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Gene: SHROOM3 |
Gene summary for SHROOM3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SHROOM3 | Gene ID | 57619 |
| Gene name | shroom family member 3 | |
| Gene Alias | APXL3 | |
| Cytomap | 4q21.1 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | B3KY47 |
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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 |
| 57619 | SHROOM3 | HTA11_3410_2000001011 | Human | Colorectum | AD | 4.74e-21 | -7.26e-01 | 0.0155 |
| 57619 | SHROOM3 | HTA11_2951_2000001011 | Human | Colorectum | AD | 4.92e-02 | -6.27e-01 | 0.0216 |
| 57619 | SHROOM3 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.03e-12 | 7.02e-01 | -0.1954 |
| 57619 | SHROOM3 | HTA11_411_2000001011 | Human | Colorectum | SER | 3.98e-08 | 8.66e-01 | -0.2602 |
| 57619 | SHROOM3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 6.47e-03 | 5.44e-01 | -0.059 |
| 57619 | SHROOM3 | HTA11_7862_2000001011 | Human | Colorectum | AD | 2.79e-02 | -5.54e-01 | -0.0179 |
| 57619 | SHROOM3 | HTA11_866_3004761011 | Human | Colorectum | AD | 8.84e-14 | -7.16e-01 | 0.096 |
| 57619 | SHROOM3 | HTA11_9408_2000001011 | Human | Colorectum | AD | 1.02e-03 | -8.63e-01 | 0.0451 |
| 57619 | SHROOM3 | HTA11_8622_2000001021 | Human | Colorectum | SER | 1.42e-03 | -4.59e-01 | 0.0528 |
| 57619 | SHROOM3 | HTA11_11156_2000001011 | Human | Colorectum | AD | 4.59e-02 | -7.01e-01 | 0.0397 |
| 57619 | SHROOM3 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 9.27e-10 | -5.40e-01 | 0.3859 |
| 57619 | SHROOM3 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.15e-05 | -7.52e-01 | 0.2585 |
| 57619 | SHROOM3 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.41e-38 | -9.53e-01 | 0.3005 |
| 57619 | SHROOM3 | F007 | Human | Colorectum | FAP | 7.94e-03 | -2.64e-01 | 0.1176 |
| 57619 | SHROOM3 | A001-C-207 | Human | Colorectum | FAP | 3.49e-04 | -3.26e-01 | 0.1278 |
| 57619 | SHROOM3 | A015-C-203 | Human | Colorectum | FAP | 2.49e-36 | -6.65e-01 | -0.1294 |
| 57619 | SHROOM3 | A015-C-204 | Human | Colorectum | FAP | 1.86e-09 | -4.49e-01 | -0.0228 |
| 57619 | SHROOM3 | A014-C-040 | Human | Colorectum | FAP | 4.41e-06 | -5.76e-01 | -0.1184 |
| 57619 | SHROOM3 | A002-C-201 | Human | Colorectum | FAP | 6.11e-10 | -3.02e-01 | 0.0324 |
| 57619 | SHROOM3 | A001-C-119 | Human | Colorectum | FAP | 1.83e-15 | -6.23e-01 | -0.1557 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | 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 |  | 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:0007015 | Colorectum | AD | actin filament organization | 167/3918 | 442/18723 | 1.65e-16 | 7.94e-14 | 167 |
| GO:0002064 | Colorectum | AD | epithelial cell development | 89/3918 | 220/18723 | 2.98e-11 | 3.52e-09 | 89 |
| GO:0022604 | Colorectum | AD | regulation of cell morphogenesis | 109/3918 | 309/18723 | 3.08e-09 | 2.07e-07 | 109 |
| GO:0008360 | Colorectum | AD | regulation of cell shape | 56/3918 | 154/18723 | 7.01e-06 | 1.73e-04 | 56 |
| GO:0060562 | Colorectum | AD | epithelial tube morphogenesis | 93/3918 | 325/18723 | 5.65e-04 | 6.00e-03 | 93 |
| GO:0014020 | Colorectum | AD | primary neural tube formation | 33/3918 | 94/18723 | 1.02e-03 | 9.50e-03 | 33 |
| GO:0001841 | Colorectum | AD | neural tube formation | 35/3918 | 102/18723 | 1.16e-03 | 1.05e-02 | 35 |
| GO:0001843 | Colorectum | AD | neural tube closure | 30/3918 | 88/18723 | 2.83e-03 | 2.12e-02 | 30 |
| GO:0060606 | Colorectum | AD | tube closure | 30/3918 | 89/18723 | 3.42e-03 | 2.49e-02 | 30 |
| GO:0035148 | Colorectum | AD | tube formation | 45/3918 | 148/18723 | 4.13e-03 | 2.87e-02 | 45 |
| GO:0001838 | Colorectum | AD | embryonic epithelial tube formation | 38/3918 | 121/18723 | 4.40e-03 | 3.01e-02 | 38 |
| GO:0072175 | Colorectum | AD | epithelial tube formation | 40/3918 | 132/18723 | 6.98e-03 | 4.29e-02 | 40 |
| GO:0021915 | Colorectum | AD | neural tube development | 45/3918 | 152/18723 | 7.05e-03 | 4.31e-02 | 45 |
| GO:00070151 | Colorectum | SER | actin filament organization | 134/2897 | 442/18723 | 1.39e-15 | 5.70e-13 | 134 |
| GO:00226041 | Colorectum | SER | regulation of cell morphogenesis | 89/2897 | 309/18723 | 1.51e-09 | 1.52e-07 | 89 |
| GO:00020641 | Colorectum | SER | epithelial cell development | 64/2897 | 220/18723 | 1.96e-07 | 1.10e-05 | 64 |
| GO:00083601 | Colorectum | SER | regulation of cell shape | 43/2897 | 154/18723 | 5.47e-05 | 1.30e-03 | 43 |
| GO:00018411 | Colorectum | SER | neural tube formation | 26/2897 | 102/18723 | 5.87e-03 | 4.29e-02 | 26 |
| GO:00070152 | Colorectum | MSS | actin filament organization | 146/3467 | 442/18723 | 1.16e-13 | 2.67e-11 | 146 |
| GO:00020642 | Colorectum | MSS | epithelial cell development | 81/3467 | 220/18723 | 1.02e-10 | 1.06e-08 | 81 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 |
| 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 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
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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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