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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 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00990721 | Colorectum | MSS | regulation of postsynaptic membrane neurotransmitter receptor levels | 21/3467 | 62/18723 | 2.87e-03 | 2.23e-02 | 21 |
GO:00510511 | Colorectum | MSS | negative regulation of transport | 110/3467 | 470/18723 | 4.20e-03 | 3.04e-02 | 110 |
GO:00031581 | Colorectum | MSS | endothelium development | 38/3467 | 136/18723 | 4.53e-03 | 3.19e-02 | 38 |
GO:0099504 | Colorectum | MSS | synaptic vesicle cycle | 48/3467 | 181/18723 | 4.85e-03 | 3.39e-02 | 48 |
GO:0031099 | Colorectum | MSS | regeneration | 51/3467 | 198/18723 | 6.99e-03 | 4.49e-02 | 51 |
GO:00454461 | Colorectum | MSS | endothelial cell differentiation | 33/3467 | 118/18723 | 7.66e-03 | 4.81e-02 | 33 |
GO:00726594 | Colorectum | FAP | protein localization to plasma membrane | 95/2622 | 284/18723 | 4.86e-17 | 9.93e-14 | 95 |
GO:19907784 | Colorectum | FAP | protein localization to cell periphery | 100/2622 | 333/18723 | 2.19e-14 | 2.68e-11 | 100 |
GO:19054753 | Colorectum | FAP | regulation of protein localization to membrane | 58/2622 | 175/18723 | 9.05e-11 | 2.92e-08 | 58 |
GO:00343293 | Colorectum | FAP | cell junction assembly | 105/2622 | 420/18723 | 1.03e-09 | 2.18e-07 | 105 |
GO:19043753 | Colorectum | FAP | regulation of protein localization to cell periphery | 43/2622 | 125/18723 | 6.69e-09 | 1.00e-06 | 43 |
GO:00020644 | Colorectum | FAP | epithelial cell development | 62/2622 | 220/18723 | 2.74e-08 | 2.54e-06 | 62 |
GO:00487324 | Colorectum | FAP | gland development | 103/2622 | 436/18723 | 3.61e-08 | 3.12e-06 | 103 |
GO:00430873 | Colorectum | FAP | regulation of GTPase activity | 85/2622 | 348/18723 | 1.20e-07 | 7.68e-06 | 85 |
GO:00109753 | Colorectum | FAP | regulation of neuron projection development | 102/2622 | 445/18723 | 2.04e-07 | 1.24e-05 | 102 |
GO:00072652 | Colorectum | FAP | Ras protein signal transduction | 80/2622 | 337/18723 | 9.61e-07 | 4.33e-05 | 80 |
GO:00313463 | Colorectum | FAP | positive regulation of cell projection organization | 82/2622 | 353/18723 | 1.78e-06 | 7.35e-05 | 82 |
GO:00097434 | Colorectum | FAP | response to carbohydrate | 63/2622 | 253/18723 | 2.52e-06 | 9.77e-05 | 63 |
GO:00990032 | Colorectum | FAP | vesicle-mediated transport in synapse | 51/2622 | 200/18723 | 1.09e-05 | 3.08e-04 | 51 |
GO:00610084 | Colorectum | FAP | hepaticobiliary system development | 41/2622 | 150/18723 | 1.32e-05 | 3.55e-04 | 41 |
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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 |
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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 |
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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. |
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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 |
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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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