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Gene: ARL4D |
Gene summary for ARL4D |
Gene summary. |
Gene information | Species | Human | Gene symbol | ARL4D | Gene ID | 379 |
Gene name | ADP ribosylation factor like GTPase 4D | |
Gene Alias | ARF4L | |
Cytomap | 17q21.31 | |
Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | P49703 |
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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 |
379 | ARL4D | LZE4T | Human | Esophagus | ESCC | 3.06e-27 | 1.40e+00 | 0.0811 |
379 | ARL4D | LZE8T | Human | Esophagus | ESCC | 1.34e-07 | 4.57e-01 | 0.067 |
379 | ARL4D | LZE20T | Human | Esophagus | ESCC | 2.36e-12 | 7.61e-01 | 0.0662 |
379 | ARL4D | LZE24T | Human | Esophagus | ESCC | 2.48e-08 | 8.15e-01 | 0.0596 |
379 | ARL4D | LZE22D3 | Human | Esophagus | HGIN | 2.14e-02 | 2.71e-01 | 0.0653 |
379 | ARL4D | LZE21T | Human | Esophagus | ESCC | 1.38e-07 | 1.26e+00 | 0.0655 |
379 | ARL4D | LZE6T | Human | Esophagus | ESCC | 1.07e-02 | 7.17e-01 | 0.0845 |
379 | ARL4D | P2T-E | Human | Esophagus | ESCC | 1.59e-20 | 3.59e-01 | 0.1177 |
379 | ARL4D | P4T-E | Human | Esophagus | ESCC | 4.60e-37 | 1.69e+00 | 0.1323 |
379 | ARL4D | P5T-E | Human | Esophagus | ESCC | 6.73e-96 | 2.36e+00 | 0.1327 |
379 | ARL4D | P8T-E | Human | Esophagus | ESCC | 2.73e-13 | 3.79e-01 | 0.0889 |
379 | ARL4D | P9T-E | Human | Esophagus | ESCC | 1.98e-17 | 7.06e-01 | 0.1131 |
379 | ARL4D | P10T-E | Human | Esophagus | ESCC | 3.29e-06 | 1.54e-01 | 0.116 |
379 | ARL4D | P11T-E | Human | Esophagus | ESCC | 1.39e-23 | 2.16e+00 | 0.1426 |
379 | ARL4D | P12T-E | Human | Esophagus | ESCC | 2.62e-72 | 1.98e+00 | 0.1122 |
379 | ARL4D | P15T-E | Human | Esophagus | ESCC | 1.17e-37 | 1.23e+00 | 0.1149 |
379 | ARL4D | P16T-E | Human | Esophagus | ESCC | 8.21e-25 | 6.70e-01 | 0.1153 |
379 | ARL4D | P17T-E | Human | Esophagus | ESCC | 9.02e-06 | 6.11e-01 | 0.1278 |
379 | ARL4D | P19T-E | Human | Esophagus | ESCC | 6.56e-03 | 8.31e-01 | 0.1662 |
379 | ARL4D | P20T-E | Human | Esophagus | ESCC | 5.31e-05 | 6.60e-01 | 0.1124 |
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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:000930617 | Esophagus | ESCC | protein secretion | 190/8552 | 359/18723 | 3.22e-03 | 1.34e-02 | 190 |
GO:003559217 | Esophagus | ESCC | establishment of protein localization to extracellular region | 190/8552 | 360/18723 | 3.77e-03 | 1.53e-02 | 190 |
GO:007169210 | Esophagus | ESCC | protein localization to extracellular region | 193/8552 | 368/18723 | 5.01e-03 | 1.92e-02 | 193 |
GO:003559212 | Liver | HCC | establishment of protein localization to extracellular region | 176/7958 | 360/18723 | 7.96e-03 | 3.15e-02 | 176 |
GO:000930612 | Liver | HCC | protein secretion | 175/7958 | 359/18723 | 9.32e-03 | 3.57e-02 | 175 |
GO:000930610 | Oral cavity | OSCC | protein secretion | 169/7305 | 359/18723 | 1.04e-03 | 5.34e-03 | 169 |
GO:003559210 | Oral cavity | OSCC | establishment of protein localization to extracellular region | 169/7305 | 360/18723 | 1.21e-03 | 6.08e-03 | 169 |
GO:00716929 | Oral cavity | OSCC | protein localization to extracellular region | 172/7305 | 368/18723 | 1.40e-03 | 6.79e-03 | 172 |
GO:00716928 | Prostate | BPH | protein localization to extracellular region | 82/3107 | 368/18723 | 2.59e-03 | 1.39e-02 | 82 |
GO:00093069 | Prostate | BPH | protein secretion | 80/3107 | 359/18723 | 2.89e-03 | 1.52e-02 | 80 |
GO:00355929 | Prostate | BPH | establishment of protein localization to extracellular region | 80/3107 | 360/18723 | 3.13e-03 | 1.63e-02 | 80 |
GO:007169214 | Prostate | Tumor | protein localization to extracellular region | 89/3246 | 368/18723 | 4.80e-04 | 3.57e-03 | 89 |
GO:000930615 | Prostate | Tumor | protein secretion | 87/3246 | 359/18723 | 5.15e-04 | 3.78e-03 | 87 |
GO:003559215 | Prostate | Tumor | establishment of protein localization to extracellular region | 87/3246 | 360/18723 | 5.65e-04 | 4.10e-03 | 87 |
GO:007169216 | Thyroid | PTC | protein localization to extracellular region | 139/5968 | 368/18723 | 8.95e-03 | 3.72e-02 | 139 |
GO:000930618 | Thyroid | PTC | protein secretion | 135/5968 | 359/18723 | 1.16e-02 | 4.58e-02 | 135 |
GO:003559218 | Thyroid | PTC | establishment of protein localization to extracellular region | 135/5968 | 360/18723 | 1.28e-02 | 4.95e-02 | 135 |
GO:007169223 | Thyroid | ATC | protein localization to extracellular region | 150/6293 | 368/18723 | 2.25e-03 | 1.05e-02 | 150 |
GO:000930623 | Thyroid | ATC | protein secretion | 146/6293 | 359/18723 | 2.83e-03 | 1.29e-02 | 146 |
GO:003559223 | Thyroid | ATC | establishment of protein localization to extracellular region | 146/6293 | 360/18723 | 3.20e-03 | 1.44e-02 | 146 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
ARL4D | insertion | Frame_Shift_Ins | novel | c.406_407insCCGTGTCAACGGCTTGGGGCTTCGGAGGGCGGGTGGG | p.Lys136ThrfsTer24 | p.K136Tfs*24 | P49703 | protein_coding | TCGA-BH-A0BD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
ARL4D | SNV | Missense_Mutation | novel | c.322N>T | p.Arg108Trp | p.R108W | P49703 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
ARL4D | SNV | Missense_Mutation | c.286G>T | p.Gly96Cys | p.G96C | P49703 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-A01K-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | folinic | CR | |
ARL4D | SNV | Missense_Mutation | c.382N>A | p.Val128Met | p.V128M | P49703 | protein_coding | deleterious(0) | probably_damaging(0.932) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
ARL4D | SNV | Missense_Mutation | c.262N>T | p.Arg88Cys | p.R88C | P49703 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD | |
ARL4D | SNV | Missense_Mutation | c.251N>A | p.Arg84Gln | p.R84Q | P49703 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-D1-A16J-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD | |
ARL4D | SNV | Missense_Mutation | novel | c.125N>G | p.Lys42Arg | p.K42R | P49703 | protein_coding | tolerated(0.06) | possibly_damaging(0.46) | TCGA-FI-A2F4-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
ARL4D | insertion | Frame_Shift_Ins | rs758198899 | c.231_232insG | p.Gln80AlafsTer28 | p.Q80Afs*28 | P49703 | protein_coding | TCGA-DI-A1BU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD | ||
ARL4D | SNV | Missense_Mutation | c.412G>T | p.Asp138Tyr | p.D138Y | P49703 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-05-4410-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
ARL4D | SNV | Missense_Mutation | c.286G>T | p.Gly96Cys | p.G96C | P49703 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-05-4430-01 | Lung | lung 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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