TCGA-A7-A0CG-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SHROOM3 | insertion | Frame_Shift_Ins | novel | c.4596_4597insA | p.Pro1533ThrfsTer10 | p.P1533Tfs*10 | Q8TF72 | protein_coding | | | TCGA-A8-A07F-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |