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Gene: GCAT |
Gene summary for GCAT |
Gene summary. |
Gene information | Species | Human | Gene symbol | GCAT | Gene ID | 23464 |
Gene name | glycine C-acetyltransferase | |
Gene Alias | KBL | |
Cytomap | 22q13.1 | |
Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | O75600 |
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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 |
23464 | GCAT | HCC2 | Human | Liver | HCC | 8.12e-35 | 5.05e+00 | 0.5341 |
23464 | GCAT | HCC5 | Human | Liver | HCC | 3.92e-03 | 2.97e+00 | 0.4932 |
23464 | GCAT | Pt14.a | Human | Liver | HCC | 4.09e-03 | 2.98e-01 | 0.0169 |
23464 | GCAT | S014 | Human | Liver | HCC | 3.75e-12 | 4.72e-01 | 0.2254 |
23464 | GCAT | S015 | Human | Liver | HCC | 9.35e-15 | 7.15e-01 | 0.2375 |
23464 | GCAT | S016 | Human | Liver | HCC | 3.38e-08 | 3.74e-01 | 0.2243 |
23464 | GCAT | S027 | Human | Liver | HCC | 9.60e-03 | 2.94e-01 | 0.2446 |
23464 | GCAT | S028 | Human | Liver | HCC | 2.13e-07 | 3.70e-01 | 0.2503 |
23464 | GCAT | S029 | Human | Liver | HCC | 1.36e-10 | 5.68e-01 | 0.2581 |
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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:00442827 | Esophagus | ESCC | small molecule catabolic process | 201/8552 | 376/18723 | 1.35e-03 | 6.41e-03 | 201 |
GO:004428221 | Liver | HCC | small molecule catabolic process | 225/7958 | 376/18723 | 6.50e-12 | 2.80e-10 | 225 |
GO:001605421 | Liver | HCC | organic acid catabolic process | 152/7958 | 240/18723 | 5.11e-11 | 1.92e-09 | 152 |
GO:00463952 | Liver | HCC | carboxylic acid catabolic process | 149/7958 | 236/18723 | 1.11e-10 | 3.87e-09 | 149 |
GO:19016052 | Liver | HCC | alpha-amino acid metabolic process | 124/7958 | 195/18723 | 2.07e-09 | 5.79e-08 | 124 |
GO:00065202 | Liver | HCC | cellular amino acid metabolic process | 167/7958 | 284/18723 | 1.91e-08 | 4.56e-07 | 167 |
GO:00090632 | Liver | HCC | cellular amino acid catabolic process | 70/7958 | 110/18723 | 6.12e-06 | 7.52e-05 | 70 |
GO:00090692 | Liver | HCC | serine family amino acid metabolic process | 29/7958 | 40/18723 | 1.17e-04 | 9.87e-04 | 29 |
GO:00090662 | Liver | HCC | aspartate family amino acid metabolic process | 34/7958 | 49/18723 | 1.28e-04 | 1.06e-03 | 34 |
GO:19016062 | Liver | HCC | alpha-amino acid catabolic process | 53/7958 | 87/18723 | 4.01e-04 | 2.71e-03 | 53 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa002602 | Liver | HCC | Glycine, serine and threonine metabolism | 28/4020 | 40/8465 | 3.28e-03 | 1.07e-02 | 5.93e-03 | 28 |
hsa002603 | Liver | HCC | Glycine, serine and threonine metabolism | 28/4020 | 40/8465 | 3.28e-03 | 1.07e-02 | 5.93e-03 | 28 |
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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 |
GCAT | SNV | Missense_Mutation | c.325G>A | p.Glu109Lys | p.E109K | O75600 | protein_coding | tolerated(0.16) | benign(0.021) | TCGA-A8-A09G-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
GCAT | SNV | Missense_Mutation | rs201266387 | c.607C>T | p.Arg203Cys | p.R203C | O75600 | protein_coding | deleterious(0.02) | benign(0.013) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
GCAT | SNV | Missense_Mutation | c.332N>C | p.Ile111Thr | p.I111T | O75600 | protein_coding | deleterious(0.02) | possibly_damaging(0.612) | TCGA-C8-A26X-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
GCAT | SNV | Missense_Mutation | novel | c.308N>A | p.Gly103Asp | p.G103D | O75600 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
GCAT | SNV | Missense_Mutation | novel | c.65N>T | p.Ser22Leu | p.S22L | O75600 | protein_coding | deleterious_low_confidence(0.01) | benign(0.169) | TCGA-EX-A69L-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
GCAT | SNV | Missense_Mutation | novel | c.155N>T | p.Ser52Phe | p.S52F | O75600 | protein_coding | deleterious(0) | probably_damaging(0.982) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
GCAT | SNV | Missense_Mutation | rs750055272 | c.1070N>A | p.Arg357His | p.R357H | O75600 | protein_coding | deleterious(0.03) | probably_damaging(0.995) | TCGA-VS-A9V1-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
GCAT | SNV | Missense_Mutation | rs200392738 | c.809N>A | p.Arg270Gln | p.R270Q | O75600 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
GCAT | SNV | Missense_Mutation | rs139816860 | c.1216N>A | p.Val406Met | p.V406M | O75600 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
GCAT | SNV | Missense_Mutation | novel | c.493G>A | p.Ala165Thr | p.A165T | O75600 | protein_coding | tolerated(0.14) | benign(0.176) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | 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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