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Gene: RAP1A |
Gene summary for RAP1A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RAP1A | Gene ID | 5906 |
| Gene name | RAP1A, member of RAS oncogene family | |
| Gene Alias | C21KG | |
| Cytomap | 1p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | A8KAH9 |
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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 |
| 5906 | RAP1A | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.22e-06 | -3.99e-01 | 0.0155 |
| 5906 | RAP1A | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.15e-04 | -3.24e-01 | 0.0674 |
| 5906 | RAP1A | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.21e-05 | -3.29e-01 | 0.3005 |
| 5906 | RAP1A | F007 | Human | Colorectum | FAP | 1.27e-03 | -3.62e-01 | 0.1176 |
| 5906 | RAP1A | A001-C-207 | Human | Colorectum | FAP | 5.35e-08 | -3.55e-01 | 0.1278 |
| 5906 | RAP1A | A015-C-203 | Human | Colorectum | FAP | 1.27e-24 | -4.54e-01 | -0.1294 |
| 5906 | RAP1A | A015-C-204 | Human | Colorectum | FAP | 3.85e-06 | -3.12e-01 | -0.0228 |
| 5906 | RAP1A | A014-C-040 | Human | Colorectum | FAP | 5.54e-04 | -4.30e-01 | -0.1184 |
| 5906 | RAP1A | A002-C-201 | Human | Colorectum | FAP | 1.77e-16 | -3.99e-01 | 0.0324 |
| 5906 | RAP1A | A002-C-203 | Human | Colorectum | FAP | 1.36e-03 | -1.74e-01 | 0.2786 |
| 5906 | RAP1A | A001-C-119 | Human | Colorectum | FAP | 1.64e-07 | -4.78e-01 | -0.1557 |
| 5906 | RAP1A | A001-C-108 | Human | Colorectum | FAP | 1.07e-15 | -3.77e-01 | -0.0272 |
| 5906 | RAP1A | A002-C-205 | Human | Colorectum | FAP | 1.57e-22 | -4.91e-01 | -0.1236 |
| 5906 | RAP1A | A001-C-104 | Human | Colorectum | FAP | 1.27e-02 | -2.63e-01 | 0.0184 |
| 5906 | RAP1A | A015-C-005 | Human | Colorectum | FAP | 2.66e-04 | -2.22e-01 | -0.0336 |
| 5906 | RAP1A | A015-C-006 | Human | Colorectum | FAP | 3.38e-14 | -4.89e-01 | -0.0994 |
| 5906 | RAP1A | A015-C-106 | Human | Colorectum | FAP | 1.78e-11 | -3.22e-01 | -0.0511 |
| 5906 | RAP1A | A002-C-114 | Human | Colorectum | FAP | 5.99e-15 | -3.90e-01 | -0.1561 |
| 5906 | RAP1A | A015-C-104 | Human | Colorectum | FAP | 1.63e-23 | -5.01e-01 | -0.1899 |
| 5906 | RAP1A | A001-C-014 | Human | Colorectum | FAP | 2.42e-10 | -3.48e-01 | 0.0135 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 | ||
| 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:003432916 | Oral cavity | OSCC | cell junction assembly | 190/7305 | 420/18723 | 4.99e-03 | 1.96e-02 | 190 |
| GO:0032963 | Oral cavity | OSCC | collagen metabolic process | 54/7305 | 104/18723 | 5.00e-03 | 1.96e-02 | 54 |
| GO:00380935 | Oral cavity | OSCC | Fc receptor signaling pathway | 29/7305 | 50/18723 | 5.01e-03 | 1.96e-02 | 29 |
| GO:00109763 | Oral cavity | OSCC | positive regulation of neuron projection development | 80/7305 | 163/18723 | 5.54e-03 | 2.14e-02 | 80 |
| GO:0032486 | Oral cavity | OSCC | Rap protein signal transduction | 11/7305 | 15/18723 | 7.49e-03 | 2.75e-02 | 11 |
| GO:00434107 | Oral cavity | OSCC | positive regulation of MAPK cascade | 213/7305 | 480/18723 | 8.71e-03 | 3.16e-02 | 213 |
| GO:00703716 | Oral cavity | OSCC | ERK1 and ERK2 cascade | 150/7305 | 330/18723 | 9.47e-03 | 3.38e-02 | 150 |
| GO:00703724 | Oral cavity | OSCC | regulation of ERK1 and ERK2 cascade | 140/7305 | 309/18723 | 1.34e-02 | 4.46e-02 | 140 |
| GO:00381792 | Oral cavity | OSCC | neurotrophin signaling pathway | 21/7305 | 36/18723 | 1.46e-02 | 4.76e-02 | 21 |
| GO:00507643 | Oral cavity | OSCC | regulation of phagocytosis | 48/7305 | 95/18723 | 1.47e-02 | 4.77e-02 | 48 |
| GO:007265919 | Oral cavity | LP | protein localization to plasma membrane | 119/4623 | 284/18723 | 1.11e-10 | 6.44e-09 | 119 |
| GO:199077817 | Oral cavity | LP | protein localization to cell periphery | 133/4623 | 333/18723 | 4.42e-10 | 2.21e-08 | 133 |
| GO:190547517 | Oral cavity | LP | regulation of protein localization to membrane | 74/4623 | 175/18723 | 2.26e-07 | 6.81e-06 | 74 |
| GO:190437517 | Oral cavity | LP | regulation of protein localization to cell periphery | 55/4623 | 125/18723 | 1.77e-06 | 4.11e-05 | 55 |
| GO:000188919 | Oral cavity | LP | liver development | 62/4623 | 147/18723 | 2.32e-06 | 5.14e-05 | 62 |
| GO:0048732110 | Oral cavity | LP | gland development | 149/4623 | 436/18723 | 4.51e-06 | 9.17e-05 | 149 |
| GO:006100819 | Oral cavity | LP | hepaticobiliary system development | 62/4623 | 150/18723 | 5.13e-06 | 1.03e-04 | 62 |
| GO:003109916 | Oral cavity | LP | regeneration | 76/4623 | 198/18723 | 1.25e-05 | 2.24e-04 | 76 |
| GO:003150313 | Oral cavity | LP | protein-containing complex localization | 82/4623 | 220/18723 | 2.08e-05 | 3.44e-04 | 82 |
| GO:000726515 | Oral cavity | LP | Ras protein signal transduction | 109/4623 | 337/18723 | 8.44e-04 | 7.36e-03 | 109 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04520 | Colorectum | AD | Adherens junction | 50/2092 | 93/8465 | 1.52e-09 | 2.83e-08 | 1.81e-08 | 50 |
| hsa04530 | Colorectum | AD | Tight junction | 76/2092 | 169/8465 | 5.49e-09 | 9.69e-08 | 6.18e-08 | 76 |
| hsa04722 | Colorectum | AD | Neurotrophin signaling pathway | 50/2092 | 119/8465 | 2.28e-05 | 2.24e-04 | 1.43e-04 | 50 |
| hsa05417 | Colorectum | AD | Lipid and atherosclerosis | 73/2092 | 215/8465 | 1.31e-03 | 8.27e-03 | 5.27e-03 | 73 |
| hsa04015 | Colorectum | AD | Rap1 signaling pathway | 71/2092 | 210/8465 | 1.72e-03 | 9.68e-03 | 6.18e-03 | 71 |
| hsa05211 | Colorectum | AD | Renal cell carcinoma | 28/2092 | 69/8465 | 2.58e-03 | 1.37e-02 | 8.75e-03 | 28 |
| hsa04510 | Colorectum | AD | Focal adhesion | 67/2092 | 203/8465 | 4.40e-03 | 2.17e-02 | 1.38e-02 | 67 |
| hsa04670 | Colorectum | AD | Leukocyte transendothelial migration | 41/2092 | 114/8465 | 4.60e-03 | 2.20e-02 | 1.40e-02 | 41 |
| hsa04720 | Colorectum | AD | Long-term potentiation | 26/2092 | 67/8465 | 7.26e-03 | 2.97e-02 | 1.89e-02 | 26 |
| hsa04972 | Colorectum | AD | Pancreatic secretion | 36/2092 | 102/8465 | 1.06e-02 | 3.98e-02 | 2.54e-02 | 36 |
| hsa045201 | Colorectum | AD | Adherens junction | 50/2092 | 93/8465 | 1.52e-09 | 2.83e-08 | 1.81e-08 | 50 |
| hsa045301 | Colorectum | AD | Tight junction | 76/2092 | 169/8465 | 5.49e-09 | 9.69e-08 | 6.18e-08 | 76 |
| hsa047221 | Colorectum | AD | Neurotrophin signaling pathway | 50/2092 | 119/8465 | 2.28e-05 | 2.24e-04 | 1.43e-04 | 50 |
| hsa054171 | Colorectum | AD | Lipid and atherosclerosis | 73/2092 | 215/8465 | 1.31e-03 | 8.27e-03 | 5.27e-03 | 73 |
| hsa040151 | Colorectum | AD | Rap1 signaling pathway | 71/2092 | 210/8465 | 1.72e-03 | 9.68e-03 | 6.18e-03 | 71 |
| hsa052111 | Colorectum | AD | Renal cell carcinoma | 28/2092 | 69/8465 | 2.58e-03 | 1.37e-02 | 8.75e-03 | 28 |
| hsa045101 | Colorectum | AD | Focal adhesion | 67/2092 | 203/8465 | 4.40e-03 | 2.17e-02 | 1.38e-02 | 67 |
| hsa046701 | Colorectum | AD | Leukocyte transendothelial migration | 41/2092 | 114/8465 | 4.60e-03 | 2.20e-02 | 1.40e-02 | 41 |
| hsa047201 | Colorectum | AD | Long-term potentiation | 26/2092 | 67/8465 | 7.26e-03 | 2.97e-02 | 1.89e-02 | 26 |
| hsa049721 | Colorectum | AD | Pancreatic secretion | 36/2092 | 102/8465 | 1.06e-02 | 3.98e-02 | 2.54e-02 | 36 |
| Page: 1 2 3 4 5 6 7 8 9 |
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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 |
| RAP1A | SNV | Missense_Mutation | rs749041743 | c.367N>A | p.Glu123Lys | p.E123K | P62834 | protein_coding | deleterious(0.03) | benign(0.072) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| RAP1A | SNV | Missense_Mutation | novel | c.55N>G | p.Leu19Val | p.L19V | P62834 | protein_coding | deleterious(0.03) | probably_damaging(0.944) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RAP1A | SNV | Missense_Mutation | c.445A>G | p.Lys149Glu | p.K149E | P62834 | protein_coding | deleterious(0) | possibly_damaging(0.727) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| RAP1A | SNV | Missense_Mutation | c.25C>A | p.Leu9Ile | p.L9I | P62834 | protein_coding | deleterious(0.02) | probably_damaging(0.913) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| RAP1A | SNV | Missense_Mutation | c.344N>A | p.Gly115Asp | p.G115D | P62834 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| RAP1A | SNV | Missense_Mutation | c.160G>A | p.Glu54Lys | p.E54K | P62834 | protein_coding | deleterious(0) | benign(0.28) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| RAP1A | SNV | Missense_Mutation | novel | c.247T>G | p.Ser83Ala | p.S83A | P62834 | protein_coding | deleterious(0.03) | probably_damaging(0.972) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| RAP1A | SNV | Missense_Mutation | c.115T>C | p.Ser39Pro | p.S39P | P62834 | protein_coding | deleterious(0.01) | probably_damaging(0.994) | TCGA-B5-A11E-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RAP1A | SNV | Missense_Mutation | c.344N>A | p.Gly115Asp | p.G115D | P62834 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-DI-A0WH-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RAP1A | SNV | Missense_Mutation | novel | c.470N>C | p.Ile157Thr | p.I157T | P62834 | protein_coding | deleterious(0.05) | possibly_damaging(0.754) | TCGA-E6-A1LX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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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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