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Gene: GCNT4 |
Gene summary for GCNT4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GCNT4 | Gene ID | 51301 |
| Gene name | glucosaminyl (N-acetyl) transferase 4 | |
| Gene Alias | C2GNT3 | |
| Cytomap | 5q13.3 | |
| Gene Type | protein-coding | GO ID | GO:0001655 | UniProtAcc | NA |
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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 |
| 51301 | GCNT4 | S43 | Human | Liver | Cirrhotic | 1.48e-16 | -5.76e-01 | -0.0187 |
| 51301 | GCNT4 | HCC1_Meng | Human | Liver | HCC | 3.01e-20 | -5.86e-01 | 0.0246 |
| 51301 | GCNT4 | HCC2_Meng | Human | Liver | HCC | 9.70e-18 | -5.73e-01 | 0.0107 |
| 51301 | GCNT4 | cirrhotic1 | Human | Liver | Cirrhotic | 6.82e-09 | -4.68e-01 | 0.0202 |
| 51301 | GCNT4 | cirrhotic2 | Human | Liver | Cirrhotic | 1.41e-12 | -2.75e-01 | 0.0201 |
| 51301 | GCNT4 | cirrhotic3 | Human | Liver | Cirrhotic | 4.70e-12 | -5.20e-01 | 0.0215 |
| 51301 | GCNT4 | p6 | Human | Liver | Cyst | 2.30e-02 | -5.87e-01 | -0.0218 |
| 51301 | GCNT4 | HCC1 | Human | Liver | HCC | 9.09e-04 | -5.87e-01 | 0.5336 |
| 51301 | GCNT4 | HCC2 | Human | Liver | HCC | 7.08e-06 | -5.87e-01 | 0.5341 |
| 51301 | GCNT4 | HCC5 | Human | Liver | HCC | 5.27e-09 | -5.87e-01 | 0.4932 |
| 51301 | GCNT4 | Pt13.a | Human | Liver | HCC | 1.29e-20 | -5.87e-01 | 0.021 |
| 51301 | GCNT4 | Pt13.b | Human | Liver | HCC | 1.98e-16 | -5.87e-01 | 0.0251 |
| 51301 | GCNT4 | Pt13.c | Human | Liver | HCC | 1.05e-10 | -5.87e-01 | 0.0076 |
| 51301 | GCNT4 | Pt14.b | Human | Liver | HCC | 1.85e-02 | -5.87e-01 | 0.018 |
| 51301 | GCNT4 | Pt14.c | Human | Liver | HCC | 2.62e-03 | -5.87e-01 | 0.0054 |
| 51301 | GCNT4 | Pt14.d | Human | Liver | HCC | 3.01e-20 | -5.87e-01 | 0.0143 |
| 51301 | GCNT4 | S014 | Human | Liver | HCC | 3.51e-13 | -5.87e-01 | 0.2254 |
| 51301 | GCNT4 | S015 | Human | Liver | HCC | 4.42e-09 | -5.87e-01 | 0.2375 |
| 51301 | GCNT4 | S016 | Human | Liver | HCC | 1.15e-16 | -5.87e-01 | 0.2243 |
| 51301 | GCNT4 | S028 | Human | Liver | HCC | 1.36e-04 | -5.03e-01 | 0.2503 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:000657511 | Liver | Cirrhotic | cellular modified amino acid metabolic process | 70/4634 | 188/18723 | 9.04e-05 | 9.69e-04 | 70 |
| GO:004887212 | Liver | Cirrhotic | homeostasis of number of cells | 89/4634 | 272/18723 | 1.76e-03 | 1.12e-02 | 89 |
| GO:004244511 | Liver | Cirrhotic | hormone metabolic process | 73/4634 | 218/18723 | 2.22e-03 | 1.36e-02 | 73 |
| GO:000657521 | Liver | HCC | cellular modified amino acid metabolic process | 119/7958 | 188/18723 | 6.47e-09 | 1.67e-07 | 119 |
| GO:004887222 | Liver | HCC | homeostasis of number of cells | 147/7958 | 272/18723 | 7.48e-05 | 6.70e-04 | 147 |
| GO:00064862 | Liver | HCC | protein glycosylation | 122/7958 | 226/18723 | 3.11e-04 | 2.21e-03 | 122 |
| GO:00434132 | Liver | HCC | macromolecule glycosylation | 122/7958 | 226/18723 | 3.11e-04 | 2.21e-03 | 122 |
| GO:00700852 | Liver | HCC | glycosylation | 128/7958 | 240/18723 | 4.35e-04 | 2.92e-03 | 128 |
| GO:0009100 | Liver | HCC | glycoprotein metabolic process | 193/7958 | 387/18723 | 1.89e-03 | 9.62e-03 | 193 |
| GO:00016553 | Liver | HCC | urogenital system development | 170/7958 | 338/18723 | 2.15e-03 | 1.08e-02 | 170 |
| GO:00018222 | Liver | HCC | kidney development | 148/7958 | 293/18723 | 3.25e-03 | 1.49e-02 | 148 |
| GO:00720012 | Liver | HCC | renal system development | 152/7958 | 302/18723 | 3.45e-03 | 1.56e-02 | 152 |
| GO:00065753 | Liver | Cyst | cellular modified amino acid metabolic process | 13/496 | 188/18723 | 1.55e-03 | 3.61e-02 | 13 |
| GO:004887232 | Liver | Cyst | homeostasis of number of cells | 16/496 | 272/18723 | 2.55e-03 | 4.87e-02 | 16 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| GCNT4 | SNV | Missense_Mutation | c.182N>G | p.Thr61Ser | p.T61S | Q9P109 | protein_coding | tolerated(0.88) | benign(0) | TCGA-A2-A0D2-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| GCNT4 | SNV | Missense_Mutation | rs201693155 | c.379N>A | p.Glu127Lys | p.E127K | Q9P109 | protein_coding | deleterious(0.01) | benign(0.159) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| GCNT4 | SNV | Missense_Mutation | novel | c.1274N>A | p.Ala425Glu | p.A425E | Q9P109 | protein_coding | tolerated(1) | benign(0.007) | TCGA-AC-A3BB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | CR |
| GCNT4 | SNV | Missense_Mutation | c.772N>T | p.Pro258Ser | p.P258S | Q9P109 | protein_coding | tolerated(1) | benign(0.012) | TCGA-E9-A1NF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD | |
| GCNT4 | SNV | Missense_Mutation | novel | c.1082A>G | p.Asp361Gly | p.D361G | Q9P109 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| GCNT4 | SNV | Missense_Mutation | rs770022108 | c.1099C>T | p.Arg367Cys | p.R367C | Q9P109 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD |
| GCNT4 | SNV | Missense_Mutation | c.407N>T | p.Ser136Phe | p.S136F | Q9P109 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| GCNT4 | SNV | Missense_Mutation | novel | c.44N>C | p.Lys15Thr | p.K15T | Q9P109 | protein_coding | tolerated(0.12) | benign(0.154) | TCGA-AA-3939-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| GCNT4 | SNV | Missense_Mutation | rs770022108 | c.1099N>T | p.Arg367Cys | p.R367C | Q9P109 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| GCNT4 | SNV | Missense_Mutation | c.795N>A | p.Phe265Leu | p.F265L | Q9P109 | protein_coding | deleterious(0.02) | possibly_damaging(0.46) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 |
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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 |
| Page: 1 |
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