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Gene: GCN1 |
Gene summary for GCN1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GCN1 | Gene ID | 10985 |
| Gene name | GCN1 activator of EIF2AK4 | |
| Gene Alias | GCN1L | |
| Cytomap | 12q24.23 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q92616 |
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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 |
| 10985 | GCN1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.01e-02 | 4.57e-02 | 0.0155 |
| 10985 | GCN1 | HTA11_347_2000001011 | Human | Colorectum | AD | 7.22e-04 | 3.09e-01 | -0.1954 |
| 10985 | GCN1 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.86e-03 | 3.21e-01 | -0.1464 |
| 10985 | GCN1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.48e-06 | 5.21e-01 | -0.059 |
| 10985 | GCN1 | HTA11_866_3004761011 | Human | Colorectum | AD | 8.20e-08 | 3.70e-01 | 0.096 |
| 10985 | GCN1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.72e-04 | 3.61e-01 | 0.294 |
| 10985 | GCN1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.79e-08 | 5.47e-01 | 0.3859 |
| 10985 | GCN1 | A015-C-203 | Human | Colorectum | FAP | 3.54e-06 | -1.05e-01 | -0.1294 |
| 10985 | GCN1 | A001-C-108 | Human | Colorectum | FAP | 3.54e-02 | -2.65e-03 | -0.0272 |
| 10985 | GCN1 | A015-C-104 | Human | Colorectum | FAP | 1.27e-06 | -6.97e-02 | -0.1899 |
| 10985 | GCN1 | A002-C-016 | Human | Colorectum | FAP | 6.22e-05 | -1.31e-01 | 0.0521 |
| 10985 | GCN1 | A002-C-116 | Human | Colorectum | FAP | 2.67e-08 | -2.23e-02 | -0.0452 |
| 10985 | GCN1 | F034 | Human | Colorectum | FAP | 9.84e-05 | -1.32e-01 | -0.0665 |
| 10985 | GCN1 | LZE7T | Human | Esophagus | ESCC | 6.61e-08 | 3.22e-01 | 0.0667 |
| 10985 | GCN1 | LZE8T | Human | Esophagus | ESCC | 2.47e-05 | 1.66e-01 | 0.067 |
| 10985 | GCN1 | LZE20T | Human | Esophagus | ESCC | 4.95e-02 | 6.43e-02 | 0.0662 |
| 10985 | GCN1 | LZE24T | Human | Esophagus | ESCC | 8.21e-10 | 1.07e-01 | 0.0596 |
| 10985 | GCN1 | LZE6T | Human | Esophagus | ESCC | 1.74e-02 | 7.79e-02 | 0.0845 |
| 10985 | GCN1 | P1T-E | Human | Esophagus | ESCC | 2.02e-09 | 3.70e-01 | 0.0875 |
| 10985 | GCN1 | P2T-E | Human | Esophagus | ESCC | 5.28e-17 | 3.31e-01 | 0.1177 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:0006417 | Colorectum | AD | regulation of translation | 141/3918 | 468/18723 | 1.32e-06 | 4.22e-05 | 141 |
| GO:0031667 | Colorectum | AD | response to nutrient levels | 138/3918 | 474/18723 | 1.22e-05 | 2.68e-04 | 138 |
| GO:0033674 | Colorectum | AD | positive regulation of kinase activity | 131/3918 | 467/18723 | 1.28e-04 | 1.85e-03 | 131 |
| GO:0042594 | Colorectum | AD | response to starvation | 63/3918 | 197/18723 | 1.77e-04 | 2.38e-03 | 63 |
| GO:0043620 | Colorectum | AD | regulation of DNA-templated transcription in response to stress | 23/3918 | 53/18723 | 1.86e-04 | 2.49e-03 | 23 |
| GO:0071496 | Colorectum | AD | cellular response to external stimulus | 94/3918 | 320/18723 | 1.98e-04 | 2.64e-03 | 94 |
| GO:0036003 | Colorectum | AD | positive regulation of transcription from RNA polymerase II promoter in response to stress | 13/3918 | 24/18723 | 3.45e-04 | 4.03e-03 | 13 |
| GO:0009267 | Colorectum | AD | cellular response to starvation | 51/3918 | 156/18723 | 3.90e-04 | 4.44e-03 | 51 |
| GO:0043618 | Colorectum | AD | regulation of transcription from RNA polymerase II promoter in response to stress | 20/3918 | 47/18723 | 6.54e-04 | 6.75e-03 | 20 |
| GO:0031668 | Colorectum | AD | cellular response to extracellular stimulus | 71/3918 | 246/18723 | 1.86e-03 | 1.52e-02 | 71 |
| GO:0031669 | Colorectum | AD | cellular response to nutrient levels | 63/3918 | 215/18723 | 2.19e-03 | 1.73e-02 | 63 |
| GO:00064172 | Colorectum | MSS | regulation of translation | 134/3467 | 468/18723 | 4.43e-08 | 2.38e-06 | 134 |
| GO:00316672 | Colorectum | MSS | response to nutrient levels | 125/3467 | 474/18723 | 1.24e-05 | 2.88e-04 | 125 |
| GO:00336742 | Colorectum | MSS | positive regulation of kinase activity | 122/3467 | 467/18723 | 2.50e-05 | 5.21e-04 | 122 |
| GO:00425942 | Colorectum | MSS | response to starvation | 56/3467 | 197/18723 | 4.25e-04 | 5.21e-03 | 56 |
| GO:00360032 | Colorectum | MSS | positive regulation of transcription from RNA polymerase II promoter in response to stress | 12/3467 | 24/18723 | 4.68e-04 | 5.50e-03 | 12 |
| GO:00436202 | Colorectum | MSS | regulation of DNA-templated transcription in response to stress | 20/3467 | 53/18723 | 7.91e-04 | 8.36e-03 | 20 |
| GO:00714962 | Colorectum | MSS | cellular response to external stimulus | 82/3467 | 320/18723 | 9.30e-04 | 9.44e-03 | 82 |
| GO:00436181 | Colorectum | MSS | regulation of transcription from RNA polymerase II promoter in response to stress | 18/3467 | 47/18723 | 1.17e-03 | 1.13e-02 | 18 |
| GO:00092672 | Colorectum | MSS | cellular response to starvation | 44/3467 | 156/18723 | 1.96e-03 | 1.69e-02 | 44 |
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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 |
| GCN1 | SNV | Missense_Mutation | c.4039G>T | p.Ala1347Ser | p.A1347S | Q92616 | protein_coding | deleterious(0.04) | probably_damaging(0.929) | TCGA-A8-A07L-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | CR | ||
| GCN1 | SNV | Missense_Mutation | c.2092N>T | p.Pro698Ser | p.P698S | Q92616 | protein_coding | tolerated(0.17) | benign(0.079) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| GCN1 | SNV | Missense_Mutation | c.3985N>G | p.His1329Asp | p.H1329D | Q92616 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AO-A03T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| GCN1 | SNV | Missense_Mutation | novel | c.2132N>T | p.Pro711Leu | p.P711L | Q92616 | protein_coding | tolerated(0.21) | benign(0.098) | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD |
| GCN1 | SNV | Missense_Mutation | rs770357732 | c.7949N>A | p.Arg2650Lys | p.R2650K | Q92616 | protein_coding | tolerated(1) | benign(0.062) | TCGA-AO-A124-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| GCN1 | SNV | Missense_Mutation | c.1711G>A | p.Ala571Thr | p.A571T | Q92616 | protein_coding | tolerated(0.39) | benign(0.013) | TCGA-AR-A251-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| GCN1 | SNV | Missense_Mutation | c.1175N>T | p.Pro392Leu | p.P392L | Q92616 | protein_coding | deleterious(0.05) | benign(0.015) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| GCN1 | SNV | Missense_Mutation | novel | c.221N>C | p.Ile74Thr | p.I74T | Q92616 | protein_coding | deleterious(0) | possibly_damaging(0.599) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| GCN1 | SNV | Missense_Mutation | c.3531N>T | p.Gln1177His | p.Q1177H | Q92616 | protein_coding | tolerated(0.05) | benign(0.082) | TCGA-D8-A1Y1-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | PD | |
| GCN1 | SNV | Missense_Mutation | c.3528N>T | p.Arg1176Ser | p.R1176S | Q92616 | protein_coding | deleterious(0.03) | probably_damaging(0.994) | TCGA-E2-A1L6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 |
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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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