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Gene: RAPGEF3 |
Gene summary for RAPGEF3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RAPGEF3 | Gene ID | 10411 |
| Gene name | Rap guanine nucleotide exchange factor 3 | |
| Gene Alias | CAMP-GEFI | |
| Cytomap | 12q13.11 | |
| Gene Type | protein-coding | GO ID | GO:0000768 | UniProtAcc | Q99777 |
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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 |
| 10411 | RAPGEF3 | C04 | Human | Oral cavity | OSCC | 3.59e-16 | 6.21e-01 | 0.2633 |
| 10411 | RAPGEF3 | C21 | Human | Oral cavity | OSCC | 1.29e-15 | 5.79e-01 | 0.2678 |
| 10411 | RAPGEF3 | C30 | Human | Oral cavity | OSCC | 3.71e-14 | 6.08e-01 | 0.3055 |
| 10411 | RAPGEF3 | C06 | Human | Oral cavity | OSCC | 4.73e-04 | 6.81e-01 | 0.2699 |
| 10411 | RAPGEF3 | SYSMH3 | Human | Oral cavity | OSCC | 2.91e-08 | 2.16e-01 | 0.2442 |
| 10411 | RAPGEF3 | SYSMH5 | Human | Oral cavity | OSCC | 2.40e-06 | 2.16e-01 | 0.0647 |
| 10411 | RAPGEF3 | male-WTA | Human | Thyroid | PTC | 2.25e-35 | 3.95e-01 | 0.1037 |
| 10411 | RAPGEF3 | PTC01 | Human | Thyroid | PTC | 2.43e-19 | 3.39e-01 | 0.1899 |
| 10411 | RAPGEF3 | PTC03 | Human | Thyroid | PTC | 9.73e-27 | 6.90e-01 | 0.1784 |
| 10411 | RAPGEF3 | PTC04 | Human | Thyroid | PTC | 3.67e-36 | 5.43e-01 | 0.1927 |
| 10411 | RAPGEF3 | PTC05 | Human | Thyroid | PTC | 3.20e-15 | 7.72e-01 | 0.2065 |
| 10411 | RAPGEF3 | PTC06 | Human | Thyroid | PTC | 1.04e-45 | 1.00e+00 | 0.2057 |
| 10411 | RAPGEF3 | PTC07 | Human | Thyroid | PTC | 1.88e-58 | 8.62e-01 | 0.2044 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:000691317 | Oral cavity | OSCC | nucleocytoplasmic transport | 204/7305 | 301/18723 | 2.65e-24 | 6.98e-22 | 204 |
| GO:005116917 | Oral cavity | OSCC | nuclear transport | 204/7305 | 301/18723 | 2.65e-24 | 6.98e-22 | 204 |
| GO:003238615 | Oral cavity | OSCC | regulation of intracellular transport | 218/7305 | 337/18723 | 6.91e-22 | 1.41e-19 | 218 |
| GO:003315718 | Oral cavity | OSCC | regulation of intracellular protein transport | 155/7305 | 229/18723 | 1.05e-18 | 1.28e-16 | 155 |
| GO:005116817 | Oral cavity | OSCC | nuclear export | 112/7305 | 154/18723 | 1.70e-17 | 1.56e-15 | 112 |
| GO:190495119 | Oral cavity | OSCC | positive regulation of establishment of protein localization | 196/7305 | 319/18723 | 2.89e-16 | 2.20e-14 | 196 |
| GO:005122219 | Oral cavity | OSCC | positive regulation of protein transport | 187/7305 | 303/18723 | 7.37e-16 | 5.49e-14 | 187 |
| GO:003238818 | Oral cavity | OSCC | positive regulation of intracellular transport | 134/7305 | 202/18723 | 2.82e-15 | 1.88e-13 | 134 |
| GO:009031610 | Oral cavity | OSCC | positive regulation of intracellular protein transport | 110/7305 | 160/18723 | 2.10e-14 | 1.19e-12 | 110 |
| GO:004682217 | Oral cavity | OSCC | regulation of nucleocytoplasmic transport | 79/7305 | 106/18723 | 1.04e-13 | 5.37e-12 | 79 |
| GO:00435434 | Oral cavity | OSCC | protein acylation | 149/7305 | 243/18723 | 1.33e-12 | 5.80e-11 | 149 |
| GO:190290520 | Oral cavity | OSCC | positive regulation of supramolecular fiber organization | 131/7305 | 209/18723 | 3.18e-12 | 1.27e-10 | 131 |
| GO:00064734 | Oral cavity | OSCC | protein acetylation | 124/7305 | 201/18723 | 5.59e-11 | 1.74e-09 | 124 |
| GO:190290320 | Oral cavity | OSCC | regulation of supramolecular fiber organization | 211/7305 | 383/18723 | 9.45e-11 | 2.88e-09 | 211 |
| GO:005149518 | Oral cavity | OSCC | positive regulation of cytoskeleton organization | 135/7305 | 226/18723 | 1.98e-10 | 5.66e-09 | 135 |
| GO:00072659 | Oral cavity | OSCC | Ras protein signal transduction | 185/7305 | 337/18723 | 1.95e-09 | 4.60e-08 | 185 |
| GO:000701520 | Oral cavity | OSCC | actin filament organization | 230/7305 | 442/18723 | 1.37e-08 | 2.77e-07 | 230 |
| GO:003297020 | Oral cavity | OSCC | regulation of actin filament-based process | 209/7305 | 397/18723 | 1.89e-08 | 3.72e-07 | 209 |
| GO:003295620 | Oral cavity | OSCC | regulation of actin cytoskeleton organization | 189/7305 | 358/18723 | 6.81e-08 | 1.21e-06 | 189 |
| GO:004682414 | Oral cavity | OSCC | positive regulation of nucleocytoplasmic transport | 45/7305 | 62/18723 | 8.26e-08 | 1.46e-06 | 45 |
| Page: 1 2 3 4 5 6 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0467030 | Oral cavity | OSCC | Leukocyte transendothelial migration | 63/3704 | 114/8465 | 8.46e-03 | 1.96e-02 | 9.95e-03 | 63 |
| hsa0401518 | Oral cavity | OSCC | Rap1 signaling pathway | 107/3704 | 210/8465 | 2.01e-02 | 4.34e-02 | 2.21e-02 | 107 |
| hsa04670113 | Oral cavity | OSCC | Leukocyte transendothelial migration | 63/3704 | 114/8465 | 8.46e-03 | 1.96e-02 | 9.95e-03 | 63 |
| hsa0401519 | Oral cavity | OSCC | Rap1 signaling pathway | 107/3704 | 210/8465 | 2.01e-02 | 4.34e-02 | 2.21e-02 | 107 |
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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 |
| RAPGEF3 | SNV | Missense_Mutation | novel | c.2546N>A | p.Ala849Glu | p.A849E | O95398 | protein_coding | deleterious(0) | benign(0.027) | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| RAPGEF3 | SNV | Missense_Mutation | c.2188C>A | p.Pro730Thr | p.P730T | O95398 | protein_coding | deleterious(0.01) | benign(0.035) | TCGA-A2-A0ET-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD | |
| RAPGEF3 | SNV | Missense_Mutation | c.1231N>T | p.His411Tyr | p.H411Y | O95398 | protein_coding | tolerated(0.3) | possibly_damaging(0.779) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RAPGEF3 | SNV | Missense_Mutation | c.889N>A | p.Gly297Ser | p.G297S | O95398 | protein_coding | deleterious(0.02) | probably_damaging(0.967) | TCGA-C8-A133-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| RAPGEF3 | insertion | Frame_Shift_Ins | novel | c.354_355insAGGGCAGTCCTGGGAAG | p.Lys120AlafsTer55 | p.K120Afs*55 | O95398 | protein_coding | TCGA-BH-A0DP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD | ||
| RAPGEF3 | deletion | Frame_Shift_Del | novel | c.2764delN | p.Glu922SerfsTer56 | p.E922Sfs*56 | O95398 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| RAPGEF3 | SNV | Missense_Mutation | novel | c.2269N>T | p.Val757Phe | p.V757F | O95398 | protein_coding | deleterious(0) | possibly_damaging(0.759) | TCGA-C5-A8YR-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| RAPGEF3 | SNV | Missense_Mutation | novel | c.1483N>A | p.Asp495Asn | p.D495N | O95398 | protein_coding | tolerated(0.46) | benign(0.325) | TCGA-5M-AAT5-01 | Colorectum | colon adenocarcinoma | Unknown | Unknown | I/II | Unknown | Unknown | Unknown |
| RAPGEF3 | SNV | Missense_Mutation | c.743A>G | p.His248Arg | p.H248R | O95398 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-A6-3809-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RAPGEF3 | SNV | Missense_Mutation | c.1121N>A | p.Gly374Asp | p.G374D | O95398 | protein_coding | deleterious(0.03) | probably_damaging(0.938) | TCGA-A6-6653-01 | Colorectum | colon adenocarcinoma | Male | >=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 |
| 10411 | RAPGEF3 | ENZYME | CRYPTOTANSHINONE | CRYPTOTANSHINONE | ||
| 10411 | RAPGEF3 | ENZYME | 8-BROMO-CAMP SODIUM | CHEMBL1256796 | ||
| 10411 | RAPGEF3 | ENZYME | HEXACHLOROPHENE | HEXACHLOROPHENE | ||
| 10411 | RAPGEF3 | ENZYME | ISOQUINOLINE-1,3(2H,4H)-DIONE | CHEMBL1210769 | ||
| 10411 | RAPGEF3 | ENZYME | LUTEOLIN | LUTEOLIN | ||
| 10411 | RAPGEF3 | ENZYME | IDARUBICIN HYDROCHLORIDE | IDARUBICIN HYDROCHLORIDE | ||
| 10411 | RAPGEF3 | ENZYME | 5,6,7,8,4'-PENTAHYDROXYFLAVONE | CHEMBL234338 | ||
| 10411 | RAPGEF3 | ENZYME | 2,4-DIHYDROXYBENZOPHENONE | 2,4-DIHYDROXYBENZOPHENONE | ||
| 10411 | RAPGEF3 | ENZYME | RAFOXANIDE | RAFOXANIDE | ||
| 10411 | RAPGEF3 | ENZYME | 9,10-PHENANTHRENEQUINONE | 9,10-PHENANTHRENEQUINONE |
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