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Gene: RAB3GAP1 |
Gene summary for RAB3GAP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RAB3GAP1 | Gene ID | 22930 |
| Gene name | RAB3 GTPase activating protein catalytic subunit 1 | |
| Gene Alias | MARTS2 | |
| Cytomap | 2q21.3 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | Q15042 |
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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 |
| 22930 | RAB3GAP1 | CCI_1 | Human | Cervix | CC | 2.79e-06 | 7.12e-01 | 0.528 |
| 22930 | RAB3GAP1 | CCI_2 | Human | Cervix | CC | 9.04e-06 | 7.41e-01 | 0.5249 |
| 22930 | RAB3GAP1 | CCI_3 | Human | Cervix | CC | 5.48e-10 | 6.59e-01 | 0.516 |
| 22930 | RAB3GAP1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.97e-15 | -5.46e-01 | 0.0155 |
| 22930 | RAB3GAP1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.99e-02 | -3.50e-01 | -0.1207 |
| 22930 | RAB3GAP1 | HTA11_866_3004761011 | Human | Colorectum | AD | 3.24e-06 | -4.20e-01 | 0.096 |
| 22930 | RAB3GAP1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.88e-10 | -4.21e-01 | 0.0674 |
| 22930 | RAB3GAP1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 4.73e-07 | -3.92e-01 | 0.3005 |
| 22930 | RAB3GAP1 | F007 | Human | Colorectum | FAP | 2.62e-04 | -2.72e-01 | 0.1176 |
| 22930 | RAB3GAP1 | A001-C-207 | Human | Colorectum | FAP | 7.72e-04 | -2.20e-01 | 0.1278 |
| 22930 | RAB3GAP1 | A015-C-203 | Human | Colorectum | FAP | 1.88e-25 | -4.37e-01 | -0.1294 |
| 22930 | RAB3GAP1 | A015-C-204 | Human | Colorectum | FAP | 3.77e-08 | -3.29e-01 | -0.0228 |
| 22930 | RAB3GAP1 | A014-C-040 | Human | Colorectum | FAP | 7.64e-05 | -3.80e-01 | -0.1184 |
| 22930 | RAB3GAP1 | A002-C-201 | Human | Colorectum | FAP | 8.20e-20 | -4.47e-01 | 0.0324 |
| 22930 | RAB3GAP1 | A002-C-203 | Human | Colorectum | FAP | 1.46e-02 | -2.17e-01 | 0.2786 |
| 22930 | RAB3GAP1 | A001-C-119 | Human | Colorectum | FAP | 2.73e-09 | -4.28e-01 | -0.1557 |
| 22930 | RAB3GAP1 | A001-C-108 | Human | Colorectum | FAP | 4.56e-20 | -3.23e-01 | -0.0272 |
| 22930 | RAB3GAP1 | A002-C-205 | Human | Colorectum | FAP | 1.23e-26 | -4.64e-01 | -0.1236 |
| 22930 | RAB3GAP1 | A001-C-104 | Human | Colorectum | FAP | 1.89e-03 | -2.67e-01 | 0.0184 |
| 22930 | RAB3GAP1 | A015-C-005 | Human | Colorectum | FAP | 1.32e-03 | -2.05e-01 | -0.0336 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 | ||
| 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 | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:190503713 | Thyroid | PTC | autophagosome organization | 55/5968 | 103/18723 | 4.75e-06 | 5.79e-05 | 55 |
| GO:190211516 | Thyroid | PTC | regulation of organelle assembly | 88/5968 | 186/18723 | 7.41e-06 | 8.65e-05 | 88 |
| GO:004308718 | Thyroid | PTC | regulation of GTPase activity | 148/5968 | 348/18723 | 1.63e-05 | 1.71e-04 | 148 |
| GO:00162395 | Thyroid | PTC | positive regulation of macroautophagy | 36/5968 | 63/18723 | 2.98e-05 | 2.86e-04 | 36 |
| GO:007178613 | Thyroid | PTC | endoplasmic reticulum tubular network organization | 14/5968 | 18/18723 | 8.31e-05 | 7.01e-04 | 14 |
| GO:19021176 | Thyroid | PTC | positive regulation of organelle assembly | 35/5968 | 67/18723 | 4.24e-04 | 2.83e-03 | 35 |
| GO:00440886 | Thyroid | PTC | regulation of vacuole organization | 25/5968 | 45/18723 | 8.54e-04 | 5.23e-03 | 25 |
| GO:00603244 | Thyroid | PTC | face development | 24/5968 | 44/18723 | 1.52e-03 | 8.49e-03 | 24 |
| GO:00603255 | Thyroid | PTC | face morphogenesis | 17/5968 | 28/18723 | 1.55e-03 | 8.63e-03 | 17 |
| GO:004354714 | Thyroid | PTC | positive regulation of GTPase activity | 103/5968 | 255/18723 | 2.38e-03 | 1.25e-02 | 103 |
| GO:00101713 | Thyroid | PTC | body morphogenesis | 23/5968 | 43/18723 | 2.66e-03 | 1.35e-02 | 23 |
| GO:00603234 | Thyroid | PTC | head morphogenesis | 18/5968 | 32/18723 | 3.72e-03 | 1.79e-02 | 18 |
| GO:00309007 | Thyroid | PTC | forebrain development | 143/5968 | 379/18723 | 8.47e-03 | 3.56e-02 | 143 |
| GO:20007855 | Thyroid | PTC | regulation of autophagosome assembly | 20/5968 | 39/18723 | 9.09e-03 | 3.76e-02 | 20 |
| GO:0009896210 | Thyroid | ATC | positive regulation of catabolic process | 290/6293 | 492/18723 | 2.15e-31 | 1.94e-28 | 290 |
| GO:0031331210 | Thyroid | ATC | positive regulation of cellular catabolic process | 258/6293 | 427/18723 | 2.09e-30 | 1.65e-27 | 258 |
| GO:007259429 | Thyroid | ATC | establishment of protein localization to organelle | 247/6293 | 422/18723 | 2.88e-26 | 1.40e-23 | 247 |
| GO:001623623 | Thyroid | ATC | macroautophagy | 169/6293 | 291/18723 | 6.56e-18 | 7.69e-16 | 169 |
| GO:001050632 | Thyroid | ATC | regulation of autophagy | 180/6293 | 317/18723 | 1.34e-17 | 1.46e-15 | 180 |
| GO:009015031 | Thyroid | ATC | establishment of protein localization to membrane | 150/6293 | 260/18723 | 1.05e-15 | 7.96e-14 | 150 |
| 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 |
| 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 |
| RAB3GAP1 | SNV | Missense_Mutation | rs757654937 | c.2187N>A | p.Met729Ile | p.M729I | Q15042 | protein_coding | deleterious(0.02) | benign(0.259) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| RAB3GAP1 | SNV | Missense_Mutation | novel | c.1604N>C | p.Lys535Thr | p.K535T | Q15042 | protein_coding | deleterious(0.03) | benign(0.241) | TCGA-E2-A150-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| RAB3GAP1 | SNV | Missense_Mutation | c.238G>A | p.Val80Ile | p.V80I | Q15042 | protein_coding | tolerated(0.33) | benign(0.197) | TCGA-GM-A2DA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | fluorouracil | PD | |
| RAB3GAP1 | SNV | Missense_Mutation | novel | c.442N>T | p.Leu148Phe | p.L148F | Q15042 | protein_coding | deleterious(0) | probably_damaging(0.941) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| RAB3GAP1 | deletion | Frame_Shift_Del | novel | c.1153_1159delNNNNNNN | p.His385GlnfsTer11 | p.H385Qfs*11 | Q15042 | protein_coding | TCGA-A8-A094-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| RAB3GAP1 | deletion | Frame_Shift_Del | novel | c.2923delN | p.Phe975LeufsTer53 | p.F975Lfs*53 | Q15042 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| RAB3GAP1 | SNV | Missense_Mutation | c.1358N>T | p.Ser453Phe | p.S453F | Q15042 | protein_coding | tolerated(0.1) | probably_damaging(0.915) | TCGA-BI-A20A-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| RAB3GAP1 | SNV | Missense_Mutation | c.1076N>G | p.Asp359Gly | p.D359G | Q15042 | protein_coding | deleterious(0) | benign(0.335) | TCGA-EK-A2PM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RAB3GAP1 | SNV | Missense_Mutation | novel | c.2680N>T | p.Ile894Phe | p.I894F | Q15042 | protein_coding | deleterious(0) | benign(0.267) | TCGA-5M-AATE-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| RAB3GAP1 | SNV | Missense_Mutation | c.560G>A | p.Arg187Gln | p.R187Q | Q15042 | protein_coding | tolerated(0.1) | probably_damaging(0.998) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=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 |
| Page: 1 |
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