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Gene: ARHGAP42 |
Gene summary for ARHGAP42 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ARHGAP42 | Gene ID | 143872 |
| Gene name | Rho GTPase activating protein 42 | |
| Gene Alias | AD031 | |
| Cytomap | 11q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | A6NI28 |
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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 |
| 143872 | ARHGAP42 | AEH-subject1 | Human | Endometrium | AEH | 8.23e-11 | 3.65e-01 | -0.3059 |
| 143872 | ARHGAP42 | AEH-subject2 | Human | Endometrium | AEH | 2.15e-12 | 4.13e-01 | -0.2525 |
| 143872 | ARHGAP42 | AEH-subject4 | Human | Endometrium | AEH | 9.81e-14 | 4.62e-01 | -0.2657 |
| 143872 | ARHGAP42 | AEH-subject5 | Human | Endometrium | AEH | 5.58e-09 | 3.54e-01 | -0.2953 |
| 143872 | ARHGAP42 | EEC-subject1 | Human | Endometrium | EEC | 8.51e-03 | 2.13e-01 | -0.2682 |
| 143872 | ARHGAP42 | EEC-subject2 | Human | Endometrium | EEC | 1.75e-10 | 4.37e-01 | -0.2607 |
| 143872 | ARHGAP42 | NAFLD1 | Human | Liver | NAFLD | 6.97e-07 | 7.39e-01 | -0.04 |
| 143872 | ARHGAP42 | S41 | Human | Liver | Cirrhotic | 9.20e-03 | 6.04e-01 | -0.0343 |
| 143872 | ARHGAP42 | HCC1_Meng | Human | Liver | HCC | 3.58e-14 | -1.54e-01 | 0.0246 |
| 143872 | ARHGAP42 | HCC2_Meng | Human | Liver | HCC | 7.54e-03 | -1.27e-01 | 0.0107 |
| 143872 | ARHGAP42 | HCC5 | Human | Liver | HCC | 3.21e-35 | 3.91e-01 | 0.4932 |
| 143872 | ARHGAP42 | TD9 | Human | Lung | IAC | 9.99e-05 | 7.54e-01 | 0.088 |
| 143872 | ARHGAP42 | RNA-P17T-P17T-4 | Human | Lung | IAC | 3.73e-02 | 4.86e-01 | 0.343 |
| 143872 | ARHGAP42 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 1.51e-04 | 4.17e-01 | -0.2116 |
| 143872 | ARHGAP42 | RNA-P25T1-P25T1-2 | Human | Lung | AIS | 4.60e-03 | 5.39e-01 | -0.1941 |
| 143872 | ARHGAP42 | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 4.31e-02 | 4.00e-01 | -0.2107 |
| 143872 | ARHGAP42 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 2.62e-04 | 3.99e-01 | -0.2119 |
| 143872 | ARHGAP42 | RNA-P3T-P3T-2 | Human | Lung | IAC | 1.69e-02 | 4.51e-01 | 0.1835 |
| 143872 | ARHGAP42 | RNA-P3T-P3T-4 | Human | Lung | IAC | 3.28e-03 | 4.71e-01 | 0.1859 |
| 143872 | ARHGAP42 | RNA-P6T1-P6T1-1 | Human | Lung | MIAC | 1.89e-10 | 1.49e+00 | -0.0238 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:00430878 | Endometrium | AEH | regulation of GTPase activity | 66/2100 | 348/18723 | 1.26e-05 | 2.77e-04 | 66 |
| GO:00510567 | Endometrium | AEH | regulation of small GTPase mediated signal transduction | 59/2100 | 302/18723 | 1.43e-05 | 3.03e-04 | 59 |
| GO:00072657 | Endometrium | AEH | Ras protein signal transduction | 63/2100 | 337/18723 | 3.09e-05 | 5.66e-04 | 63 |
| GO:00030126 | Endometrium | AEH | muscle system process | 78/2100 | 452/18723 | 6.89e-05 | 1.06e-03 | 78 |
| GO:00435477 | Endometrium | AEH | positive regulation of GTPase activity | 48/2100 | 255/18723 | 2.18e-04 | 2.67e-03 | 48 |
| GO:0006936 | Endometrium | AEH | muscle contraction | 59/2100 | 347/18723 | 7.32e-04 | 6.99e-03 | 59 |
| GO:00465786 | Endometrium | AEH | regulation of Ras protein signal transduction | 36/2100 | 189/18723 | 1.01e-03 | 8.97e-03 | 36 |
| GO:00072667 | Endometrium | AEH | Rho protein signal transduction | 28/2100 | 137/18723 | 1.17e-03 | 1.01e-02 | 28 |
| GO:00902579 | Endometrium | AEH | regulation of muscle system process | 44/2100 | 252/18723 | 1.92e-03 | 1.51e-02 | 44 |
| GO:00069374 | Endometrium | AEH | regulation of muscle contraction | 32/2100 | 169/18723 | 2.06e-03 | 1.60e-02 | 32 |
| GO:0045986 | Endometrium | AEH | negative regulation of smooth muscle contraction | 6/2100 | 15/18723 | 4.03e-03 | 2.69e-02 | 6 |
| GO:00350236 | Endometrium | AEH | regulation of Rho protein signal transduction | 18/2100 | 86/18723 | 6.39e-03 | 3.79e-02 | 18 |
| GO:00906304 | Endometrium | AEH | activation of GTPase activity | 22/2100 | 115/18723 | 8.42e-03 | 4.60e-02 | 22 |
| GO:005105612 | Endometrium | EEC | regulation of small GTPase mediated signal transduction | 61/2168 | 302/18723 | 9.42e-06 | 2.08e-04 | 61 |
| GO:004308712 | Endometrium | EEC | regulation of GTPase activity | 67/2168 | 348/18723 | 1.84e-05 | 3.43e-04 | 67 |
| GO:000726513 | Endometrium | EEC | Ras protein signal transduction | 64/2168 | 337/18723 | 4.31e-05 | 7.10e-04 | 64 |
| GO:000301213 | Endometrium | EEC | muscle system process | 79/2168 | 452/18723 | 1.16e-04 | 1.55e-03 | 79 |
| GO:004354712 | Endometrium | EEC | positive regulation of GTPase activity | 50/2168 | 255/18723 | 1.26e-04 | 1.66e-03 | 50 |
| GO:000726613 | Endometrium | EEC | Rho protein signal transduction | 30/2168 | 137/18723 | 4.05e-04 | 4.31e-03 | 30 |
| GO:004657813 | Endometrium | EEC | regulation of Ras protein signal transduction | 37/2168 | 189/18723 | 9.23e-04 | 8.32e-03 | 37 |
| Page: 1 2 3 4 5 6 7 |
| 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 |
| ARHGAP42 | SNV | Missense_Mutation | c.1849N>T | p.Pro617Ser | p.P617S | A6NI28 | protein_coding | tolerated(0.65) | benign(0.112) | TCGA-A1-A0SK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| ARHGAP42 | SNV | Missense_Mutation | rs367900224 | c.2456N>A | p.Arg819His | p.R819H | A6NI28 | protein_coding | deleterious(0) | possibly_damaging(0.511) | TCGA-A2-A4S1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ARHGAP42 | SNV | Missense_Mutation | c.568G>C | p.Glu190Gln | p.E190Q | A6NI28 | protein_coding | deleterious(0.02) | possibly_damaging(0.893) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| ARHGAP42 | SNV | Missense_Mutation | novel | c.2318A>C | p.Asp773Ala | p.D773A | A6NI28 | protein_coding | tolerated_low_confidence(0.16) | benign(0.272) | TCGA-AN-A0AT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ARHGAP42 | SNV | Missense_Mutation | c.565C>G | p.Gln189Glu | p.Q189E | A6NI28 | protein_coding | deleterious(0.01) | benign(0.264) | TCGA-AO-A124-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| ARHGAP42 | SNV | Missense_Mutation | rs774941750 | c.2402N>G | p.Ala801Gly | p.A801G | A6NI28 | protein_coding | tolerated(0.06) | probably_damaging(0.935) | TCGA-AQ-A1H3-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
| ARHGAP42 | SNV | Missense_Mutation | rs746263248 | c.940C>T | p.Leu314Phe | p.L314F | A6NI28 | protein_coding | tolerated(0.09) | possibly_damaging(0.621) | TCGA-AR-A251-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD |
| ARHGAP42 | SNV | Missense_Mutation | c.1979G>C | p.Gly660Ala | p.G660A | A6NI28 | protein_coding | tolerated(0.33) | benign(0) | TCGA-BH-A18P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| ARHGAP42 | SNV | Missense_Mutation | c.1852G>C | p.Asp618His | p.D618H | A6NI28 | protein_coding | tolerated(0.08) | possibly_damaging(0.707) | TCGA-C8-A8HQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| ARHGAP42 | SNV | Missense_Mutation | c.303N>T | p.Arg101Ser | p.R101S | A6NI28 | protein_coding | deleterious(0) | possibly_damaging(0.852) | TCGA-E9-A1R4-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD |
| Page: 1 2 3 4 5 6 7 8 |
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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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