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Gene: RAB3GAP2 |
Gene summary for RAB3GAP2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RAB3GAP2 | Gene ID | 25782 |
| Gene name | RAB3 GTPase activating non-catalytic protein subunit 2 | |
| Gene Alias | MARTS1 | |
| Cytomap | 1q41 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | Q9H2M9 |
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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 |
| 25782 | RAB3GAP2 | C04 | Human | Oral cavity | OSCC | 1.28e-08 | 6.18e-01 | 0.2633 |
| 25782 | RAB3GAP2 | C21 | Human | Oral cavity | OSCC | 1.10e-24 | 7.64e-01 | 0.2678 |
| 25782 | RAB3GAP2 | C30 | Human | Oral cavity | OSCC | 1.40e-21 | 9.28e-01 | 0.3055 |
| 25782 | RAB3GAP2 | C51 | Human | Oral cavity | OSCC | 4.21e-08 | 4.74e-01 | 0.2674 |
| 25782 | RAB3GAP2 | EOLP-1 | Human | Oral cavity | EOLP | 3.97e-04 | 2.75e-01 | -0.0202 |
| 25782 | RAB3GAP2 | NEOLP-1 | Human | Oral cavity | NEOLP | 6.02e-04 | 2.90e-01 | -0.0194 |
| 25782 | RAB3GAP2 | SYSMH1 | Human | Oral cavity | OSCC | 1.25e-11 | 3.57e-01 | 0.1127 |
| 25782 | RAB3GAP2 | SYSMH2 | Human | Oral cavity | OSCC | 2.52e-03 | 3.04e-01 | 0.2326 |
| 25782 | RAB3GAP2 | SYSMH3 | Human | Oral cavity | OSCC | 2.51e-11 | 4.10e-01 | 0.2442 |
| 25782 | RAB3GAP2 | HTA12-26-1 | Human | Pancreas | PDAC | 8.14e-17 | 8.30e-01 | 0.3728 |
| 25782 | RAB3GAP2 | HTA12-29-1 | Human | Pancreas | PDAC | 2.54e-15 | 5.63e-01 | 0.3722 |
| 25782 | RAB3GAP2 | male-WTA | Human | Thyroid | PTC | 6.57e-19 | 1.41e-01 | 0.1037 |
| 25782 | RAB3GAP2 | PTC01 | Human | Thyroid | PTC | 3.15e-08 | 1.36e-01 | 0.1899 |
| 25782 | RAB3GAP2 | PTC03 | Human | Thyroid | PTC | 4.76e-08 | 2.15e-01 | 0.1784 |
| 25782 | RAB3GAP2 | PTC04 | Human | Thyroid | PTC | 4.18e-25 | 3.09e-01 | 0.1927 |
| 25782 | RAB3GAP2 | PTC05 | Human | Thyroid | PTC | 7.31e-17 | 7.12e-01 | 0.2065 |
| 25782 | RAB3GAP2 | PTC06 | Human | Thyroid | PTC | 3.66e-28 | 5.75e-01 | 0.2057 |
| 25782 | RAB3GAP2 | PTC07 | Human | Thyroid | PTC | 1.91e-29 | 4.27e-01 | 0.2044 |
| 25782 | RAB3GAP2 | ATC11 | Human | Thyroid | ATC | 8.75e-04 | 3.02e-01 | 0.3386 |
| 25782 | RAB3GAP2 | ATC12 | Human | Thyroid | ATC | 5.52e-16 | 2.21e-01 | 0.34 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| 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:00725949 | Cervix | CC | establishment of protein localization to organelle | 99/2311 | 422/18723 | 1.23e-10 | 2.11e-08 | 99 |
| GO:000989610 | Cervix | CC | positive regulation of catabolic process | 109/2311 | 492/18723 | 5.26e-10 | 6.99e-08 | 109 |
| GO:00430877 | Cervix | CC | regulation of GTPase activity | 79/2311 | 348/18723 | 4.21e-08 | 2.60e-06 | 79 |
| GO:003133110 | Cervix | CC | positive regulation of cellular catabolic process | 91/2311 | 427/18723 | 9.64e-08 | 5.25e-06 | 91 |
| GO:00901509 | Cervix | CC | establishment of protein localization to membrane | 54/2311 | 260/18723 | 7.67e-05 | 1.05e-03 | 54 |
| GO:00162367 | Cervix | CC | macroautophagy | 58/2311 | 291/18723 | 1.40e-04 | 1.70e-03 | 58 |
| GO:00709726 | Cervix | CC | protein localization to endoplasmic reticulum | 21/2311 | 74/18723 | 1.69e-04 | 2.00e-03 | 21 |
| GO:00105067 | Cervix | CC | regulation of autophagy | 61/2311 | 317/18723 | 2.61e-04 | 2.87e-03 | 61 |
| GO:19021153 | Cervix | CC | regulation of organelle assembly | 40/2311 | 186/18723 | 2.92e-04 | 3.15e-03 | 40 |
| GO:19021171 | Cervix | CC | positive regulation of organelle assembly | 19/2311 | 67/18723 | 3.42e-04 | 3.58e-03 | 19 |
| GO:00725995 | Cervix | CC | establishment of protein localization to endoplasmic reticulum | 13/2311 | 46/18723 | 2.95e-03 | 1.94e-02 | 13 |
| GO:00000452 | Cervix | CC | autophagosome assembly | 21/2311 | 99/18723 | 8.67e-03 | 4.46e-02 | 21 |
| GO:0072594110 | Esophagus | ESCC | establishment of protein localization to organelle | 311/8552 | 422/18723 | 3.02e-32 | 2.13e-29 | 311 |
| GO:001623617 | Esophagus | ESCC | macroautophagy | 216/8552 | 291/18723 | 1.94e-23 | 4.57e-21 | 216 |
| GO:0009896111 | Esophagus | ESCC | positive regulation of catabolic process | 332/8552 | 492/18723 | 4.36e-23 | 9.22e-21 | 332 |
| GO:0031331111 | Esophagus | ESCC | positive regulation of cellular catabolic process | 292/8552 | 427/18723 | 8.67e-22 | 1.53e-19 | 292 |
| GO:001050617 | Esophagus | ESCC | regulation of autophagy | 220/8552 | 317/18723 | 6.72e-18 | 6.36e-16 | 220 |
| GO:0090150110 | Esophagus | ESCC | establishment of protein localization to membrane | 182/8552 | 260/18723 | 1.27e-15 | 8.19e-14 | 182 |
| GO:000703314 | Esophagus | ESCC | vacuole organization | 127/8552 | 180/18723 | 1.04e-11 | 3.85e-10 | 127 |
| GO:001624114 | Esophagus | ESCC | regulation of macroautophagy | 102/8552 | 141/18723 | 1.09e-10 | 3.27e-09 | 102 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| RAB3GAP2 | SNV | Missense_Mutation | c.1387N>G | p.Gln463Glu | p.Q463E | Q9H2M9 | protein_coding | deleterious(0.02) | possibly_damaging(0.576) | TCGA-AC-A2FG-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | CR | |
| RAB3GAP2 | SNV | Missense_Mutation | c.2945N>C | p.Val982Ala | p.V982A | Q9H2M9 | protein_coding | tolerated(0.74) | benign(0) | TCGA-AN-A0XV-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| RAB3GAP2 | SNV | Missense_Mutation | novel | c.98N>A | p.Ala33Asp | p.A33D | Q9H2M9 | protein_coding | tolerated_low_confidence(0.36) | benign(0.165) | TCGA-B6-A0IA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RAB3GAP2 | SNV | Missense_Mutation | c.2222N>G | p.Phe741Cys | p.F741C | Q9H2M9 | protein_coding | deleterious(0.01) | probably_damaging(0.935) | TCGA-BH-A0AZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | CR | |
| RAB3GAP2 | SNV | Missense_Mutation | c.3200N>T | p.Ser1067Phe | p.S1067F | Q9H2M9 | protein_coding | deleterious(0) | probably_damaging(0.984) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RAB3GAP2 | SNV | Missense_Mutation | c.2416G>A | p.Val806Met | p.V806M | Q9H2M9 | protein_coding | tolerated(0.25) | possibly_damaging(0.875) | TCGA-BH-A0BZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | CR | |
| RAB3GAP2 | SNV | Missense_Mutation | c.3859N>A | p.Gly1287Arg | p.G1287R | Q9H2M9 | protein_coding | deleterious(0) | possibly_damaging(0.894) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| RAB3GAP2 | SNV | Missense_Mutation | c.3476C>G | p.Ser1159Cys | p.S1159C | Q9H2M9 | protein_coding | tolerated(0.18) | benign(0.003) | TCGA-C8-A1HM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | CR | |
| RAB3GAP2 | SNV | Missense_Mutation | c.1847N>C | p.Leu616Ser | p.L616S | Q9H2M9 | protein_coding | deleterious(0.02) | benign(0.035) | TCGA-E2-A15A-06 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | |
| RAB3GAP2 | insertion | Frame_Shift_Ins | novel | c.1276_1277insTCCTTGTTCTAATATTTTTACCATATTG | p.Arg426LeufsTer25 | p.R426Lfs*25 | Q9H2M9 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
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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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