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Gene: ARHGEF5 |
Gene summary for ARHGEF5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ARHGEF5 | Gene ID | 7984 |
| Gene name | Rho guanine nucleotide exchange factor 5 | |
| Gene Alias | GEF5 | |
| Cytomap | 7q35 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | Q12774 |
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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 |
| 7984 | ARHGEF5 | HTA11_2487_2000001011 | Human | Colorectum | SER | 9.17e-05 | 3.33e-01 | -0.1808 |
| 7984 | ARHGEF5 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.19e-02 | 2.66e-01 | -0.0811 |
| 7984 | ARHGEF5 | HTA11_78_2000001011 | Human | Colorectum | AD | 5.17e-03 | 2.06e-01 | -0.1088 |
| 7984 | ARHGEF5 | HTA11_347_2000001011 | Human | Colorectum | AD | 5.26e-07 | 2.99e-01 | -0.1954 |
| 7984 | ARHGEF5 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.38e-02 | 5.76e-01 | -0.2602 |
| 7984 | ARHGEF5 | HTA11_2112_2000001011 | Human | Colorectum | SER | 2.77e-03 | 4.75e-01 | -0.2196 |
| 7984 | ARHGEF5 | HTA11_83_2000001011 | Human | Colorectum | SER | 4.95e-04 | 4.03e-01 | -0.1526 |
| 7984 | ARHGEF5 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.94e-06 | 2.52e-01 | -0.1464 |
| 7984 | ARHGEF5 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.50e-10 | 4.34e-01 | -0.059 |
| 7984 | ARHGEF5 | HTA11_866_3004761011 | Human | Colorectum | AD | 3.27e-02 | 1.87e-01 | 0.096 |
| 7984 | ARHGEF5 | HTA11_10711_2000001011 | Human | Colorectum | AD | 2.96e-03 | 2.17e-01 | 0.0338 |
| 7984 | ARHGEF5 | HTA11_6818_2000001011 | Human | Colorectum | AD | 4.13e-02 | 2.92e-01 | 0.0112 |
| 7984 | ARHGEF5 | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.34e-03 | 2.37e-01 | 0.0588 |
| 7984 | ARHGEF5 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 7.78e-04 | 2.45e-01 | 0.294 |
| 7984 | ARHGEF5 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.15e-03 | 3.04e-01 | 0.281 |
| 7984 | ARHGEF5 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.15e-09 | 3.78e-01 | 0.3859 |
| 7984 | ARHGEF5 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 4.56e-04 | 2.89e-01 | 0.2585 |
| 7984 | ARHGEF5 | LZE4T | Human | Esophagus | ESCC | 7.58e-11 | 4.61e-01 | 0.0811 |
| 7984 | ARHGEF5 | LZE5T | Human | Esophagus | ESCC | 4.77e-03 | 1.69e-01 | 0.0514 |
| 7984 | ARHGEF5 | LZE7T | Human | Esophagus | ESCC | 2.02e-05 | 3.22e-01 | 0.0667 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| 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:190290522 | Liver | HCC | positive regulation of supramolecular fiber organization | 131/7958 | 209/18723 | 2.85e-09 | 7.69e-08 | 131 |
| GO:005149522 | Liver | HCC | positive regulation of cytoskeleton organization | 138/7958 | 226/18723 | 1.26e-08 | 3.12e-07 | 138 |
| GO:003297022 | Liver | HCC | regulation of actin filament-based process | 222/7958 | 397/18723 | 3.81e-08 | 8.30e-07 | 222 |
| GO:003295622 | Liver | HCC | regulation of actin cytoskeleton organization | 202/7958 | 358/18723 | 6.18e-08 | 1.29e-06 | 202 |
| GO:190458911 | Liver | HCC | regulation of protein import | 46/7958 | 63/18723 | 8.72e-07 | 1.33e-05 | 46 |
| GO:011005322 | Liver | HCC | regulation of actin filament organization | 158/7958 | 278/18723 | 9.01e-07 | 1.37e-05 | 158 |
| GO:005101722 | Liver | HCC | actin filament bundle assembly | 96/7958 | 157/18723 | 1.81e-06 | 2.52e-05 | 96 |
| GO:006157222 | Liver | HCC | actin filament bundle organization | 97/7958 | 161/18723 | 4.04e-06 | 5.22e-05 | 97 |
| GO:190459111 | Liver | HCC | positive regulation of protein import | 32/7958 | 43/18723 | 2.16e-05 | 2.30e-04 | 32 |
| GO:007190021 | Liver | HCC | regulation of protein serine/threonine kinase activity | 189/7958 | 359/18723 | 5.97e-05 | 5.47e-04 | 189 |
| GO:003103222 | Liver | HCC | actomyosin structure organization | 109/7958 | 196/18723 | 1.39e-04 | 1.13e-03 | 109 |
| GO:00510902 | Liver | HCC | regulation of DNA-binding transcription factor activity | 220/7958 | 440/18723 | 8.04e-04 | 4.82e-03 | 220 |
| GO:004586021 | Liver | HCC | positive regulation of protein kinase activity | 194/7958 | 386/18723 | 1.16e-03 | 6.54e-03 | 194 |
| GO:003367411 | Liver | HCC | positive regulation of kinase activity | 230/7958 | 467/18723 | 1.72e-03 | 8.95e-03 | 230 |
| GO:003003822 | Liver | HCC | contractile actin filament bundle assembly | 60/7958 | 106/18723 | 2.34e-03 | 1.16e-02 | 60 |
| GO:004314922 | Liver | HCC | stress fiber assembly | 60/7958 | 106/18723 | 2.34e-03 | 1.16e-02 | 60 |
| GO:003223312 | Liver | HCC | positive regulation of actin filament bundle assembly | 38/7958 | 63/18723 | 3.27e-03 | 1.50e-02 | 38 |
| GO:00510913 | Liver | HCC | positive regulation of DNA-binding transcription factor activity | 131/7958 | 260/18723 | 5.98e-03 | 2.45e-02 | 131 |
| GO:003223122 | Liver | HCC | regulation of actin filament bundle assembly | 57/7958 | 105/18723 | 9.73e-03 | 3.66e-02 | 57 |
| GO:011002022 | Liver | HCC | regulation of actomyosin structure organization | 54/7958 | 100/18723 | 1.33e-02 | 4.76e-02 | 54 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| 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 |
| ARHGEF5 | SNV | Missense_Mutation | novel | c.2579G>T | p.Gly860Val | p.G860V | Q12774 | protein_coding | tolerated(0.09) | benign(0.166) | TCGA-A7-A6VX-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | CR |
| ARHGEF5 | SNV | Missense_Mutation | c.4748A>G | p.His1583Arg | p.H1583R | Q12774 | protein_coding | deleterious(0.04) | benign(0.163) | TCGA-A8-A08P-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | CR | |
| ARHGEF5 | SNV | Missense_Mutation | novel | c.3595N>T | p.His1199Tyr | p.H1199Y | Q12774 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| ARHGEF5 | SNV | Missense_Mutation | novel | c.1059G>T | p.Glu353Asp | p.E353D | Q12774 | protein_coding | tolerated(0.12) | benign(0.143) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ARHGEF5 | SNV | Missense_Mutation | rs774773903 | c.44C>G | p.Ser15Cys | p.S15C | Q12774 | protein_coding | deleterious(0) | benign(0.053) | TCGA-C8-A8HQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ARHGEF5 | SNV | Missense_Mutation | rs755202652 | c.3620N>A | p.Arg1207Gln | p.R1207Q | Q12774 | protein_coding | tolerated(0.19) | benign(0.313) | TCGA-D8-A1Y1-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | PD |
| ARHGEF5 | SNV | Missense_Mutation | novel | c.907G>A | p.Gly303Ser | p.G303S | Q12774 | protein_coding | tolerated(0.33) | benign(0.005) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| ARHGEF5 | SNV | Missense_Mutation | c.394G>C | p.Glu132Gln | p.E132Q | Q12774 | protein_coding | tolerated(0.1) | benign(0.086) | TCGA-C5-A1BJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| ARHGEF5 | SNV | Missense_Mutation | rs746273665 | c.542G>C | p.Arg181Thr | p.R181T | Q12774 | protein_coding | tolerated(0.61) | benign(0.025) | TCGA-DS-A7WI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| ARHGEF5 | SNV | Missense_Mutation | rs761138536 | c.390N>C | p.Gln130His | p.Q130H | Q12774 | protein_coding | deleterious(0.01) | benign(0.438) | TCGA-IR-A3LI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| 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 |
| Page: 1 |
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