|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: RABGEF1 |
Gene summary for RABGEF1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RABGEF1 | Gene ID | 27342 |
| Gene name | RAB guanine nucleotide exchange factor 1 | |
| Gene Alias | RABEX5 | |
| Cytomap | 7q11.21 | |
| Gene Type | protein-coding | GO ID | GO:0006605 | UniProtAcc | A0A0A0MSJ3 |
Top |
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 |
| 27342 | RABGEF1 | AEH-subject1 | Human | Endometrium | AEH | 6.36e-40 | 7.53e-01 | -0.3059 |
| 27342 | RABGEF1 | AEH-subject2 | Human | Endometrium | AEH | 1.13e-10 | 3.78e-01 | -0.2525 |
| 27342 | RABGEF1 | AEH-subject3 | Human | Endometrium | AEH | 9.15e-21 | 5.50e-01 | -0.2576 |
| 27342 | RABGEF1 | AEH-subject4 | Human | Endometrium | AEH | 2.54e-15 | 4.97e-01 | -0.2657 |
| 27342 | RABGEF1 | AEH-subject5 | Human | Endometrium | AEH | 2.24e-18 | 4.82e-01 | -0.2953 |
| 27342 | RABGEF1 | EEC-subject1 | Human | Endometrium | EEC | 1.16e-39 | 8.05e-01 | -0.2682 |
| 27342 | RABGEF1 | EEC-subject2 | Human | Endometrium | EEC | 5.24e-17 | 4.65e-01 | -0.2607 |
| 27342 | RABGEF1 | EEC-subject3 | Human | Endometrium | EEC | 1.68e-13 | 4.65e-01 | -0.2525 |
| 27342 | RABGEF1 | EEC-subject4 | Human | Endometrium | EEC | 5.56e-13 | 3.54e-01 | -0.2571 |
| 27342 | RABGEF1 | EEC-subject5 | Human | Endometrium | EEC | 2.09e-20 | 4.70e-01 | -0.249 |
| 27342 | RABGEF1 | GSM5276934 | Human | Endometrium | EEC | 7.45e-03 | 1.77e-01 | -0.0913 |
| 27342 | RABGEF1 | LZE2T | Human | Esophagus | ESCC | 1.46e-04 | 6.58e-01 | 0.082 |
| 27342 | RABGEF1 | LZE4T | Human | Esophagus | ESCC | 4.42e-09 | 2.62e-01 | 0.0811 |
| 27342 | RABGEF1 | LZE7T | Human | Esophagus | ESCC | 4.89e-03 | 2.12e-01 | 0.0667 |
| 27342 | RABGEF1 | LZE8T | Human | Esophagus | ESCC | 9.94e-08 | 2.07e-01 | 0.067 |
| 27342 | RABGEF1 | LZE20T | Human | Esophagus | ESCC | 5.55e-05 | 1.60e-01 | 0.0662 |
| 27342 | RABGEF1 | LZE22T | Human | Esophagus | ESCC | 4.09e-03 | 3.25e-01 | 0.068 |
| 27342 | RABGEF1 | LZE24T | Human | Esophagus | ESCC | 1.01e-13 | 3.72e-01 | 0.0596 |
| 27342 | RABGEF1 | LZE21T | Human | Esophagus | ESCC | 1.47e-02 | 1.69e-01 | 0.0655 |
| 27342 | RABGEF1 | LZE6T | Human | Esophagus | ESCC | 1.72e-03 | 1.98e-01 | 0.0845 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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. |
Top |
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:000660516 | Endometrium | AEH | protein targeting | 68/2100 | 314/18723 | 6.30e-08 | 3.38e-06 | 68 |
| GO:009015010 | Endometrium | AEH | establishment of protein localization to membrane | 51/2100 | 260/18723 | 4.74e-05 | 7.85e-04 | 51 |
| GO:000660517 | Endometrium | EEC | protein targeting | 69/2168 | 314/18723 | 9.61e-08 | 4.69e-06 | 69 |
| GO:009015015 | Endometrium | EEC | establishment of protein localization to membrane | 52/2168 | 260/18723 | 5.46e-05 | 8.64e-04 | 52 |
| GO:0006605111 | Esophagus | ESCC | protein targeting | 229/8552 | 314/18723 | 4.93e-23 | 1.01e-20 | 229 |
| GO:0090150110 | Esophagus | ESCC | establishment of protein localization to membrane | 182/8552 | 260/18723 | 1.27e-15 | 8.19e-14 | 182 |
| GO:00066124 | Esophagus | ESCC | protein targeting to membrane | 83/8552 | 131/18723 | 3.31e-05 | 2.73e-04 | 83 |
| GO:000660512 | Liver | HCC | protein targeting | 219/7958 | 314/18723 | 7.74e-23 | 1.49e-20 | 219 |
| GO:009015012 | Liver | HCC | establishment of protein localization to membrane | 168/7958 | 260/18723 | 4.07e-13 | 2.13e-11 | 168 |
| GO:00066121 | Liver | HCC | protein targeting to membrane | 75/7958 | 131/18723 | 4.58e-04 | 3.04e-03 | 75 |
| GO:00066058 | Lung | IAC | protein targeting | 51/2061 | 314/18723 | 2.91e-03 | 2.61e-02 | 51 |
| GO:00901508 | Lung | IAC | establishment of protein localization to membrane | 43/2061 | 260/18723 | 4.25e-03 | 3.39e-02 | 43 |
| GO:000660513 | Lung | AIS | protein targeting | 49/1849 | 314/18723 | 8.56e-04 | 1.17e-02 | 49 |
| GO:009015013 | Lung | AIS | establishment of protein localization to membrane | 42/1849 | 260/18723 | 9.73e-04 | 1.28e-02 | 42 |
| GO:000660518 | Prostate | BPH | protein targeting | 102/3107 | 314/18723 | 2.51e-12 | 2.05e-10 | 102 |
| GO:009015016 | Prostate | BPH | establishment of protein localization to membrane | 77/3107 | 260/18723 | 1.06e-07 | 2.56e-06 | 77 |
| GO:000660519 | Prostate | Tumor | protein targeting | 109/3246 | 314/18723 | 6.11e-14 | 7.30e-12 | 109 |
| GO:009015017 | Prostate | Tumor | establishment of protein localization to membrane | 77/3246 | 260/18723 | 6.46e-07 | 1.33e-05 | 77 |
| GO:000660526 | Skin | AK | protein targeting | 53/1910 | 314/18723 | 1.67e-04 | 1.94e-03 | 53 |
| GO:009015023 | Skin | AK | establishment of protein localization to membrane | 45/1910 | 260/18723 | 2.84e-04 | 2.99e-03 | 45 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| RABGEF1 | SNV | Missense_Mutation | rs770537510 | c.854N>T | p.Ala285Val | p.A285V | Q9UJ41 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-A7-A6VV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | CR |
| RABGEF1 | SNV | Missense_Mutation | rs749603235 | c.1402N>A | p.Glu468Lys | p.E468K | Q9UJ41 | protein_coding | tolerated(0.13) | benign(0.085) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| RABGEF1 | SNV | Missense_Mutation | novel | c.232N>A | p.Glu78Lys | p.E78K | Q9UJ41 | protein_coding | deleterious(0.02) | possibly_damaging(0.679) | TCGA-AC-A3W6-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| RABGEF1 | SNV | Missense_Mutation | c.329G>A | p.Arg110His | p.R110H | Q9UJ41 | protein_coding | tolerated(0.1) | possibly_damaging(0.517) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| RABGEF1 | SNV | Missense_Mutation | novel | c.886C>T | p.Arg296Cys | p.R296C | Q9UJ41 | protein_coding | deleterious(0.02) | benign(0.251) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RABGEF1 | SNV | Missense_Mutation | c.580N>C | p.Glu194Gln | p.E194Q | Q9UJ41 | protein_coding | tolerated(0.06) | benign(0.365) | TCGA-FU-A23L-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| RABGEF1 | SNV | Missense_Mutation | c.329N>A | p.Arg110His | p.R110H | Q9UJ41 | protein_coding | tolerated(0.1) | possibly_damaging(0.517) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| RABGEF1 | SNV | Missense_Mutation | rs756436887 | c.1061N>A | p.Arg354His | p.R354H | Q9UJ41 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| RABGEF1 | SNV | Missense_Mutation | c.1288C>A | p.Leu430Ile | p.L430I | Q9UJ41 | protein_coding | tolerated(0.17) | benign(0.104) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| RABGEF1 | SNV | Missense_Mutation | c.1319N>T | p.Arg440Met | p.R440M | Q9UJ41 | protein_coding | deleterious(0.01) | possibly_damaging(0.619) | TCGA-AZ-4615-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | xeloda | PD |
| Page: 1 2 3 4 5 6 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |