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Gene: GPATCH4 |
Gene summary for GPATCH4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | GPATCH4 | Gene ID | 54865 |
Gene name | G-patch domain containing 4 | |
Gene Alias | GPATC4 | |
Cytomap | 1q22-q23.1 | |
Gene Type | protein-coding | GO ID | GO:0003674 | UniProtAcc | A8KAG1 |
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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 |
54865 | GPATCH4 | LZE2T | Human | Esophagus | ESCC | 1.15e-04 | 6.44e-01 | 0.082 |
54865 | GPATCH4 | LZE4T | Human | Esophagus | ESCC | 6.52e-04 | 2.20e-01 | 0.0811 |
54865 | GPATCH4 | LZE7T | Human | Esophagus | ESCC | 1.00e-02 | 2.81e-01 | 0.0667 |
54865 | GPATCH4 | LZE8T | Human | Esophagus | ESCC | 1.50e-02 | 1.52e-01 | 0.067 |
54865 | GPATCH4 | LZE20T | Human | Esophagus | ESCC | 4.27e-02 | 1.48e-01 | 0.0662 |
54865 | GPATCH4 | LZE24T | Human | Esophagus | ESCC | 4.49e-11 | 3.73e-01 | 0.0596 |
54865 | GPATCH4 | LZE6T | Human | Esophagus | ESCC | 9.23e-05 | 3.04e-01 | 0.0845 |
54865 | GPATCH4 | P1T-E | Human | Esophagus | ESCC | 8.50e-06 | 2.65e-01 | 0.0875 |
54865 | GPATCH4 | P2T-E | Human | Esophagus | ESCC | 7.91e-27 | 5.51e-01 | 0.1177 |
54865 | GPATCH4 | P4T-E | Human | Esophagus | ESCC | 1.04e-15 | 5.05e-01 | 0.1323 |
54865 | GPATCH4 | P5T-E | Human | Esophagus | ESCC | 7.88e-25 | 6.23e-01 | 0.1327 |
54865 | GPATCH4 | P8T-E | Human | Esophagus | ESCC | 3.40e-13 | 2.39e-01 | 0.0889 |
54865 | GPATCH4 | P9T-E | Human | Esophagus | ESCC | 1.70e-24 | 7.33e-01 | 0.1131 |
54865 | GPATCH4 | P10T-E | Human | Esophagus | ESCC | 6.72e-16 | 3.08e-01 | 0.116 |
54865 | GPATCH4 | P11T-E | Human | Esophagus | ESCC | 1.38e-08 | 3.81e-01 | 0.1426 |
54865 | GPATCH4 | P12T-E | Human | Esophagus | ESCC | 5.08e-16 | 1.98e-01 | 0.1122 |
54865 | GPATCH4 | P15T-E | Human | Esophagus | ESCC | 6.84e-20 | 5.68e-01 | 0.1149 |
54865 | GPATCH4 | P16T-E | Human | Esophagus | ESCC | 9.56e-17 | 3.57e-01 | 0.1153 |
54865 | GPATCH4 | P17T-E | Human | Esophagus | ESCC | 1.61e-09 | 7.31e-01 | 0.1278 |
54865 | GPATCH4 | P20T-E | Human | Esophagus | ESCC | 3.32e-13 | 4.09e-01 | 0.1124 |
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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 |
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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 |
GPATCH4 | SNV | Missense_Mutation | c.322N>C | p.Asn108His | p.N108H | protein_coding | tolerated(0.06) | possibly_damaging(0.887) | TCGA-BR-4357-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | ||
GPATCH4 | SNV | Missense_Mutation | rs780369480 | c.109N>T | p.Arg37Trp | p.R37W | protein_coding | deleterious(0.05) | benign(0.244) | TCGA-BR-8487-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
GPATCH4 | SNV | Missense_Mutation | c.220N>G | p.Phe74Val | p.F74V | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-D7-6526-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | cisplatin | SD | ||
GPATCH4 | SNV | Missense_Mutation | c.371G>A | p.Gly124Glu | p.G124E | protein_coding | tolerated(0.43) | benign(0.003) | TCGA-F1-6875-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
GPATCH4 | SNV | Missense_Mutation | c.181C>T | p.Pro61Ser | p.P61S | protein_coding | tolerated(0.06) | possibly_damaging(0.535) | TCGA-HU-A4GN-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | mitomycin | PD | ||
GPATCH4 | SNV | Missense_Mutation | novel | c.67N>A | p.Gln23Lys | p.Q23K | protein_coding | deleterious(0.01) | probably_damaging(0.998) | TCGA-VQ-A8DT-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | fluorouracil | PD | |
GPATCH4 | SNV | Missense_Mutation | novel | c.396N>T | p.Glu132Asp | p.E132D | protein_coding | tolerated(0.08) | benign(0.241) | TCGA-VQ-A8P2-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unspecific | Complete Response | ||
GPATCH4 | SNV | Missense_Mutation | rs762613137 | c.302N>A | p.Arg101His | p.R101H | protein_coding | tolerated(0.2) | benign(0) | TCGA-VQ-A8PO-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
GPATCH4 | SNV | Missense_Mutation | novel | c.59C>A | p.Ala20Asp | p.A20D | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-VQ-A91D-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | PD | |
GPATCH4 | deletion | Frame_Shift_Del | c.629delN | p.Lys210ArgfsTer73 | p.K210Rfs*73 | protein_coding | TCGA-BR-4201-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | cisplatin | 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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