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Gene: ARHGAP4 |
Gene summary for ARHGAP4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ARHGAP4 | Gene ID | 393 |
| Gene name | Rho GTPase activating protein 4 | |
| Gene Alias | C1 | |
| Cytomap | Xq28 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | P98171 |
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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 |
| 393 | ARHGAP4 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.97e-12 | 4.57e-01 | -0.0811 |
| 393 | ARHGAP4 | HTA11_78_2000001011 | Human | Colorectum | AD | 2.40e-04 | 2.30e-01 | -0.1088 |
| 393 | ARHGAP4 | HTA11_83_2000001011 | Human | Colorectum | SER | 9.94e-10 | 4.44e-01 | -0.1526 |
| 393 | ARHGAP4 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.61e-03 | 2.30e-01 | -0.1001 |
| 393 | ARHGAP4 | HTA11_1391_2000001011 | Human | Colorectum | AD | 7.63e-14 | 5.26e-01 | -0.059 |
| 393 | ARHGAP4 | HTA11_8622_2000001021 | Human | Colorectum | SER | 1.31e-05 | 3.88e-01 | 0.0528 |
| 393 | ARHGAP4 | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.54e-05 | 2.96e-01 | 0.0338 |
| 393 | ARHGAP4 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.37e-25 | 5.93e-01 | 0.0674 |
| 393 | ARHGAP4 | HTA11_6818_2000001021 | Human | Colorectum | AD | 2.12e-10 | 4.67e-01 | 0.0588 |
| 393 | ARHGAP4 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 9.27e-07 | 3.02e-01 | 0.294 |
| 393 | ARHGAP4 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.50e-10 | 3.75e-01 | 0.3859 |
| 393 | ARHGAP4 | HCC1_Meng | Human | Liver | HCC | 4.84e-15 | 6.46e-02 | 0.0246 |
| 393 | ARHGAP4 | HCC2 | Human | Liver | HCC | 2.51e-10 | 2.37e+00 | 0.5341 |
| 393 | ARHGAP4 | HCC5 | Human | Liver | HCC | 4.17e-02 | 3.62e-01 | 0.4932 |
| 393 | ARHGAP4 | S014 | Human | Liver | HCC | 2.80e-18 | 5.28e-01 | 0.2254 |
| 393 | ARHGAP4 | S015 | Human | Liver | HCC | 6.27e-14 | 4.91e-01 | 0.2375 |
| 393 | ARHGAP4 | S016 | Human | Liver | HCC | 5.36e-25 | 5.66e-01 | 0.2243 |
| 393 | ARHGAP4 | S027 | Human | Liver | HCC | 3.49e-23 | 1.48e+00 | 0.2446 |
| 393 | ARHGAP4 | S028 | Human | Liver | HCC | 1.68e-44 | 1.39e+00 | 0.2503 |
| 393 | ARHGAP4 | S029 | Human | Liver | HCC | 4.94e-38 | 1.32e+00 | 0.2581 |
| Page: 1 2 |
| 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 | ||
| 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:0072659 | Colorectum | AD | protein localization to plasma membrane | 122/3918 | 284/18723 | 2.86e-17 | 1.49e-14 | 122 |
| GO:1990778 | Colorectum | AD | protein localization to cell periphery | 129/3918 | 333/18723 | 5.51e-14 | 1.15e-11 | 129 |
| GO:0032535 | Colorectum | AD | regulation of cellular component size | 142/3918 | 383/18723 | 1.74e-13 | 3.41e-11 | 142 |
| GO:0032970 | Colorectum | AD | regulation of actin filament-based process | 142/3918 | 397/18723 | 4.05e-12 | 5.90e-10 | 142 |
| GO:0090150 | Colorectum | AD | establishment of protein localization to membrane | 100/3918 | 260/18723 | 6.01e-11 | 6.33e-09 | 100 |
| GO:0032956 | Colorectum | AD | regulation of actin cytoskeleton organization | 127/3918 | 358/18723 | 1.03e-10 | 1.04e-08 | 127 |
| GO:0016197 | Colorectum | AD | endosomal transport | 90/3918 | 230/18723 | 1.88e-10 | 1.73e-08 | 90 |
| GO:1905475 | Colorectum | AD | regulation of protein localization to membrane | 73/3918 | 175/18723 | 3.37e-10 | 2.93e-08 | 73 |
| GO:1903076 | Colorectum | AD | regulation of protein localization to plasma membrane | 48/3918 | 104/18723 | 7.17e-09 | 4.36e-07 | 48 |
| GO:1904375 | Colorectum | AD | regulation of protein localization to cell periphery | 54/3918 | 125/18723 | 1.52e-08 | 9.00e-07 | 54 |
| GO:0098876 | Colorectum | AD | vesicle-mediated transport to the plasma membrane | 57/3918 | 136/18723 | 2.30e-08 | 1.27e-06 | 57 |
| GO:0061951 | Colorectum | AD | establishment of protein localization to plasma membrane | 31/3918 | 60/18723 | 1.37e-07 | 6.42e-06 | 31 |
| GO:0032386 | Colorectum | AD | regulation of intracellular transport | 109/3918 | 337/18723 | 5.33e-07 | 1.95e-05 | 109 |
| GO:0033157 | Colorectum | AD | regulation of intracellular protein transport | 80/3918 | 229/18723 | 5.81e-07 | 2.09e-05 | 80 |
| GO:0043087 | Colorectum | AD | regulation of GTPase activity | 110/3918 | 348/18723 | 1.64e-06 | 5.03e-05 | 110 |
| GO:0016049 | Colorectum | AD | cell growth | 143/3918 | 482/18723 | 2.83e-06 | 8.09e-05 | 143 |
| GO:0001558 | Colorectum | AD | regulation of cell growth | 124/3918 | 414/18723 | 7.67e-06 | 1.86e-04 | 124 |
| GO:0007265 | Colorectum | AD | Ras protein signal transduction | 104/3918 | 337/18723 | 1.01e-05 | 2.35e-04 | 104 |
| GO:0051056 | Colorectum | AD | regulation of small GTPase mediated signal transduction | 94/3918 | 302/18723 | 1.81e-05 | 3.76e-04 | 94 |
| GO:0001667 | Colorectum | AD | ameboidal-type cell migration | 137/3918 | 475/18723 | 2.17e-05 | 4.33e-04 | 137 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
| 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 |
| ARHGAP4 | SNV | Missense_Mutation | novel | c.2188C>A | p.Gln730Lys | p.Q730K | P98171 | protein_coding | deleterious(0.03) | benign(0.069) | TCGA-AC-A2FM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| ARHGAP4 | SNV | Missense_Mutation | c.884N>T | p.Ala295Val | p.A295V | P98171 | protein_coding | deleterious(0) | possibly_damaging(0.632) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ARHGAP4 | SNV | Missense_Mutation | novel | c.2551N>T | p.Val851Leu | p.V851L | P98171 | protein_coding | tolerated(0.43) | benign(0.039) | TCGA-E9-A1RC-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | tamoxiphen | SD |
| ARHGAP4 | insertion | In_Frame_Ins | novel | c.820_821insTAC | p.Glu274delinsValGln | p.E274delinsVQ | P98171 | protein_coding | TCGA-AO-A0J5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Other, specify in notesBisphosphonate | zoledronic | PD | ||
| ARHGAP4 | insertion | Nonsense_Mutation | novel | c.819_820insCGTGGCTAAGATTT | p.Glu274ArgfsTer3 | p.E274Rfs*3 | P98171 | protein_coding | TCGA-AO-A0J5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Other, specify in notesBisphosphonate | zoledronic | PD | ||
| ARHGAP4 | SNV | Missense_Mutation | c.1121N>A | p.Arg374His | p.R374H | P98171 | protein_coding | deleterious(0) | probably_damaging(0.98) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| ARHGAP4 | SNV | Missense_Mutation | novel | c.567N>T | p.Glu189Asp | p.E189D | P98171 | protein_coding | deleterious(0) | benign(0.345) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| ARHGAP4 | SNV | Missense_Mutation | novel | c.1145N>A | p.Gly382Glu | p.G382E | P98171 | protein_coding | deleterious(0.01) | probably_damaging(0.961) | TCGA-C5-A1M5-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| ARHGAP4 | SNV | Missense_Mutation | novel | c.1091N>C | p.Val364Ala | p.V364A | P98171 | protein_coding | tolerated(0.37) | benign(0.003) | TCGA-C5-A1ME-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| ARHGAP4 | SNV | Missense_Mutation | novel | c.787N>T | p.Pro263Ser | p.P263S | P98171 | protein_coding | tolerated_low_confidence(0.79) | benign(0.025) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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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