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Gene: ARFGEF3 |
Gene summary for ARFGEF3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ARFGEF3 | Gene ID | 57221 |
| Gene name | ARFGEF family member 3 | |
| Gene Alias | A7322 | |
| Cytomap | 6q23.3-q24.1 | |
| Gene Type | protein-coding | GO ID | GO:0006996 | UniProtAcc | Q5TH69 |
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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 |
| 57221 | ARFGEF3 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.18e-04 | 5.80e-01 | -0.1088 |
| 57221 | ARFGEF3 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 2.12e-05 | 1.10e+00 | 0.3487 |
| 57221 | ARFGEF3 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.72e-09 | 7.19e-01 | 0.281 |
| 57221 | ARFGEF3 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.89e-03 | -1.36e-01 | 0.3005 |
| 57221 | ARFGEF3 | A001-C-207 | Human | Colorectum | FAP | 4.53e-02 | -1.40e-02 | 0.1278 |
| 57221 | ARFGEF3 | A015-C-203 | Human | Colorectum | FAP | 1.06e-27 | -3.57e-01 | -0.1294 |
| 57221 | ARFGEF3 | A015-C-204 | Human | Colorectum | FAP | 3.57e-05 | -2.02e-01 | -0.0228 |
| 57221 | ARFGEF3 | A014-C-040 | Human | Colorectum | FAP | 3.16e-03 | -3.02e-01 | -0.1184 |
| 57221 | ARFGEF3 | A002-C-201 | Human | Colorectum | FAP | 2.18e-07 | -2.16e-01 | 0.0324 |
| 57221 | ARFGEF3 | A001-C-119 | Human | Colorectum | FAP | 5.91e-05 | -2.98e-01 | -0.1557 |
| 57221 | ARFGEF3 | A001-C-108 | Human | Colorectum | FAP | 2.53e-12 | -1.13e-01 | -0.0272 |
| 57221 | ARFGEF3 | A002-C-205 | Human | Colorectum | FAP | 4.33e-19 | -4.17e-01 | -0.1236 |
| 57221 | ARFGEF3 | A015-C-006 | Human | Colorectum | FAP | 2.95e-10 | -2.48e-01 | -0.0994 |
| 57221 | ARFGEF3 | A015-C-106 | Human | Colorectum | FAP | 4.40e-08 | -1.83e-01 | -0.0511 |
| 57221 | ARFGEF3 | A002-C-114 | Human | Colorectum | FAP | 7.74e-14 | -3.14e-01 | -0.1561 |
| 57221 | ARFGEF3 | A015-C-104 | Human | Colorectum | FAP | 5.86e-26 | -2.19e-01 | -0.1899 |
| 57221 | ARFGEF3 | A001-C-014 | Human | Colorectum | FAP | 2.21e-13 | -2.05e-01 | 0.0135 |
| 57221 | ARFGEF3 | A002-C-016 | Human | Colorectum | FAP | 1.87e-18 | -2.17e-01 | 0.0521 |
| 57221 | ARFGEF3 | A015-C-002 | Human | Colorectum | FAP | 3.03e-09 | -4.05e-01 | -0.0763 |
| 57221 | ARFGEF3 | A001-C-203 | Human | Colorectum | FAP | 8.30e-06 | -1.31e-01 | -0.0481 |
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| ∗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:0032012 | Lung | IAC | regulation of ARF protein signal transduction | 8/2061 | 19/18723 | 5.25e-04 | 7.44e-03 | 8 |
| GO:005105611 | Lung | AIS | regulation of small GTPase mediated signal transduction | 66/1849 | 302/18723 | 4.26e-10 | 9.53e-08 | 66 |
| GO:000726512 | Lung | AIS | Ras protein signal transduction | 60/1849 | 337/18723 | 4.68e-06 | 2.31e-04 | 60 |
| GO:004657812 | Lung | AIS | regulation of Ras protein signal transduction | 39/1849 | 189/18723 | 6.68e-06 | 2.95e-04 | 39 |
| GO:00320111 | Lung | AIS | ARF protein signal transduction | 8/1849 | 19/18723 | 2.48e-04 | 4.83e-03 | 8 |
| GO:00320121 | Lung | AIS | regulation of ARF protein signal transduction | 8/1849 | 19/18723 | 2.48e-04 | 4.83e-03 | 8 |
| GO:005105621 | Lung | MIAC | regulation of small GTPase mediated signal transduction | 35/967 | 302/18723 | 6.81e-06 | 6.35e-04 | 35 |
| GO:00072658 | Prostate | BPH | Ras protein signal transduction | 101/3107 | 337/18723 | 5.64e-10 | 2.79e-08 | 101 |
| GO:00510568 | Prostate | BPH | regulation of small GTPase mediated signal transduction | 78/3107 | 302/18723 | 2.69e-05 | 3.16e-04 | 78 |
| GO:00465787 | Prostate | BPH | regulation of Ras protein signal transduction | 53/3107 | 189/18723 | 5.08e-05 | 5.24e-04 | 53 |
| GO:000726514 | Prostate | Tumor | Ras protein signal transduction | 101/3246 | 337/18723 | 6.29e-09 | 2.44e-07 | 101 |
| GO:005105613 | Prostate | Tumor | regulation of small GTPase mediated signal transduction | 80/3246 | 302/18723 | 3.96e-05 | 4.57e-04 | 80 |
| GO:004657814 | Prostate | Tumor | regulation of Ras protein signal transduction | 53/3246 | 189/18723 | 1.63e-04 | 1.46e-03 | 53 |
| Page: 1 2 |
| 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 |
| ARFGEF3 | SNV | Missense_Mutation | c.3230C>G | p.Pro1077Arg | p.P1077R | Q5TH69 | protein_coding | deleterious(0) | benign(0.34) | TCGA-A2-A0D2-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| ARFGEF3 | SNV | Missense_Mutation | novel | c.2314G>T | p.Val772Leu | p.V772L | Q5TH69 | protein_coding | deleterious(0.02) | benign(0) | TCGA-AC-A8OQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ARFGEF3 | SNV | Missense_Mutation | c.2404N>A | p.Ala802Thr | p.A802T | Q5TH69 | protein_coding | deleterious(0.01) | benign(0.368) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| ARFGEF3 | SNV | Missense_Mutation | c.1184C>T | p.Ser395Leu | p.S395L | Q5TH69 | protein_coding | deleterious(0) | benign(0.006) | TCGA-BH-A1FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| ARFGEF3 | SNV | Missense_Mutation | c.2213N>T | p.Ala738Val | p.A738V | Q5TH69 | protein_coding | tolerated(0.11) | benign(0.101) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ARFGEF3 | SNV | Missense_Mutation | novel | c.1907N>T | p.Ser636Leu | p.S636L | Q5TH69 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.977) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ARFGEF3 | SNV | Missense_Mutation | novel | c.2347N>G | p.Gln783Glu | p.Q783E | Q5TH69 | protein_coding | tolerated(0.29) | benign(0.073) | TCGA-D8-A4Z1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| ARFGEF3 | SNV | Missense_Mutation | c.2250N>A | p.His750Gln | p.H750Q | Q5TH69 | protein_coding | tolerated(0.63) | benign(0.082) | TCGA-GM-A2DB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxol | CR | |
| ARFGEF3 | SNV | Missense_Mutation | novel | c.2380C>T | p.Leu794Phe | p.L794F | Q5TH69 | protein_coding | deleterious(0) | probably_damaging(0.942) | TCGA-LL-A9Q3-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Immunotherapy | herceptin | CR |
| ARFGEF3 | insertion | Frame_Shift_Ins | novel | c.2346_2347insG | p.Gln783AlafsTer5 | p.Q783Afs*5 | Q5TH69 | protein_coding | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 |
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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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