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Gene: RAP2A |
Gene summary for RAP2A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RAP2A | Gene ID | 5911 |
| Gene name | RAP2A, member of RAS oncogene family | |
| Gene Alias | K-REV | |
| Cytomap | 13q32.1 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | P10114 |
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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 |
| 5911 | RAP2A | P2T-E | Human | Esophagus | ESCC | 1.45e-20 | 4.33e-02 | 0.1177 |
| 5911 | RAP2A | P4T-E | Human | Esophagus | ESCC | 2.87e-08 | 1.17e-01 | 0.1323 |
| 5911 | RAP2A | P5T-E | Human | Esophagus | ESCC | 1.80e-06 | 4.75e-03 | 0.1327 |
| 5911 | RAP2A | P8T-E | Human | Esophagus | ESCC | 4.22e-03 | 9.76e-03 | 0.0889 |
| 5911 | RAP2A | P9T-E | Human | Esophagus | ESCC | 2.56e-06 | 3.69e-02 | 0.1131 |
| 5911 | RAP2A | P10T-E | Human | Esophagus | ESCC | 1.09e-08 | 9.12e-02 | 0.116 |
| 5911 | RAP2A | P11T-E | Human | Esophagus | ESCC | 1.75e-03 | 9.55e-02 | 0.1426 |
| 5911 | RAP2A | P12T-E | Human | Esophagus | ESCC | 1.44e-08 | 6.95e-02 | 0.1122 |
| 5911 | RAP2A | P15T-E | Human | Esophagus | ESCC | 1.67e-06 | 2.25e-02 | 0.1149 |
| 5911 | RAP2A | P16T-E | Human | Esophagus | ESCC | 6.52e-19 | 3.56e-01 | 0.1153 |
| 5911 | RAP2A | P21T-E | Human | Esophagus | ESCC | 1.27e-06 | 3.41e-02 | 0.1617 |
| 5911 | RAP2A | P22T-E | Human | Esophagus | ESCC | 2.01e-02 | -1.41e-02 | 0.1236 |
| 5911 | RAP2A | P24T-E | Human | Esophagus | ESCC | 2.10e-09 | 1.07e-02 | 0.1287 |
| 5911 | RAP2A | P26T-E | Human | Esophagus | ESCC | 1.04e-07 | 3.54e-03 | 0.1276 |
| 5911 | RAP2A | P30T-E | Human | Esophagus | ESCC | 6.70e-08 | 1.17e-01 | 0.137 |
| 5911 | RAP2A | P31T-E | Human | Esophagus | ESCC | 1.76e-08 | 8.04e-03 | 0.1251 |
| 5911 | RAP2A | P32T-E | Human | Esophagus | ESCC | 1.45e-12 | 9.12e-02 | 0.1666 |
| 5911 | RAP2A | P37T-E | Human | Esophagus | ESCC | 1.23e-09 | 9.17e-02 | 0.1371 |
| 5911 | RAP2A | P39T-E | Human | Esophagus | ESCC | 2.29e-04 | -3.97e-02 | 0.0894 |
| 5911 | RAP2A | P47T-E | Human | Esophagus | ESCC | 4.57e-16 | -2.97e-04 | 0.1067 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:0072659110 | Esophagus | ESCC | protein localization to plasma membrane | 193/8552 | 284/18723 | 1.95e-14 | 1.03e-12 | 193 |
| GO:199077819 | Esophagus | ESCC | protein localization to cell periphery | 217/8552 | 333/18723 | 4.08e-13 | 1.88e-11 | 217 |
| GO:003109818 | Esophagus | ESCC | stress-activated protein kinase signaling cascade | 154/8552 | 247/18723 | 8.53e-08 | 1.44e-06 | 154 |
| GO:000726510 | Esophagus | ESCC | Ras protein signal transduction | 201/8552 | 337/18723 | 1.44e-07 | 2.30e-06 | 201 |
| GO:005140318 | Esophagus | ESCC | stress-activated MAPK cascade | 147/8552 | 239/18723 | 5.43e-07 | 7.18e-06 | 147 |
| GO:004677710 | Esophagus | ESCC | protein autophosphorylation | 138/8552 | 227/18723 | 2.98e-06 | 3.38e-05 | 138 |
| GO:003153218 | Esophagus | ESCC | actin cytoskeleton reorganization | 72/8552 | 107/18723 | 5.03e-06 | 5.31e-05 | 72 |
| GO:007030217 | Esophagus | ESCC | regulation of stress-activated protein kinase signaling cascade | 119/8552 | 195/18723 | 1.07e-05 | 1.01e-04 | 119 |
| GO:003287217 | Esophagus | ESCC | regulation of stress-activated MAPK cascade | 116/8552 | 192/18723 | 2.63e-05 | 2.21e-04 | 116 |
| GO:00072549 | Esophagus | ESCC | JNK cascade | 102/8552 | 167/18723 | 4.22e-05 | 3.39e-04 | 102 |
| GO:000941020 | Esophagus | ESCC | response to xenobiotic stimulus | 253/8552 | 462/18723 | 4.55e-05 | 3.58e-04 | 253 |
| GO:001097516 | Esophagus | ESCC | regulation of neuron projection development | 240/8552 | 445/18723 | 2.48e-04 | 1.53e-03 | 240 |
| GO:00463289 | Esophagus | ESCC | regulation of JNK cascade | 80/8552 | 133/18723 | 5.35e-04 | 2.95e-03 | 80 |
| GO:00319521 | Esophagus | ESCC | regulation of protein autophosphorylation | 29/8552 | 43/18723 | 3.25e-03 | 1.35e-02 | 29 |
| GO:00300339 | Esophagus | ESCC | microvillus assembly | 13/8552 | 16/18723 | 4.05e-03 | 1.62e-02 | 13 |
| GO:001635816 | Esophagus | ESCC | dendrite development | 130/8552 | 243/18723 | 8.33e-03 | 2.95e-02 | 130 |
| GO:00319541 | Esophagus | ESCC | positive regulation of protein autophosphorylation | 19/8552 | 27/18723 | 8.35e-03 | 2.95e-02 | 19 |
| GO:007265921 | Liver | HCC | protein localization to plasma membrane | 177/7958 | 284/18723 | 1.02e-11 | 4.18e-10 | 177 |
| GO:199077821 | Liver | HCC | protein localization to cell periphery | 200/7958 | 333/18723 | 6.07e-11 | 2.23e-09 | 200 |
| GO:000941022 | Liver | HCC | response to xenobiotic stimulus | 248/7958 | 462/18723 | 6.47e-07 | 1.02e-05 | 248 |
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| 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 |
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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 |
| RAP2A | SNV | Missense_Mutation | novel | c.463G>A | p.Glu155Lys | p.E155K | P10114 | protein_coding | deleterious(0.02) | benign(0.111) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RAP2A | SNV | Missense_Mutation | c.503N>T | p.Ala168Val | p.A168V | P10114 | protein_coding | tolerated(0.17) | benign(0.017) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RAP2A | SNV | Missense_Mutation | novel | c.507N>T | p.Gln169His | p.Q169H | P10114 | protein_coding | tolerated(0.16) | benign(0.001) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RAP2A | SNV | Missense_Mutation | c.429N>T | p.Met143Ile | p.M143I | P10114 | protein_coding | tolerated(0.43) | benign(0.001) | TCGA-AX-A05S-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unspecific | Carboplatin & Paclitaxel | PD | |
| RAP2A | SNV | Missense_Mutation | c.439N>A | p.Ala147Thr | p.A147T | P10114 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD | |
| RAP2A | SNV | Missense_Mutation | novel | c.463G>A | p.Glu155Lys | p.E155K | P10114 | protein_coding | deleterious(0.02) | benign(0.111) | TCGA-E6-A1LX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RAP2A | SNV | Missense_Mutation | novel | c.463N>A | p.Glu155Lys | p.E155K | P10114 | protein_coding | deleterious(0.02) | benign(0.111) | TCGA-EO-A22R-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RAP2A | insertion | Nonsense_Mutation | novel | c.505_506insTCACAGTGGATGATAAAATGAGTTTTATGAAATGATGTTTT | p.Gln169LeufsTer12 | p.Q169Lfs*12 | P10114 | protein_coding | TCGA-BG-A0MQ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| RAP2A | SNV | Missense_Mutation | c.429N>T | p.Met143Ile | p.M143I | P10114 | protein_coding | tolerated(0.43) | benign(0.001) | TCGA-55-6969-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| RAP2A | SNV | Missense_Mutation | novel | c.490A>T | p.Met164Leu | p.M164L | P10114 | protein_coding | deleterious(0.01) | benign(0.009) | TCGA-55-6975-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
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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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