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Gene: RAB5A |
Gene summary for RAB5A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RAB5A | Gene ID | 5868 |
| Gene name | RAB5A, member RAS oncogene family | |
| Gene Alias | RAB5 | |
| Cytomap | 3p24.3 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | P20339 |
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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 |
| 5868 | RAB5A | LZE4T | Human | Esophagus | ESCC | 8.30e-09 | 1.54e-01 | 0.0811 |
| 5868 | RAB5A | LZE5T | Human | Esophagus | ESCC | 1.08e-03 | 1.47e-01 | 0.0514 |
| 5868 | RAB5A | LZE7T | Human | Esophagus | ESCC | 7.16e-08 | 1.06e-01 | 0.0667 |
| 5868 | RAB5A | LZE8T | Human | Esophagus | ESCC | 5.37e-08 | 7.38e-02 | 0.067 |
| 5868 | RAB5A | LZE20T | Human | Esophagus | ESCC | 2.18e-09 | 1.22e-02 | 0.0662 |
| 5868 | RAB5A | LZE24T | Human | Esophagus | ESCC | 3.78e-15 | 6.35e-01 | 0.0596 |
| 5868 | RAB5A | LZE21T | Human | Esophagus | ESCC | 1.07e-03 | -7.13e-02 | 0.0655 |
| 5868 | RAB5A | P1T-E | Human | Esophagus | ESCC | 2.65e-02 | 2.68e-01 | 0.0875 |
| 5868 | RAB5A | P2T-E | Human | Esophagus | ESCC | 3.56e-28 | 6.10e-02 | 0.1177 |
| 5868 | RAB5A | P4T-E | Human | Esophagus | ESCC | 7.17e-17 | 5.19e-01 | 0.1323 |
| 5868 | RAB5A | P5T-E | Human | Esophagus | ESCC | 7.26e-25 | 2.02e-02 | 0.1327 |
| 5868 | RAB5A | P8T-E | Human | Esophagus | ESCC | 6.15e-16 | 4.33e-01 | 0.0889 |
| 5868 | RAB5A | P9T-E | Human | Esophagus | ESCC | 3.86e-14 | 4.21e-02 | 0.1131 |
| 5868 | RAB5A | P10T-E | Human | Esophagus | ESCC | 3.47e-21 | 3.12e-01 | 0.116 |
| 5868 | RAB5A | P11T-E | Human | Esophagus | ESCC | 9.49e-09 | 5.05e-01 | 0.1426 |
| 5868 | RAB5A | P12T-E | Human | Esophagus | ESCC | 8.70e-24 | 5.81e-01 | 0.1122 |
| 5868 | RAB5A | P15T-E | Human | Esophagus | ESCC | 1.13e-15 | 3.29e-01 | 0.1149 |
| 5868 | RAB5A | P16T-E | Human | Esophagus | ESCC | 1.33e-15 | 2.74e-01 | 0.1153 |
| 5868 | RAB5A | P17T-E | Human | Esophagus | ESCC | 2.53e-02 | 2.54e-01 | 0.1278 |
| 5868 | RAB5A | P19T-E | Human | Esophagus | ESCC | 5.23e-03 | 4.20e-01 | 0.1662 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| 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:0016032111 | Esophagus | ESCC | viral process | 301/8552 | 415/18723 | 3.34e-29 | 1.32e-26 | 301 |
| GO:001623617 | Esophagus | ESCC | macroautophagy | 216/8552 | 291/18723 | 1.94e-23 | 4.57e-21 | 216 |
| GO:0019058111 | Esophagus | ESCC | viral life cycle | 226/8552 | 317/18723 | 1.17e-20 | 1.76e-18 | 226 |
| GO:0019079111 | Esophagus | ESCC | viral genome replication | 102/8552 | 131/18723 | 4.31e-14 | 2.19e-12 | 102 |
| GO:001648210 | Esophagus | ESCC | cytosolic transport | 124/8552 | 168/18723 | 9.69e-14 | 4.69e-12 | 124 |
| GO:000703314 | Esophagus | ESCC | vacuole organization | 127/8552 | 180/18723 | 1.04e-11 | 3.85e-10 | 127 |
| GO:001605517 | Esophagus | ESCC | Wnt signaling pathway | 268/8552 | 444/18723 | 2.32e-10 | 6.58e-09 | 268 |
| GO:019873817 | Esophagus | ESCC | cell-cell signaling by wnt | 269/8552 | 446/18723 | 2.41e-10 | 6.79e-09 | 269 |
| GO:003253520 | Esophagus | ESCC | regulation of cellular component size | 227/8552 | 383/18723 | 4.77e-08 | 8.60e-07 | 227 |
| GO:003010018 | Esophagus | ESCC | regulation of endocytosis | 135/8552 | 211/18723 | 5.75e-08 | 1.02e-06 | 135 |
| GO:190503712 | Esophagus | ESCC | autophagosome organization | 73/8552 | 103/18723 | 1.88e-07 | 2.93e-06 | 73 |
| GO:00989278 | Esophagus | ESCC | vesicle-mediated transport between endosomal compartments | 36/8552 | 43/18723 | 2.90e-07 | 4.20e-06 | 36 |
| GO:006007016 | Esophagus | ESCC | canonical Wnt signaling pathway | 180/8552 | 303/18723 | 9.15e-07 | 1.17e-05 | 180 |
| GO:000004513 | Esophagus | ESCC | autophagosome assembly | 69/8552 | 99/18723 | 1.10e-06 | 1.38e-05 | 69 |
| GO:00450226 | Esophagus | ESCC | early endosome to late endosome transport | 33/8552 | 40/18723 | 1.80e-06 | 2.11e-05 | 33 |
| GO:190211514 | Esophagus | ESCC | regulation of organelle assembly | 116/8552 | 186/18723 | 3.15e-06 | 3.53e-05 | 116 |
| GO:004311218 | Esophagus | ESCC | receptor metabolic process | 104/8552 | 166/18723 | 7.44e-06 | 7.37e-05 | 104 |
| GO:000689818 | Esophagus | ESCC | receptor-mediated endocytosis | 142/8552 | 244/18723 | 5.22e-05 | 4.05e-04 | 142 |
| GO:003969411 | Esophagus | ESCC | viral RNA genome replication | 27/8552 | 35/18723 | 1.48e-04 | 9.88e-04 | 27 |
| GO:006049118 | Esophagus | ESCC | regulation of cell projection assembly | 110/8552 | 188/18723 | 2.60e-04 | 1.58e-03 | 110 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05014210 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa05132211 | Esophagus | ESCC | Salmonella infection | 191/4205 | 249/8465 | 6.51e-19 | 5.45e-17 | 2.79e-17 | 191 |
| hsa04144210 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
| hsa05022210 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
| hsa0414530 | Esophagus | ESCC | Phagosome | 100/4205 | 152/8465 | 3.81e-05 | 1.72e-04 | 8.82e-05 | 100 |
| hsa0496223 | Esophagus | ESCC | Vasopressin-regulated water reabsorption | 33/4205 | 44/8465 | 5.27e-04 | 1.78e-03 | 9.13e-04 | 33 |
| hsa051527 | Esophagus | ESCC | Tuberculosis | 111/4205 | 180/8465 | 7.14e-04 | 2.32e-03 | 1.19e-03 | 111 |
| hsa0501438 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa05132310 | Esophagus | ESCC | Salmonella infection | 191/4205 | 249/8465 | 6.51e-19 | 5.45e-17 | 2.79e-17 | 191 |
| hsa0414437 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
| hsa0502238 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
| hsa04145114 | Esophagus | ESCC | Phagosome | 100/4205 | 152/8465 | 3.81e-05 | 1.72e-04 | 8.82e-05 | 100 |
| hsa0496233 | Esophagus | ESCC | Vasopressin-regulated water reabsorption | 33/4205 | 44/8465 | 5.27e-04 | 1.78e-03 | 9.13e-04 | 33 |
| hsa0515212 | Esophagus | ESCC | Tuberculosis | 111/4205 | 180/8465 | 7.14e-04 | 2.32e-03 | 1.19e-03 | 111 |
| hsa0501414 | Liver | Cirrhotic | Amyotrophic lateral sclerosis | 187/2530 | 364/8465 | 1.56e-18 | 6.50e-17 | 4.01e-17 | 187 |
| hsa0502214 | Liver | Cirrhotic | Pathways of neurodegeneration - multiple diseases | 217/2530 | 476/8465 | 7.30e-14 | 2.03e-12 | 1.25e-12 | 217 |
| hsa0513222 | Liver | Cirrhotic | Salmonella infection | 121/2530 | 249/8465 | 2.47e-10 | 5.13e-09 | 3.16e-09 | 121 |
| hsa0414412 | Liver | Cirrhotic | Endocytosis | 119/2530 | 251/8465 | 2.33e-09 | 4.56e-08 | 2.81e-08 | 119 |
| hsa0414514 | Liver | Cirrhotic | Phagosome | 73/2530 | 152/8465 | 1.61e-06 | 1.78e-05 | 1.10e-05 | 73 |
| hsa0501415 | Liver | Cirrhotic | Amyotrophic lateral sclerosis | 187/2530 | 364/8465 | 1.56e-18 | 6.50e-17 | 4.01e-17 | 187 |
| Page: 1 2 3 4 |
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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 |
| RAB5A | SNV | Missense_Mutation | c.404N>T | p.Ala135Val | p.A135V | P20339 | protein_coding | tolerated(0.17) | benign(0.114) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RAB5A | SNV | Missense_Mutation | c.418N>G | p.Lys140Glu | p.K140E | P20339 | protein_coding | tolerated(0.18) | benign(0.006) | TCGA-D5-6932-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| RAB5A | SNV | Missense_Mutation | c.339N>A | p.Asn113Lys | p.N113K | P20339 | protein_coding | tolerated(0.84) | benign(0.009) | TCGA-G4-6304-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | PD | |
| RAB5A | SNV | Missense_Mutation | novel | c.268N>A | p.Tyr90Asn | p.Y90N | P20339 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-DY-A1DG-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| RAB5A | SNV | Missense_Mutation | c.339N>A | p.Asn113Lys | p.N113K | P20339 | protein_coding | tolerated(0.84) | benign(0.009) | TCGA-EI-6882-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| RAB5A | SNV | Missense_Mutation | rs144198452 | c.16N>A | p.Ala6Thr | p.A6T | P20339 | protein_coding | tolerated(0.29) | benign(0.003) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| RAB5A | SNV | Missense_Mutation | c.101N>T | p.Ser34Leu | p.S34L | P20339 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RAB5A | SNV | Missense_Mutation | novel | c.73N>A | p.Leu25Ile | p.L25I | P20339 | protein_coding | deleterious(0.02) | possibly_damaging(0.725) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RAB5A | SNV | Missense_Mutation | novel | c.73C>A | p.Leu25Ile | p.L25I | P20339 | protein_coding | deleterious(0.02) | possibly_damaging(0.725) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| RAB5A | SNV | Missense_Mutation | rs749601586 | c.406G>A | p.Asp136Asn | p.D136N | P20339 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| 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 |
| 5868 | RAB5A | NA | HGF | 16423831 |
| Page: 1 |
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