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Gene: GCH1 |
Gene summary for GCH1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | GCH1 | Gene ID | 2643 |
Gene name | GTP cyclohydrolase 1 | |
Gene Alias | DYT14 | |
Cytomap | 14q22.2 | |
Gene Type | protein-coding | GO ID | GO:0000302 | UniProtAcc | A0A024R642 |
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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 |
2643 | GCH1 | LZE4T | Human | Esophagus | ESCC | 6.12e-03 | -4.10e-02 | 0.0811 |
2643 | GCH1 | LZE8T | Human | Esophagus | ESCC | 4.89e-05 | 6.04e-02 | 0.067 |
2643 | GCH1 | LZE20T | Human | Esophagus | ESCC | 2.94e-08 | 3.40e-01 | 0.0662 |
2643 | GCH1 | LZE24T | Human | Esophagus | ESCC | 1.04e-08 | 4.93e-01 | 0.0596 |
2643 | GCH1 | P1T-E | Human | Esophagus | ESCC | 3.27e-12 | 6.75e-01 | 0.0875 |
2643 | GCH1 | P2T-E | Human | Esophagus | ESCC | 5.53e-12 | 1.60e-01 | 0.1177 |
2643 | GCH1 | P4T-E | Human | Esophagus | ESCC | 1.16e-20 | 3.46e-01 | 0.1323 |
2643 | GCH1 | P5T-E | Human | Esophagus | ESCC | 1.08e-04 | 5.22e-02 | 0.1327 |
2643 | GCH1 | P8T-E | Human | Esophagus | ESCC | 6.26e-20 | 3.52e-01 | 0.0889 |
2643 | GCH1 | P9T-E | Human | Esophagus | ESCC | 4.01e-07 | 5.73e-02 | 0.1131 |
2643 | GCH1 | P10T-E | Human | Esophagus | ESCC | 6.76e-09 | -9.29e-03 | 0.116 |
2643 | GCH1 | P11T-E | Human | Esophagus | ESCC | 8.27e-05 | 5.86e-01 | 0.1426 |
2643 | GCH1 | P12T-E | Human | Esophagus | ESCC | 9.34e-22 | 3.87e-01 | 0.1122 |
2643 | GCH1 | P15T-E | Human | Esophagus | ESCC | 5.26e-22 | 3.97e-01 | 0.1149 |
2643 | GCH1 | P16T-E | Human | Esophagus | ESCC | 2.51e-13 | 1.94e-03 | 0.1153 |
2643 | GCH1 | P20T-E | Human | Esophagus | ESCC | 4.14e-05 | 1.68e-01 | 0.1124 |
2643 | GCH1 | P21T-E | Human | Esophagus | ESCC | 3.25e-08 | -1.24e-02 | 0.1617 |
2643 | GCH1 | P22T-E | Human | Esophagus | ESCC | 1.12e-05 | 3.46e-02 | 0.1236 |
2643 | GCH1 | P23T-E | Human | Esophagus | ESCC | 1.20e-09 | 3.86e-01 | 0.108 |
2643 | GCH1 | P24T-E | Human | Esophagus | ESCC | 1.14e-07 | 1.93e-01 | 0.1287 |
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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:000697920 | Oral cavity | OSCC | response to oxidative stress | 273/7305 | 446/18723 | 8.35e-22 | 1.65e-19 | 273 |
GO:006219720 | Oral cavity | OSCC | cellular response to chemical stress | 204/7305 | 337/18723 | 6.89e-16 | 5.19e-14 | 204 |
GO:000030220 | Oral cavity | OSCC | response to reactive oxygen species | 143/7305 | 222/18723 | 1.32e-14 | 7.88e-13 | 143 |
GO:003459920 | Oral cavity | OSCC | cellular response to oxidative stress | 173/7305 | 288/18723 | 2.90e-13 | 1.43e-11 | 173 |
GO:003461419 | Oral cavity | OSCC | cellular response to reactive oxygen species | 96/7305 | 155/18723 | 5.98e-09 | 1.27e-07 | 96 |
GO:003461218 | Oral cavity | OSCC | response to tumor necrosis factor | 143/7305 | 253/18723 | 1.09e-08 | 2.23e-07 | 143 |
GO:200037716 | Oral cavity | OSCC | regulation of reactive oxygen species metabolic process | 92/7305 | 157/18723 | 4.96e-07 | 7.27e-06 | 92 |
GO:003249617 | Oral cavity | OSCC | response to lipopolysaccharide | 178/7305 | 343/18723 | 7.27e-07 | 1.03e-05 | 178 |
GO:00060667 | Oral cavity | OSCC | alcohol metabolic process | 179/7305 | 353/18723 | 4.54e-06 | 5.21e-05 | 179 |
GO:00343417 | Oral cavity | OSCC | response to interferon-gamma | 81/7305 | 141/18723 | 6.77e-06 | 7.43e-05 | 81 |
GO:000963618 | Oral cavity | OSCC | response to toxic substance | 137/7305 | 262/18723 | 7.94e-06 | 8.52e-05 | 137 |
GO:000223717 | Oral cavity | OSCC | response to molecule of bacterial origin | 181/7305 | 363/18723 | 1.48e-05 | 1.49e-04 | 181 |
GO:00461652 | Oral cavity | OSCC | alcohol biosynthetic process | 77/7305 | 140/18723 | 8.77e-05 | 6.70e-04 | 77 |
GO:00423985 | Oral cavity | OSCC | cellular modified amino acid biosynthetic process | 31/7305 | 46/18723 | 9.03e-05 | 6.88e-04 | 31 |
GO:007259316 | Oral cavity | OSCC | reactive oxygen species metabolic process | 122/7305 | 239/18723 | 9.73e-05 | 7.34e-04 | 122 |
GO:00425594 | Oral cavity | OSCC | pteridine-containing compound biosynthetic process | 13/7305 | 15/18723 | 2.07e-04 | 1.36e-03 | 13 |
GO:199074818 | Oral cavity | OSCC | cellular detoxification | 63/7305 | 116/18723 | 5.80e-04 | 3.31e-03 | 63 |
GO:009886918 | Oral cavity | OSCC | cellular oxidant detoxification | 55/7305 | 101/18723 | 1.16e-03 | 5.89e-03 | 55 |
GO:00513533 | Oral cavity | OSCC | positive regulation of oxidoreductase activity | 35/7305 | 59/18723 | 1.24e-03 | 6.23e-03 | 35 |
GO:009723718 | Oral cavity | OSCC | cellular response to toxic substance | 65/7305 | 124/18723 | 1.63e-03 | 7.74e-03 | 65 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa012405 | Esophagus | ESCC | Biosynthesis of cofactors | 97/4205 | 153/8465 | 3.88e-04 | 1.35e-03 | 6.94e-04 | 97 |
hsa0124012 | Esophagus | ESCC | Biosynthesis of cofactors | 97/4205 | 153/8465 | 3.88e-04 | 1.35e-03 | 6.94e-04 | 97 |
hsa012404 | Oral cavity | OSCC | Biosynthesis of cofactors | 88/3704 | 153/8465 | 3.84e-04 | 1.20e-03 | 6.12e-04 | 88 |
hsa0124011 | Oral cavity | OSCC | Biosynthesis of cofactors | 88/3704 | 153/8465 | 3.84e-04 | 1.20e-03 | 6.12e-04 | 88 |
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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 |
GCH1 | SNV | Missense_Mutation | c.166N>A | p.Glu56Lys | p.E56K | P30793 | protein_coding | tolerated(0.18) | benign(0.007) | TCGA-E2-A15R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
GCH1 | SNV | Missense_Mutation | novel | c.561N>C | p.Lys187Asn | p.K187N | P30793 | protein_coding | deleterious(0.01) | probably_damaging(0.983) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
GCH1 | SNV | Missense_Mutation | novel | c.111N>T | p.Glu37Asp | p.E37D | P30793 | protein_coding | tolerated(0.37) | benign(0.001) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
GCH1 | SNV | Missense_Mutation | c.676G>A | p.Val226Met | p.V226M | P30793 | protein_coding | deleterious(0.03) | possibly_damaging(0.602) | TCGA-A6-6653-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
GCH1 | SNV | Missense_Mutation | c.404N>C | p.Ile135Thr | p.I135T | P30793 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-D5-6530-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
GCH1 | SNV | Missense_Mutation | c.355N>A | p.Asp119Asn | p.D119N | P30793 | protein_coding | tolerated(0.37) | benign(0.003) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
GCH1 | SNV | Missense_Mutation | novel | c.749G>T | p.Ser250Ile | p.S250I | P30793 | protein_coding | deleterious(0) | possibly_damaging(0.657) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
GCH1 | SNV | Missense_Mutation | rs886042892 | c.284N>T | p.Pro95Leu | p.P95L | P30793 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-B5-A1MX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Hormone Therapy | megace | SD |
GCH1 | SNV | Missense_Mutation | c.384N>T | p.Glu128Asp | p.E128D | P30793 | protein_coding | deleterious(0.03) | benign(0.352) | TCGA-D1-A103-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
GCH1 | SNV | Missense_Mutation | c.159N>C | p.Trp53Cys | p.W53C | P30793 | protein_coding | tolerated(0.1) | benign(0.001) | TCGA-EC-A24G-01 | Endometrium | uterine corpus endometrioid 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 |
2643 | GCH1 | ENZYME | ProSavin | |||
2643 | GCH1 | ENZYME | Guanine | GUANINE |
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