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Gene: GSTM4 |
Gene summary for GSTM4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | GSTM4 | Gene ID | 2948 |
Gene name | glutathione S-transferase mu 4 | |
Gene Alias | GSTM4-4 | |
Cytomap | 1p13.3 | |
Gene Type | protein-coding | GO ID | GO:0001676 | UniProtAcc | A0A140VKE3 |
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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 |
2948 | GSTM4 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.48e-02 | 1.44e-01 | 0.0155 |
2948 | GSTM4 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.60e-05 | 2.70e-01 | -0.1808 |
2948 | GSTM4 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.02e-03 | 2.65e-01 | -0.0811 |
2948 | GSTM4 | HTA11_347_2000001011 | Human | Colorectum | AD | 4.96e-13 | 3.54e-01 | -0.1954 |
2948 | GSTM4 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.56e-07 | 2.37e-01 | -0.1464 |
2948 | GSTM4 | HTA11_866_2000001011 | Human | Colorectum | AD | 9.67e-04 | 1.74e-01 | -0.1001 |
2948 | GSTM4 | HTA11_1391_2000001011 | Human | Colorectum | AD | 5.21e-09 | 4.09e-01 | -0.059 |
2948 | GSTM4 | HTA11_5216_2000001011 | Human | Colorectum | SER | 9.16e-03 | 4.36e-01 | -0.1462 |
2948 | GSTM4 | HTA11_546_2000001011 | Human | Colorectum | AD | 1.53e-02 | 2.50e-01 | -0.0842 |
2948 | GSTM4 | HTA11_10623_2000001011 | Human | Colorectum | AD | 9.57e-07 | 4.00e-01 | -0.0177 |
2948 | GSTM4 | HTA11_7696_3000711011 | Human | Colorectum | AD | 3.04e-09 | 2.62e-01 | 0.0674 |
2948 | GSTM4 | HTA11_7469_2000001011 | Human | Colorectum | AD | 1.50e-03 | 5.13e-01 | -0.0124 |
2948 | GSTM4 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.23e-11 | 3.11e-01 | 0.3859 |
2948 | GSTM4 | LZE2T | Human | Esophagus | ESCC | 7.32e-16 | 2.45e+00 | 0.082 |
2948 | GSTM4 | LZE4T | Human | Esophagus | ESCC | 1.81e-23 | 8.66e-01 | 0.0811 |
2948 | GSTM4 | LZE7T | Human | Esophagus | ESCC | 9.67e-04 | 6.74e-01 | 0.0667 |
2948 | GSTM4 | LZE21T | Human | Esophagus | ESCC | 2.10e-04 | 3.33e-01 | 0.0655 |
2948 | GSTM4 | LZE6T | Human | Esophagus | ESCC | 3.53e-03 | 1.44e-01 | 0.0845 |
2948 | GSTM4 | P1T-E | Human | Esophagus | ESCC | 7.52e-05 | 4.04e-01 | 0.0875 |
2948 | GSTM4 | P2T-E | Human | Esophagus | ESCC | 6.18e-28 | 5.32e-01 | 0.1177 |
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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:0006631 | Colorectum | AD | fatty acid metabolic process | 114/3918 | 390/18723 | 5.58e-05 | 9.44e-04 | 114 |
GO:0006790 | Colorectum | AD | sulfur compound metabolic process | 101/3918 | 339/18723 | 6.46e-05 | 1.07e-03 | 101 |
GO:0009410 | Colorectum | AD | response to xenobiotic stimulus | 128/3918 | 462/18723 | 2.69e-04 | 3.31e-03 | 128 |
GO:0006575 | Colorectum | AD | cellular modified amino acid metabolic process | 59/3918 | 188/18723 | 4.80e-04 | 5.27e-03 | 59 |
GO:00067901 | Colorectum | SER | sulfur compound metabolic process | 73/2897 | 339/18723 | 1.75e-03 | 1.81e-02 | 73 |
GO:00066311 | Colorectum | SER | fatty acid metabolic process | 79/2897 | 390/18723 | 6.34e-03 | 4.56e-02 | 79 |
GO:00065751 | Colorectum | MSS | cellular modified amino acid metabolic process | 55/3467 | 188/18723 | 2.16e-04 | 3.01e-03 | 55 |
GO:00067902 | Colorectum | MSS | sulfur compound metabolic process | 85/3467 | 339/18723 | 1.52e-03 | 1.39e-02 | 85 |
GO:00066312 | Colorectum | MSS | fatty acid metabolic process | 95/3467 | 390/18723 | 2.20e-03 | 1.84e-02 | 95 |
GO:00094101 | Colorectum | MSS | response to xenobiotic stimulus | 110/3467 | 462/18723 | 2.36e-03 | 1.92e-02 | 110 |
GO:0046394 | Colorectum | MSS | carboxylic acid biosynthetic process | 76/3467 | 314/18723 | 6.71e-03 | 4.38e-02 | 76 |
GO:0016053 | Colorectum | MSS | organic acid biosynthetic process | 76/3467 | 316/18723 | 7.88e-03 | 4.84e-02 | 76 |
GO:00067906 | Esophagus | ESCC | sulfur compound metabolic process | 201/8552 | 339/18723 | 2.64e-07 | 3.94e-06 | 201 |
GO:00066318 | Esophagus | ESCC | fatty acid metabolic process | 217/8552 | 390/18723 | 4.21e-05 | 3.39e-04 | 217 |
GO:000941020 | Esophagus | ESCC | response to xenobiotic stimulus | 253/8552 | 462/18723 | 4.55e-05 | 3.58e-04 | 253 |
GO:00065757 | Esophagus | ESCC | cellular modified amino acid metabolic process | 112/8552 | 188/18723 | 8.31e-05 | 6.06e-04 | 112 |
GO:00463948 | Esophagus | ESCC | carboxylic acid biosynthetic process | 175/8552 | 314/18723 | 1.98e-04 | 1.26e-03 | 175 |
GO:00160538 | Esophagus | ESCC | organic acid biosynthetic process | 175/8552 | 316/18723 | 3.04e-04 | 1.82e-03 | 175 |
GO:000674912 | Esophagus | ESCC | glutathione metabolic process | 42/8552 | 64/18723 | 1.01e-03 | 5.12e-03 | 42 |
GO:000663112 | Liver | Cirrhotic | fatty acid metabolic process | 165/4634 | 390/18723 | 1.29e-14 | 1.26e-12 | 165 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05208 | Colorectum | AD | Chemical carcinogenesis - reactive oxygen species | 126/2092 | 223/8465 | 1.01e-24 | 1.68e-22 | 1.07e-22 | 126 |
hsa05418 | Colorectum | AD | Fluid shear stress and atherosclerosis | 54/2092 | 139/8465 | 1.41e-04 | 1.16e-03 | 7.37e-04 | 54 |
hsa05225 | Colorectum | AD | Hepatocellular carcinoma | 59/2092 | 168/8465 | 1.50e-03 | 8.69e-03 | 5.54e-03 | 59 |
hsa00480 | Colorectum | AD | Glutathione metabolism | 23/2092 | 57/8465 | 6.52e-03 | 2.76e-02 | 1.76e-02 | 23 |
hsa052081 | Colorectum | AD | Chemical carcinogenesis - reactive oxygen species | 126/2092 | 223/8465 | 1.01e-24 | 1.68e-22 | 1.07e-22 | 126 |
hsa054181 | Colorectum | AD | Fluid shear stress and atherosclerosis | 54/2092 | 139/8465 | 1.41e-04 | 1.16e-03 | 7.37e-04 | 54 |
hsa052251 | Colorectum | AD | Hepatocellular carcinoma | 59/2092 | 168/8465 | 1.50e-03 | 8.69e-03 | 5.54e-03 | 59 |
hsa004801 | Colorectum | AD | Glutathione metabolism | 23/2092 | 57/8465 | 6.52e-03 | 2.76e-02 | 1.76e-02 | 23 |
hsa052082 | Colorectum | SER | Chemical carcinogenesis - reactive oxygen species | 103/1580 | 223/8465 | 1.60e-21 | 7.57e-20 | 5.50e-20 | 103 |
hsa054182 | Colorectum | SER | Fluid shear stress and atherosclerosis | 40/1580 | 139/8465 | 2.28e-03 | 1.75e-02 | 1.27e-02 | 40 |
hsa052083 | Colorectum | SER | Chemical carcinogenesis - reactive oxygen species | 103/1580 | 223/8465 | 1.60e-21 | 7.57e-20 | 5.50e-20 | 103 |
hsa054183 | Colorectum | SER | Fluid shear stress and atherosclerosis | 40/1580 | 139/8465 | 2.28e-03 | 1.75e-02 | 1.27e-02 | 40 |
hsa052084 | Colorectum | MSS | Chemical carcinogenesis - reactive oxygen species | 118/1875 | 223/8465 | 2.71e-24 | 4.54e-22 | 2.78e-22 | 118 |
hsa054184 | Colorectum | MSS | Fluid shear stress and atherosclerosis | 51/1875 | 139/8465 | 6.06e-05 | 5.80e-04 | 3.55e-04 | 51 |
hsa052252 | Colorectum | MSS | Hepatocellular carcinoma | 56/1875 | 168/8465 | 5.04e-04 | 3.45e-03 | 2.11e-03 | 56 |
hsa004802 | Colorectum | MSS | Glutathione metabolism | 22/1875 | 57/8465 | 3.58e-03 | 1.64e-02 | 1.01e-02 | 22 |
hsa01524 | Colorectum | MSS | Platinum drug resistance | 25/1875 | 73/8465 | 1.17e-02 | 3.99e-02 | 2.44e-02 | 25 |
hsa052085 | Colorectum | MSS | Chemical carcinogenesis - reactive oxygen species | 118/1875 | 223/8465 | 2.71e-24 | 4.54e-22 | 2.78e-22 | 118 |
hsa054185 | Colorectum | MSS | Fluid shear stress and atherosclerosis | 51/1875 | 139/8465 | 6.06e-05 | 5.80e-04 | 3.55e-04 | 51 |
hsa052253 | Colorectum | MSS | Hepatocellular carcinoma | 56/1875 | 168/8465 | 5.04e-04 | 3.45e-03 | 2.11e-03 | 56 |
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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 |
GSTM4 | SNV | Missense_Mutation | novel | c.614C>G | p.Pro205Arg | p.P205R | Q03013 | protein_coding | tolerated(0.25) | benign(0.012) | TCGA-CR-7402-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | SD |
GSTM4 | SNV | Missense_Mutation | novel | c.34G>A | p.Gly12Arg | p.G12R | Q03013 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-IQ-A61G-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | PD |
GSTM4 | SNV | Missense_Mutation | novel | c.35G>A | p.Gly12Glu | p.G12E | Q03013 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-IQ-A61G-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | PD |
GSTM4 | SNV | Missense_Mutation | c.637N>A | p.Ala213Thr | p.A213T | Q03013 | protein_coding | deleterious(0) | probably_damaging(0.93) | TCGA-BR-6452-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
GSTM4 | SNV | Missense_Mutation | rs761147429 | c.286C>T | p.Arg96Cys | p.R96C | Q03013 | protein_coding | deleterious(0.01) | benign(0.181) | TCGA-BR-8382-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
GSTM4 | SNV | Missense_Mutation | c.311C>A | p.Ala104Asp | p.A104D | Q03013 | protein_coding | deleterious(0) | possibly_damaging(0.528) | TCGA-FP-A4BE-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
GSTM4 | SNV | Missense_Mutation | rs766374788 | c.503N>A | p.Arg168His | p.R168H | Q03013 | protein_coding | deleterious(0.02) | benign(0.031) | TCGA-VQ-A8PP-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | PD |
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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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