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Gene: RAP1GDS1 |
Gene summary for RAP1GDS1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RAP1GDS1 | Gene ID | 5910 |
| Gene name | Rap1 GTPase-GDP dissociation stimulator 1 | |
| Gene Alias | GDS1 | |
| Cytomap | 4q23 | |
| Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | P52306 |
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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 |
| 5910 | RAP1GDS1 | CCI_1 | Human | Cervix | CC | 1.97e-02 | 5.20e-01 | 0.528 |
| 5910 | RAP1GDS1 | CCI_2 | Human | Cervix | CC | 9.94e-04 | 4.30e-01 | 0.5249 |
| 5910 | RAP1GDS1 | CCI_3 | Human | Cervix | CC | 1.39e-11 | 7.26e-01 | 0.516 |
| 5910 | RAP1GDS1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 4.22e-19 | -5.94e-01 | 0.0155 |
| 5910 | RAP1GDS1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 8.98e-12 | -6.38e-01 | -0.1808 |
| 5910 | RAP1GDS1 | HTA11_2112_2000001011 | Human | Colorectum | SER | 2.81e-02 | -7.51e-01 | -0.2196 |
| 5910 | RAP1GDS1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.85e-06 | -5.97e-01 | -0.1207 |
| 5910 | RAP1GDS1 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.58e-03 | -5.12e-01 | -0.1526 |
| 5910 | RAP1GDS1 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.81e-16 | -5.11e-01 | -0.1464 |
| 5910 | RAP1GDS1 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.30e-06 | -3.84e-01 | -0.1001 |
| 5910 | RAP1GDS1 | HTA11_5212_2000001011 | Human | Colorectum | AD | 4.28e-03 | -6.58e-01 | -0.2061 |
| 5910 | RAP1GDS1 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.85e-13 | -6.13e-01 | 0.096 |
| 5910 | RAP1GDS1 | HTA11_8622_2000001021 | Human | Colorectum | SER | 1.65e-04 | -6.91e-01 | 0.0528 |
| 5910 | RAP1GDS1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 3.26e-06 | -5.67e-01 | 0.0338 |
| 5910 | RAP1GDS1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 6.45e-11 | -4.42e-01 | 0.0674 |
| 5910 | RAP1GDS1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.69e-03 | -3.05e-01 | 0.294 |
| 5910 | RAP1GDS1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.78e-10 | -3.69e-01 | 0.3859 |
| 5910 | RAP1GDS1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.59e-02 | -5.48e-01 | 0.2585 |
| 5910 | RAP1GDS1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 6.86e-18 | -6.10e-01 | 0.3005 |
| 5910 | RAP1GDS1 | A001-C-207 | Human | Colorectum | FAP | 2.84e-04 | -2.38e-01 | 0.1278 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:00430877 | Cervix | CC | regulation of GTPase activity | 79/2311 | 348/18723 | 4.21e-08 | 2.60e-06 | 79 |
| GO:00435476 | Cervix | CC | positive regulation of GTPase activity | 53/2311 | 255/18723 | 8.72e-05 | 1.16e-03 | 53 |
| GO:00324698 | Cervix | CC | endoplasmic reticulum calcium ion homeostasis | 10/2311 | 25/18723 | 4.52e-04 | 4.49e-03 | 10 |
| GO:0043087 | Colorectum | AD | regulation of GTPase activity | 110/3918 | 348/18723 | 1.64e-06 | 5.03e-05 | 110 |
| GO:0032469 | Colorectum | AD | endoplasmic reticulum calcium ion homeostasis | 16/3918 | 25/18723 | 3.80e-06 | 1.04e-04 | 16 |
| GO:0043547 | Colorectum | AD | positive regulation of GTPase activity | 75/3918 | 255/18723 | 7.95e-04 | 7.91e-03 | 75 |
| GO:0051560 | Colorectum | AD | mitochondrial calcium ion homeostasis | 13/3918 | 26/18723 | 9.41e-04 | 8.92e-03 | 13 |
| GO:00324691 | Colorectum | SER | endoplasmic reticulum calcium ion homeostasis | 13/2897 | 25/18723 | 2.34e-05 | 6.64e-04 | 13 |
| GO:00430871 | Colorectum | SER | regulation of GTPase activity | 77/2897 | 348/18723 | 5.90e-04 | 8.07e-03 | 77 |
| GO:00515601 | Colorectum | SER | mitochondrial calcium ion homeostasis | 11/2897 | 26/18723 | 9.60e-04 | 1.15e-02 | 11 |
| GO:0003012 | Colorectum | SER | muscle system process | 92/2897 | 452/18723 | 2.98e-03 | 2.63e-02 | 92 |
| GO:0051561 | Colorectum | SER | positive regulation of mitochondrial calcium ion concentration | 6/2897 | 11/18723 | 3.12e-03 | 2.70e-02 | 6 |
| GO:00324692 | Colorectum | MSS | endoplasmic reticulum calcium ion homeostasis | 16/3467 | 25/18723 | 6.86e-07 | 2.48e-05 | 16 |
| GO:00430872 | Colorectum | MSS | regulation of GTPase activity | 101/3467 | 348/18723 | 1.00e-06 | 3.46e-05 | 101 |
| GO:00435471 | Colorectum | MSS | positive regulation of GTPase activity | 68/3467 | 255/18723 | 7.97e-04 | 8.38e-03 | 68 |
| GO:00515602 | Colorectum | MSS | mitochondrial calcium ion homeostasis | 12/3467 | 26/18723 | 1.16e-03 | 1.12e-02 | 12 |
| GO:00030121 | Colorectum | MSS | muscle system process | 105/3467 | 452/18723 | 6.39e-03 | 4.26e-02 | 105 |
| GO:00515611 | Colorectum | MSS | positive regulation of mitochondrial calcium ion concentration | 6/3467 | 11/18723 | 7.89e-03 | 4.84e-02 | 6 |
| GO:00430873 | Colorectum | FAP | regulation of GTPase activity | 85/2622 | 348/18723 | 1.20e-07 | 7.68e-06 | 85 |
| GO:00435472 | Colorectum | FAP | positive regulation of GTPase activity | 61/2622 | 255/18723 | 1.39e-05 | 3.73e-04 | 61 |
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| 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 |
| RAP1GDS1 | SNV | Missense_Mutation | c.764A>G | p.Asn255Ser | p.N255S | P52306 | protein_coding | tolerated(0.18) | benign(0.076) | TCGA-A8-A093-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| RAP1GDS1 | SNV | Missense_Mutation | c.1528N>C | p.Glu510Gln | p.E510Q | P52306 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RAP1GDS1 | SNV | Missense_Mutation | c.1619N>G | p.His540Arg | p.H540R | P52306 | protein_coding | deleterious(0.04) | benign(0.025) | TCGA-D8-A1JD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| RAP1GDS1 | SNV | Missense_Mutation | c.1518N>G | p.Ile506Met | p.I506M | P52306 | protein_coding | deleterious(0.01) | probably_damaging(0.921) | TCGA-EW-A1J3-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD | |
| RAP1GDS1 | deletion | Frame_Shift_Del | novel | c.893delN | p.Leu299TyrfsTer57 | p.L299Yfs*57 | P52306 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| RAP1GDS1 | SNV | Missense_Mutation | rs377518587 | c.149G>A | p.Gly50Glu | p.G50E | P52306 | protein_coding | deleterious(0) | probably_damaging(0.954) | TCGA-EA-A3HT-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| RAP1GDS1 | insertion | In_Frame_Ins | novel | c.1287_1288insGAATTCAGTTGT | p.Met429_Leu430insGluPheSerCys | p.M429_L430insEFSC | P52306 | protein_coding | TCGA-DS-A1OA-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | carboplatin | PD | ||
| RAP1GDS1 | SNV | Missense_Mutation | c.568N>A | p.Leu190Met | p.L190M | P52306 | protein_coding | tolerated(0.19) | probably_damaging(0.998) | TCGA-AA-3655-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| RAP1GDS1 | SNV | Missense_Mutation | novel | c.1234N>A | p.Leu412Ile | p.L412I | P52306 | protein_coding | tolerated(0.07) | possibly_damaging(0.756) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RAP1GDS1 | SNV | Missense_Mutation | c.1598N>T | p.Ala533Val | p.A533V | P52306 | protein_coding | deleterious(0.05) | possibly_damaging(0.786) | TCGA-AY-6197-01 | 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 |
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