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Gene: ARL4A |
Gene summary for ARL4A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ARL4A | Gene ID | 10124 |
| Gene name | ADP ribosylation factor like GTPase 4A | |
| Gene Alias | ARL4 | |
| Cytomap | 7p21.3 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | A0A024R9Z2 |
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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 |
| 10124 | ARL4A | GSM4909277 | Human | Breast | Precancer | 3.48e-02 | 5.62e-01 | 0.0177 |
| 10124 | ARL4A | GSM4909281 | Human | Breast | IDC | 1.75e-06 | -4.01e-01 | 0.21 |
| 10124 | ARL4A | GSM4909285 | Human | Breast | IDC | 1.41e-03 | -2.86e-01 | 0.21 |
| 10124 | ARL4A | GSM4909286 | Human | Breast | IDC | 5.57e-11 | -4.49e-01 | 0.1081 |
| 10124 | ARL4A | GSM4909293 | Human | Breast | IDC | 5.54e-03 | -3.04e-01 | 0.1581 |
| 10124 | ARL4A | GSM4909296 | Human | Breast | IDC | 8.56e-03 | -3.27e-01 | 0.1524 |
| 10124 | ARL4A | GSM4909297 | Human | Breast | IDC | 2.65e-06 | -2.11e-01 | 0.1517 |
| 10124 | ARL4A | GSM4909299 | Human | Breast | IDC | 2.23e-24 | 6.20e-01 | 0.035 |
| 10124 | ARL4A | GSM4909301 | Human | Breast | IDC | 4.53e-13 | -4.61e-01 | 0.1577 |
| 10124 | ARL4A | GSM4909302 | Human | Breast | IDC | 6.95e-12 | -4.31e-01 | 0.1545 |
| 10124 | ARL4A | GSM4909308 | Human | Breast | IDC | 1.24e-06 | -3.95e-01 | 0.158 |
| 10124 | ARL4A | GSM4909309 | Human | Breast | IDC | 2.26e-06 | 4.18e-01 | 0.0483 |
| 10124 | ARL4A | GSM4909311 | Human | Breast | IDC | 1.02e-16 | -4.34e-01 | 0.1534 |
| 10124 | ARL4A | GSM4909312 | Human | Breast | IDC | 2.76e-06 | -3.90e-01 | 0.1552 |
| 10124 | ARL4A | GSM4909315 | Human | Breast | IDC | 4.05e-03 | -3.46e-01 | 0.21 |
| 10124 | ARL4A | GSM4909316 | Human | Breast | IDC | 6.88e-03 | -4.58e-01 | 0.21 |
| 10124 | ARL4A | GSM4909319 | Human | Breast | IDC | 4.61e-22 | -4.70e-01 | 0.1563 |
| 10124 | ARL4A | GSM4909320 | Human | Breast | IDC | 1.19e-07 | -5.09e-01 | 0.1575 |
| 10124 | ARL4A | GSM4909321 | Human | Breast | IDC | 1.55e-11 | -3.85e-01 | 0.1559 |
| 10124 | ARL4A | brca10 | Human | Breast | Precancer | 4.31e-04 | -3.68e-01 | -0.0029 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:00454444 | Breast | Precancer | fat cell differentiation | 26/1080 | 229/18723 | 7.60e-04 | 9.04e-03 | 26 |
| GO:004544412 | Breast | IDC | fat cell differentiation | 30/1434 | 229/18723 | 2.72e-03 | 2.41e-02 | 30 |
| GO:004544421 | Breast | DCIS | fat cell differentiation | 30/1390 | 229/18723 | 1.70e-03 | 1.68e-02 | 30 |
| GO:00454445 | Cervix | CC | fat cell differentiation | 53/2311 | 229/18723 | 3.72e-06 | 9.75e-05 | 53 |
| GO:0050873 | Cervix | CC | brown fat cell differentiation | 13/2311 | 50/18723 | 6.42e-03 | 3.58e-02 | 13 |
| GO:00454449 | Esophagus | ESCC | fat cell differentiation | 135/8552 | 229/18723 | 3.38e-05 | 2.78e-04 | 135 |
| GO:00454442 | Liver | Cirrhotic | fat cell differentiation | 73/4634 | 229/18723 | 8.57e-03 | 3.97e-02 | 73 |
| GO:00454441 | Liver | HCC | fat cell differentiation | 120/7958 | 229/18723 | 1.52e-03 | 8.05e-03 | 120 |
| GO:00454448 | Oral cavity | OSCC | fat cell differentiation | 120/7305 | 229/18723 | 2.48e-05 | 2.32e-04 | 120 |
| GO:004544418 | Thyroid | PTC | fat cell differentiation | 102/5968 | 229/18723 | 3.66e-05 | 3.40e-04 | 102 |
| GO:004544423 | Thyroid | ATC | fat cell differentiation | 105/6293 | 229/18723 | 7.42e-05 | 5.62e-04 | 105 |
| Page: 1 |
| 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 |
| ARL4A | SNV | Missense_Mutation | c.415N>G | p.Arg139Gly | p.R139G | P40617 | protein_coding | tolerated(0.05) | benign(0.383) | TCGA-A2-A1G0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD | |
| ARL4A | SNV | Missense_Mutation | novel | c.340G>A | p.Glu114Lys | p.E114K | P40617 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-MA-AA41-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| ARL4A | SNV | Missense_Mutation | novel | c.368A>C | p.Glu123Ala | p.E123A | P40617 | protein_coding | deleterious(0.05) | benign(0.083) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| ARL4A | SNV | Missense_Mutation | novel | c.99G>T | p.Lys33Asn | p.K33N | P40617 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| ARL4A | SNV | Missense_Mutation | novel | c.414G>C | p.Leu138Phe | p.L138F | P40617 | protein_coding | deleterious(0) | probably_damaging(0.961) | TCGA-AJ-A3QS-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
| ARL4A | SNV | Missense_Mutation | rs749392270 | c.316N>A | p.Glu106Lys | p.E106K | P40617 | protein_coding | deleterious(0.01) | probably_damaging(0.918) | TCGA-AJ-A5DW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ARL4A | SNV | Missense_Mutation | novel | c.104N>T | p.Thr35Ile | p.T35I | P40617 | protein_coding | deleterious(0) | probably_damaging(0.975) | TCGA-AP-A1DO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ARL4A | SNV | Missense_Mutation | c.71T>C | p.Val24Ala | p.V24A | P40617 | protein_coding | tolerated(0.21) | benign(0.031) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| ARL4A | SNV | Missense_Mutation | novel | c.542A>G | p.Lys181Arg | p.K181R | P40617 | protein_coding | tolerated(0.42) | benign(0.021) | TCGA-BK-A6W3-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ARL4A | SNV | Missense_Mutation | novel | c.377G>A | p.Gly126Glu | p.G126E | P40617 | protein_coding | deleterious(0.03) | probably_damaging(0.993) | TCGA-D1-A1NS-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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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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