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Gene: RAB12 |
Gene summary for RAB12 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RAB12 | Gene ID | 201475 |
| Gene name | RAB12, member RAS oncogene family | |
| Gene Alias | RAB12 | |
| Cytomap | 18p11.22 | |
| Gene Type | protein-coding | GO ID | GO:0006807 | UniProtAcc | Q6IQ22 |
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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 |
| 201475 | RAB12 | CA_HPV_3 | Human | Cervix | CC | 1.31e-04 | 9.49e-02 | 0.0414 |
| 201475 | RAB12 | CCI_2 | Human | Cervix | CC | 2.50e-04 | 5.80e-01 | 0.5249 |
| 201475 | RAB12 | CCI_3 | Human | Cervix | CC | 6.94e-05 | 5.23e-01 | 0.516 |
| 201475 | RAB12 | HCC1_Meng | Human | Liver | HCC | 3.24e-11 | -5.07e-02 | 0.0246 |
| 201475 | RAB12 | HCC1 | Human | Liver | HCC | 5.93e-03 | 2.15e+00 | 0.5336 |
| 201475 | RAB12 | HCC2 | Human | Liver | HCC | 8.44e-03 | 2.00e+00 | 0.5341 |
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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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:007265910 | Cervix | CC | protein localization to plasma membrane | 73/2311 | 284/18723 | 4.95e-10 | 6.73e-08 | 73 |
| GO:00072656 | Cervix | CC | Ras protein signal transduction | 79/2311 | 337/18723 | 9.49e-09 | 7.77e-07 | 79 |
| GO:19907788 | Cervix | CC | protein localization to cell periphery | 78/2311 | 333/18723 | 1.22e-08 | 9.73e-07 | 78 |
| GO:19016538 | Cervix | CC | cellular response to peptide | 72/2311 | 359/18723 | 1.89e-05 | 3.48e-04 | 72 |
| GO:00434349 | Cervix | CC | response to peptide hormone | 77/2311 | 414/18723 | 1.40e-04 | 1.70e-03 | 77 |
| GO:00713757 | Cervix | CC | cellular response to peptide hormone stimulus | 57/2311 | 290/18723 | 2.32e-04 | 2.59e-03 | 57 |
| GO:00328698 | Cervix | CC | cellular response to insulin stimulus | 42/2311 | 203/18723 | 4.95e-04 | 4.83e-03 | 42 |
| GO:00070347 | Cervix | CC | vacuolar transport | 34/2311 | 157/18723 | 7.03e-04 | 6.40e-03 | 34 |
| GO:00328688 | Cervix | CC | response to insulin | 50/2311 | 264/18723 | 1.28e-03 | 1.02e-02 | 50 |
| GO:00171574 | Cervix | CC | regulation of exocytosis | 39/2311 | 202/18723 | 2.90e-03 | 1.93e-02 | 39 |
| GO:00070416 | Cervix | CC | lysosomal transport | 24/2311 | 114/18723 | 5.81e-03 | 3.33e-02 | 24 |
| GO:00068873 | Cervix | CC | exocytosis | 59/2311 | 352/18723 | 8.74e-03 | 4.48e-02 | 59 |
| GO:003286821 | Liver | HCC | response to insulin | 172/7958 | 264/18723 | 7.14e-14 | 4.23e-12 | 172 |
| GO:003286921 | Liver | HCC | cellular response to insulin stimulus | 137/7958 | 203/18723 | 4.69e-13 | 2.44e-11 | 137 |
| GO:004343422 | Liver | HCC | response to peptide hormone | 247/7958 | 414/18723 | 9.55e-13 | 4.77e-11 | 247 |
| GO:007265921 | Liver | HCC | protein localization to plasma membrane | 177/7958 | 284/18723 | 1.02e-11 | 4.18e-10 | 177 |
| GO:000703421 | Liver | HCC | vacuolar transport | 108/7958 | 157/18723 | 2.22e-11 | 8.69e-10 | 108 |
| GO:007137521 | Liver | HCC | cellular response to peptide hormone stimulus | 179/7958 | 290/18723 | 2.54e-11 | 9.88e-10 | 179 |
| GO:199077821 | Liver | HCC | protein localization to cell periphery | 200/7958 | 333/18723 | 6.07e-11 | 2.23e-09 | 200 |
| GO:190165321 | Liver | HCC | cellular response to peptide | 211/7958 | 359/18723 | 2.86e-10 | 9.63e-09 | 211 |
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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 |
| RAB12 | SNV | Missense_Mutation | c.646G>A | p.Glu216Lys | p.E216K | Q6IQ22 | protein_coding | tolerated(0.06) | probably_damaging(0.98) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RAB12 | SNV | Missense_Mutation | novel | c.308N>C | p.Arg103Thr | p.R103T | Q6IQ22 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-C8-A12T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RAB12 | SNV | Missense_Mutation | novel | c.668N>T | p.Ser223Leu | p.S223L | Q6IQ22 | protein_coding | tolerated(0.08) | probably_damaging(0.978) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RAB12 | SNV | Missense_Mutation | c.697N>C | p.Glu233Gln | p.E233Q | Q6IQ22 | protein_coding | deleterious(0.04) | probably_damaging(0.986) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| RAB12 | SNV | Missense_Mutation | novel | c.668N>T | p.Ser223Leu | p.S223L | Q6IQ22 | protein_coding | tolerated(0.08) | probably_damaging(0.978) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| RAB12 | SNV | Missense_Mutation | novel | c.347N>G | p.Lys116Arg | p.K116R | Q6IQ22 | protein_coding | tolerated(0.73) | benign(0.139) | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RAB12 | SNV | Missense_Mutation | rs184470375 | c.482N>T | p.Thr161Met | p.T161M | Q6IQ22 | protein_coding | tolerated(0.11) | benign(0.006) | TCGA-CM-6162-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | oxaliplatin | SD |
| RAB12 | SNV | Missense_Mutation | novel | c.414G>T | p.Lys138Asn | p.K138N | Q6IQ22 | protein_coding | tolerated(0.15) | possibly_damaging(0.894) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| RAB12 | SNV | Missense_Mutation | novel | c.451C>A | p.Leu151Ile | p.L151I | Q6IQ22 | protein_coding | tolerated(0.22) | possibly_damaging(0.503) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| RAB12 | SNV | Missense_Mutation | c.389T>G | p.Phe130Cys | p.F130C | Q6IQ22 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | 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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