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Gene: SHROOM4 |
Gene summary for SHROOM4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SHROOM4 | Gene ID | 57477 |
Gene name | shroom family member 4 | |
Gene Alias | MRXSSDS | |
Cytomap | Xp11.22 | |
Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | Q9ULL8 |
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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 |
57477 | SHROOM4 | PTC07 | Human | Thyroid | PTC | 1.30e-64 | 1.03e+00 | 0.2044 |
57477 | SHROOM4 | ATC13 | Human | Thyroid | ATC | 5.96e-08 | 1.45e-01 | 0.34 |
57477 | SHROOM4 | ATC5 | Human | Thyroid | ATC | 5.88e-09 | 1.65e-01 | 0.34 |
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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. |
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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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:000701522 | Liver | HCC | actin filament organization | 252/7958 | 442/18723 | 3.83e-10 | 1.25e-08 | 252 |
GO:00070158 | Lung | IAC | actin filament organization | 92/2061 | 442/18723 | 1.01e-09 | 1.93e-07 | 92 |
GO:000701513 | Lung | AIS | actin filament organization | 88/1849 | 442/18723 | 1.02e-10 | 3.13e-08 | 88 |
GO:000701533 | Lung | MIAC | actin filament organization | 50/967 | 442/18723 | 1.64e-07 | 3.81e-05 | 50 |
GO:0007015112 | Thyroid | PTC | actin filament organization | 225/5968 | 442/18723 | 3.76e-17 | 3.44e-15 | 225 |
GO:0007015210 | Thyroid | ATC | actin filament organization | 227/6293 | 442/18723 | 5.96e-15 | 3.85e-13 | 227 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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 |
SHROOM4 | SNV | Missense_Mutation | novel | c.2968N>G | p.His990Asp | p.H990D | Q9ULL8 | protein_coding | deleterious(0.02) | possibly_damaging(0.879) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
SHROOM4 | SNV | Missense_Mutation | novel | c.2243N>T | p.Pro748Leu | p.P748L | Q9ULL8 | protein_coding | tolerated(0.16) | benign(0.003) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
SHROOM4 | SNV | Missense_Mutation | rs370831168 | c.320N>C | p.Leu107Pro | p.L107P | Q9ULL8 | protein_coding | tolerated(0.2) | possibly_damaging(0.854) | TCGA-A8-A07L-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | CR | |
SHROOM4 | SNV | Missense_Mutation | c.3016N>C | p.Glu1006Gln | p.E1006Q | Q9ULL8 | protein_coding | deleterious(0.01) | benign(0.031) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
SHROOM4 | SNV | Missense_Mutation | c.2512N>T | p.His838Tyr | p.H838Y | Q9ULL8 | protein_coding | deleterious(0.02) | probably_damaging(0.932) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
SHROOM4 | SNV | Missense_Mutation | c.4189G>A | p.Asp1397Asn | p.D1397N | Q9ULL8 | protein_coding | deleterious(0.04) | probably_damaging(0.995) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SHROOM4 | SNV | Missense_Mutation | rs200144471 | c.3346C>T | p.Arg1116Cys | p.R1116C | Q9ULL8 | protein_coding | deleterious(0) | probably_damaging(0.94) | TCGA-BH-A0BT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
SHROOM4 | SNV | Missense_Mutation | c.1142N>G | p.Ser381Cys | p.S381C | Q9ULL8 | protein_coding | tolerated(0.13) | benign(0.001) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SHROOM4 | SNV | Missense_Mutation | c.3666C>G | p.His1222Gln | p.H1222Q | Q9ULL8 | protein_coding | tolerated(0.16) | benign(0.015) | TCGA-E2-A15S-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
SHROOM4 | SNV | Missense_Mutation | novel | c.2066N>C | p.Gln689Pro | p.Q689P | Q9ULL8 | protein_coding | tolerated(0.06) | benign(0.01) | TCGA-E2-A1II-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
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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 |
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