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Gene: RAP1A |
Gene summary for RAP1A |
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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 |
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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 |
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∗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 |
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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 |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0072659 | Colorectum | AD | protein localization to plasma membrane | 122/3918 | 284/18723 | 2.86e-17 | 1.49e-14 | 122 |
GO:1990778 | Colorectum | AD | protein localization to cell periphery | 129/3918 | 333/18723 | 5.51e-14 | 1.15e-11 | 129 |
GO:0002064 | Colorectum | AD | epithelial cell development | 89/3918 | 220/18723 | 2.98e-11 | 3.52e-09 | 89 |
GO:0048732 | Colorectum | AD | gland development | 149/3918 | 436/18723 | 6.07e-11 | 6.33e-09 | 149 |
GO:1905475 | Colorectum | AD | regulation of protein localization to membrane | 73/3918 | 175/18723 | 3.37e-10 | 2.93e-08 | 73 |
GO:1904375 | Colorectum | AD | regulation of protein localization to cell periphery | 54/3918 | 125/18723 | 1.52e-08 | 9.00e-07 | 54 |
GO:0034329 | Colorectum | AD | cell junction assembly | 136/3918 | 420/18723 | 2.02e-08 | 1.15e-06 | 136 |
GO:0009743 | Colorectum | AD | response to carbohydrate | 86/3918 | 253/18723 | 8.43e-07 | 2.90e-05 | 86 |
GO:0043087 | Colorectum | AD | regulation of GTPase activity | 110/3918 | 348/18723 | 1.64e-06 | 5.03e-05 | 110 |
GO:1990090 | Colorectum | AD | cellular response to nerve growth factor stimulus | 26/3918 | 53/18723 | 4.87e-06 | 1.28e-04 | 26 |
GO:0061008 | Colorectum | AD | hepaticobiliary system development | 55/3918 | 150/18723 | 6.34e-06 | 1.59e-04 | 55 |
GO:0001889 | Colorectum | AD | liver development | 54/3918 | 147/18723 | 7.20e-06 | 1.77e-04 | 54 |
GO:0007265 | Colorectum | AD | Ras protein signal transduction | 104/3918 | 337/18723 | 1.01e-05 | 2.35e-04 | 104 |
GO:0061028 | Colorectum | AD | establishment of endothelial barrier | 23/3918 | 46/18723 | 1.14e-05 | 2.57e-04 | 23 |
GO:1990089 | Colorectum | AD | response to nerve growth factor | 26/3918 | 56/18723 | 1.71e-05 | 3.59e-04 | 26 |
GO:0010975 | Colorectum | AD | regulation of neuron projection development | 129/3918 | 445/18723 | 2.88e-05 | 5.37e-04 | 129 |
GO:0097421 | Colorectum | AD | liver regeneration | 18/3918 | 35/18723 | 6.33e-05 | 1.05e-03 | 18 |
GO:0031346 | Colorectum | AD | positive regulation of cell projection organization | 104/3918 | 353/18723 | 8.26e-05 | 1.30e-03 | 104 |
GO:0033674 | Colorectum | AD | positive regulation of kinase activity | 131/3918 | 467/18723 | 1.28e-04 | 1.85e-03 | 131 |
GO:0001885 | Colorectum | AD | endothelial cell development | 26/3918 | 64/18723 | 2.67e-04 | 3.29e-03 | 26 |
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 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0453015 | Liver | NAFLD | Tight junction | 33/1043 | 169/8465 | 4.52e-03 | 4.12e-02 | 3.32e-02 | 33 |
hsa0451011 | Liver | NAFLD | Focal adhesion | 38/1043 | 203/8465 | 5.13e-03 | 4.43e-02 | 3.57e-02 | 38 |
hsa0452022 | Liver | Cirrhotic | Adherens junction | 52/2530 | 93/8465 | 1.36e-07 | 1.97e-06 | 1.21e-06 | 52 |
hsa0453022 | Liver | Cirrhotic | Tight junction | 82/2530 | 169/8465 | 2.14e-07 | 2.85e-06 | 1.76e-06 | 82 |
hsa0451021 | Liver | Cirrhotic | Focal adhesion | 93/2530 | 203/8465 | 9.27e-07 | 1.10e-05 | 6.80e-06 | 93 |
hsa052116 | Liver | Cirrhotic | Renal cell carcinoma | 33/2530 | 69/8465 | 1.24e-03 | 6.64e-03 | 4.09e-03 | 33 |
hsa0467022 | Liver | Cirrhotic | Leukocyte transendothelial migration | 49/2530 | 114/8465 | 1.92e-03 | 8.55e-03 | 5.27e-03 | 49 |
hsa0541722 | Liver | Cirrhotic | Lipid and atherosclerosis | 80/2530 | 215/8465 | 1.18e-02 | 3.81e-02 | 2.35e-02 | 80 |
hsa0452032 | Liver | Cirrhotic | Adherens junction | 52/2530 | 93/8465 | 1.36e-07 | 1.97e-06 | 1.21e-06 | 52 |
hsa0453032 | Liver | Cirrhotic | Tight junction | 82/2530 | 169/8465 | 2.14e-07 | 2.85e-06 | 1.76e-06 | 82 |
hsa0451031 | Liver | Cirrhotic | Focal adhesion | 93/2530 | 203/8465 | 9.27e-07 | 1.10e-05 | 6.80e-06 | 93 |
hsa0521111 | Liver | Cirrhotic | Renal cell carcinoma | 33/2530 | 69/8465 | 1.24e-03 | 6.64e-03 | 4.09e-03 | 33 |
hsa0467032 | Liver | Cirrhotic | Leukocyte transendothelial migration | 49/2530 | 114/8465 | 1.92e-03 | 8.55e-03 | 5.27e-03 | 49 |
hsa0541732 | Liver | Cirrhotic | Lipid and atherosclerosis | 80/2530 | 215/8465 | 1.18e-02 | 3.81e-02 | 2.35e-02 | 80 |
hsa0452042 | Liver | HCC | Adherens junction | 68/4020 | 93/8465 | 3.99e-07 | 4.46e-06 | 2.48e-06 | 68 |
hsa0453042 | Liver | HCC | Tight junction | 110/4020 | 169/8465 | 2.45e-06 | 2.28e-05 | 1.27e-05 | 110 |
hsa0521121 | Liver | HCC | Renal cell carcinoma | 51/4020 | 69/8465 | 6.76e-06 | 5.53e-05 | 3.07e-05 | 51 |
hsa0451041 | Liver | HCC | Focal adhesion | 125/4020 | 203/8465 | 3.12e-05 | 1.88e-04 | 1.04e-04 | 125 |
hsa0472210 | Liver | HCC | Neurotrophin signaling pathway | 74/4020 | 119/8465 | 8.27e-04 | 3.26e-03 | 1.81e-03 | 74 |
hsa0467042 | Liver | HCC | Leukocyte transendothelial migration | 68/4020 | 114/8465 | 5.79e-03 | 1.64e-02 | 9.15e-03 | 68 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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. |
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Somatic mutation of malignant transformation related genes |
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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 |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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