TissGeneSummary for RAB38 |
Gene summary |
Basic gene information | Gene symbol | RAB38 |
Gene name | RAB38, member RAS oncogene family | |
Synonyms | NY-MEL-1|rrGTPbp | |
Cytomap | UCSC genome browser: 11q14 | |
Type of gene | protein-coding | |
RefGenes | NM_022337.2, | |
Description | Rab-related GTP-binding proteinmelanoma antigen NY-MEL-1ras-related protein Rab-38 | |
Modification date | 20141207 | |
dbXrefs | MIM : 606281 | |
HGNC : HGNC | ||
Ensembl : ENSG00000123892 | ||
HPRD : 05889 | ||
Vega : OTTHUMG00000167288 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RAB38 | |
BioGPS: 23682 | ||
Pathway | NCI Pathway Interaction Database: RAB38 | |
KEGG: RAB38 | ||
REACTOME: RAB38 | ||
Pathway Commons: RAB38 | ||
Context | iHOP: RAB38 | |
ligand binding site mutation search in PubMed: RAB38 | ||
UCL Cancer Institute: RAB38 | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | TiGER,GTEx | |
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | Skin | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | SKCM | |
Reference showing the relevant tissue of RAB38 | ||
Description by TissGene annotations | Cancer gene Have significant anti-correlated miRNA |
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO term | PubMed ID |
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TissGeneExp for RAB38 |
Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01) |
Gene expressions across normal tissues of GTEx data (GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct) - Here, we shows the matched tissue types only among our 28 cancer types. |
Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
LUSC | 1.904548905 | 0.074433219 | 1.830115686 | 1.00E-10 | 3.78E-10 |
KIRP | 0.719540082 | -0.548672418 | 1.2682125 | 5.24E-08 | 3.40E-07 |
PRAD | -2.563084918 | -1.102788764 | -1.460296154 | 6.61E-12 | 2.28E-10 |
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TissGene-miRNA for RAB38 |
Significantly anti-correlated miRNAs of TissGene across 28 cancer types (Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016) (TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21) (TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16) (Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25)) |
Cancer type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
UCS | hsa-miR-30b-5p | MIMAT0000420 | 0.01 | -0.34 | 56 |
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TissGeneMut for RAB38 |
TissGeneSNV for RAB38 |
nsSNV counts per each loci. Different colors of circles represent different cancer types. Circle size denotes number of samples. (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) * Click on the image to enlarge it in a new window. |
Somatic nucleotide variants of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of mutated samples) The numbers in parentheses are numbers of samples with mutation (nsSNVs). (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.C208F | LUAD | 1 |
p.D167N | UCEC | 1 |
p.E189K | PRAD | 1 |
p.L48R | COAD | 1 |
p.A3D | LUAD | 1 |
p.R71I | LGG | 1 |
p.V193M | UCEC | 1 |
p.A102S | HNSC | 1 |
p.M137K | LUAD | 1 |
p.F46L | BLCA | 1 |
p.I26M | BLCA | 1 |
p.T76M | BLCA | 1 |
p.G207V | GBM | 1 |
p.A40V | PAAD | 1 |
p.Y79H | STAD | 1 |
p.S204G | LUAD | 1 |
p.L112V | UVM | 1 |
p.I26M | LUSC | 1 |
p.G151S | UCS | 1 |
p.T76M | STAD | 1 |
p.K194R | LUSC | 1 |
p.W53* | SARC | 1 |
p.V50E | BRCA | 1 |
p.E70D | BLCA | 1 |
p.T200I | UCS | 1 |
p.P190S | SKCM | 1 |
p.I26T | BLCA | 1 |
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TissGeneCNV for RAB38 |
Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples) (TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16) |
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TissGeneFusions for RAB38 |
Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
Chimerdb3.0 | FusionScan | BRCA | TCGA-C8-A12Q-01A | RAB38-CA10 | In-Frame | chr11:87908350 | chr17:50149753 |
Chimerdb3.0 | FusionScan | ESCA | TCGA-VR-A8EY-01A | RAB38-SCAMP1 | Out-of-Frame | chr11:87882842 | chr5:77684660 |
Chimerdb3.0 | FusionScan | LUAD | TCGA-55-8089-01A | CTSC-RAB38 | In-Frame | chr11:88029300 | chr11:87883123 |
Chimerdb3.0 | FusionScan | LUAD | TCGA-64-1681-01A | CTSC-RAB38 | In-Frame | chr11:88029300 | chr11:87883123 |
Chimerdb3.0 | FusionScan | LUSC | TCGA-52-7622-01A | CTSC-RAB38 | In-Frame | chr11:88029300 | chr11:87883123 |
Chimerdb3.0 | TopHat-Fusion | HNSC | TCGA-CV-7235-01A | CTSC-RAB38 | In-Frame | chr11:88029300 | chr11:87883122 |
Chimerdb3.0 | TopHat-Fusion | HNSC | TCGA-CV-7235-01A | CTSC-RAB38 | In-Frame | chr11:88033697 | chr11:87883122 |
TCGAfusionPortal | PRADA | BRCA | TCGA-C8-A12Q-01A | RAB38-CA10 | In-frame | Chr11:87908351 | Chr17:50149753 |
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TissGeneNet for RAB38 |
Co-expressed gene networks based on protein-protein interaction data (CePIN) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (PINA2 ppi data) |
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TissGeneProg for RAB38 |
Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image to enlarge it in a new window. |
Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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TissGeneClin for RAB38 |
TissGeneDrug for RAB38 |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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TissGeneDisease for RAB38 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0079504 | Hermanski-Pudlak Syndrome | 4 | BeFree |
umls:C0078918 | Albinism, Oculocutaneous | 2 | BeFree |
umls:C0001925 | Albuminuria | 1 | RGD |
umls:C0008525 | Choroideremia | 1 | BeFree |
umls:C0025202 | melanoma | 1 | BeFree |
umls:C0033687 | Proteinuria | 1 | RGD |
umls:C0162835 | Hypopigmentation disorder | 1 | BeFree |
umls:C0338451 | Frontotemporal dementia | 1 | GWASCAT |
umls:C1876214 | ALBINOIDISM, OCULOCUTANEOUS, AUTOSOMAL DOMINANT | 1 | BeFree |