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Gene: RAB38 |
Gene summary for RAB38 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RAB38 | Gene ID | 23682 |
| Gene name | RAB38, member RAS oncogene family | |
| Gene Alias | NY-MEL-1 | |
| Cytomap | 11q14.2 | |
| Gene Type | protein-coding | GO ID | GO:0006629 | UniProtAcc | A0A024R191 |
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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 |
| 23682 | RAB38 | Tumor | Human | Cervix | CC | 3.99e-52 | 8.88e-01 | 0.1241 |
| 23682 | RAB38 | sample3 | Human | Cervix | CC | 1.68e-50 | 7.90e-01 | 0.1387 |
| 23682 | RAB38 | T3 | Human | Cervix | CC | 1.76e-48 | 8.21e-01 | 0.1389 |
| 23682 | RAB38 | LZE2T | Human | Esophagus | ESCC | 1.97e-03 | 3.91e-01 | 0.082 |
| 23682 | RAB38 | LZE4T | Human | Esophagus | ESCC | 5.62e-13 | 4.15e-01 | 0.0811 |
| 23682 | RAB38 | LZE8T | Human | Esophagus | ESCC | 8.90e-05 | 3.87e-01 | 0.067 |
| 23682 | RAB38 | LZE20T | Human | Esophagus | ESCC | 1.85e-09 | 1.96e-01 | 0.0662 |
| 23682 | RAB38 | LZE24T | Human | Esophagus | ESCC | 4.40e-06 | 2.36e-01 | 0.0596 |
| 23682 | RAB38 | LZE6T | Human | Esophagus | ESCC | 7.52e-03 | 3.90e-01 | 0.0845 |
| 23682 | RAB38 | P1T-E | Human | Esophagus | ESCC | 1.74e-08 | 4.04e-01 | 0.0875 |
| 23682 | RAB38 | P2T-E | Human | Esophagus | ESCC | 2.38e-10 | 2.70e-01 | 0.1177 |
| 23682 | RAB38 | P4T-E | Human | Esophagus | ESCC | 8.15e-33 | 9.91e-01 | 0.1323 |
| 23682 | RAB38 | P5T-E | Human | Esophagus | ESCC | 2.27e-32 | 7.92e-01 | 0.1327 |
| 23682 | RAB38 | P8T-E | Human | Esophagus | ESCC | 1.26e-08 | 3.00e-01 | 0.0889 |
| 23682 | RAB38 | P9T-E | Human | Esophagus | ESCC | 3.14e-32 | 8.52e-01 | 0.1131 |
| 23682 | RAB38 | P10T-E | Human | Esophagus | ESCC | 2.42e-06 | 1.33e-01 | 0.116 |
| 23682 | RAB38 | P11T-E | Human | Esophagus | ESCC | 3.16e-17 | 1.11e+00 | 0.1426 |
| 23682 | RAB38 | P12T-E | Human | Esophagus | ESCC | 1.82e-07 | 2.87e-01 | 0.1122 |
| 23682 | RAB38 | P15T-E | Human | Esophagus | ESCC | 1.52e-13 | 3.16e-01 | 0.1149 |
| 23682 | RAB38 | P16T-E | Human | Esophagus | ESCC | 2.37e-16 | 4.17e-01 | 0.1153 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| 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 |
| ∗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:00160506 | Cervix | CC | vesicle organization | 54/2311 | 300/18723 | 2.71e-03 | 1.85e-02 | 54 |
| GO:001605014 | Esophagus | ESCC | vesicle organization | 211/8552 | 300/18723 | 2.85e-18 | 2.87e-16 | 211 |
| GO:00086544 | Esophagus | ESCC | phospholipid biosynthetic process | 162/8552 | 253/18723 | 2.59e-09 | 5.73e-08 | 162 |
| GO:00464744 | Esophagus | ESCC | glycerophospholipid biosynthetic process | 135/8552 | 211/18723 | 5.75e-08 | 1.02e-06 | 135 |
| GO:00450175 | Esophagus | ESCC | glycerolipid biosynthetic process | 154/8552 | 252/18723 | 5.20e-07 | 6.96e-06 | 154 |
| GO:00066446 | Esophagus | ESCC | phospholipid metabolic process | 218/8552 | 383/18723 | 5.37e-06 | 5.59e-05 | 218 |
| GO:00330593 | Esophagus | ESCC | cellular pigmentation | 40/8552 | 53/18723 | 9.67e-06 | 9.21e-05 | 40 |
| GO:00066561 | Esophagus | ESCC | phosphatidylcholine biosynthetic process | 24/8552 | 29/18723 | 4.50e-05 | 3.55e-04 | 24 |
| GO:00066505 | Esophagus | ESCC | glycerophospholipid metabolic process | 174/8552 | 306/18723 | 4.92e-05 | 3.85e-04 | 174 |
| GO:00487531 | Esophagus | ESCC | pigment granule organization | 23/8552 | 29/18723 | 2.25e-04 | 1.40e-03 | 23 |
| GO:00324381 | Esophagus | ESCC | melanosome organization | 22/8552 | 28/18723 | 3.95e-04 | 2.26e-03 | 22 |
| GO:00464864 | Esophagus | ESCC | glycerolipid metabolic process | 211/8552 | 392/18723 | 6.51e-04 | 3.46e-03 | 211 |
| GO:00514521 | Esophagus | ESCC | intracellular pH reduction | 29/8552 | 42/18723 | 1.87e-03 | 8.46e-03 | 29 |
| GO:0090382 | Esophagus | ESCC | phagosome maturation | 19/8552 | 25/18723 | 2.03e-03 | 9.08e-03 | 19 |
| GO:00458511 | Esophagus | ESCC | pH reduction | 31/8552 | 46/18723 | 2.42e-03 | 1.06e-02 | 31 |
| GO:00434731 | Esophagus | ESCC | pigmentation | 59/8552 | 98/18723 | 2.64e-03 | 1.12e-02 | 59 |
| GO:0035646 | Esophagus | ESCC | endosome to melanosome transport | 9/8552 | 10/18723 | 5.09e-03 | 1.92e-02 | 9 |
| GO:0043485 | Esophagus | ESCC | endosome to pigment granule transport | 9/8552 | 10/18723 | 5.09e-03 | 1.92e-02 | 9 |
| GO:0048757 | Esophagus | ESCC | pigment granule maturation | 9/8552 | 10/18723 | 5.09e-03 | 1.92e-02 | 9 |
| GO:01501724 | Esophagus | ESCC | regulation of phosphatidylcholine metabolic process | 9/8552 | 10/18723 | 5.09e-03 | 1.92e-02 | 9 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| RAB38 | SNV | Missense_Mutation | novel | c.118N>T | p.Ala40Ser | p.A40S | P57729 | protein_coding | tolerated(0.27) | possibly_damaging(0.859) | TCGA-A7-A0DB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| RAB38 | SNV | Missense_Mutation | c.8N>T | p.Ala3Val | p.A3V | P57729 | protein_coding | tolerated(0.15) | benign(0.02) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| RAB38 | SNV | Missense_Mutation | c.149N>A | p.Val50Glu | p.V50E | P57729 | protein_coding | deleterious(0.03) | probably_damaging(0.98) | TCGA-BH-A1FM-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| RAB38 | insertion | Frame_Shift_Ins | novel | c.66_67insGAGCAATTTAACTCCC | p.Thr23GlufsTer82 | p.T23Efs*82 | P57729 | protein_coding | TCGA-AN-A0FV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| RAB38 | SNV | Missense_Mutation | novel | c.548N>G | p.Asp183Gly | p.D183G | P57729 | protein_coding | tolerated(0.21) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RAB38 | SNV | Missense_Mutation | c.272A>T | p.Asp91Val | p.D91V | P57729 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-A02R-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RAB38 | SNV | Missense_Mutation | rs765696305 | c.313N>G | p.Lys105Glu | p.K105E | P57729 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RAB38 | SNV | Missense_Mutation | rs777409146 | c.505N>A | p.Ala169Thr | p.A169T | P57729 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| RAB38 | SNV | Missense_Mutation | novel | c.483N>T | p.Lys161Asn | p.K161N | P57729 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
| RAB38 | SNV | Missense_Mutation | novel | c.230G>A | p.Arg77Lys | p.R77K | P57729 | protein_coding | deleterious(0) | probably_damaging(0.919) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | 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 |
| Page: 1 |
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