Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for STAB2
Basic gene info.Gene symbolSTAB2
Gene namestabilin 2
SynonymsFEEL2|FELE-2|FELL2|FEX2|HARE
CytomapUCSC genome browser: 12q23.3
Genomic locationchr12 :103981068-104160502
Type of geneprotein-coding
RefGenesNM_017564.9,
Ensembl idENSG00000136011
DescriptionCD44-like precursor FELLFAS1 EGF-like and X-link domain containing adhesion molecule-2fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-2hepatic hyaluronan clearance receptorhyaluronan receptor for endocytosishy
Modification date20141207
dbXrefs MIM : 608561
HGNC : HGNC
Ensembl : ENSG00000136011
HPRD : 10542
Vega : OTTHUMG00000170056
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_STAB2
BioGPS: 55576
Gene Expression Atlas: ENSG00000136011
The Human Protein Atlas: ENSG00000136011
PathwayNCI Pathway Interaction Database: STAB2
KEGG: STAB2
REACTOME: STAB2
ConsensusPathDB
Pathway Commons: STAB2
MetabolismMetaCyc: STAB2
HUMANCyc: STAB2
RegulationEnsembl's Regulation: ENSG00000136011
miRBase: chr12 :103,981,068-104,160,502
TargetScan: NM_017564
cisRED: ENSG00000136011
ContextiHOP: STAB2
cancer metabolism search in PubMed: STAB2
UCL Cancer Institute: STAB2
Assigned class in ccmGDBC

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Phenotypic Information for STAB2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: STAB2
Familial Cancer Database: STAB2
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_HYALURONAN_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: STAB2
MedGen: STAB2 (Human Medical Genetics with Condition)
ClinVar: STAB2
PhenotypeMGI: STAB2 (International Mouse Phenotyping Consortium)
PhenomicDB: STAB2

Mutations for STAB2
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastSTAB2chr12104116524104116524chr12127640816127640816
ovarySTAB2chr12104150505104150525MTSS1chr8125663004125663024
pancreasSTAB2chr12104152953104152973STAB2chr12104156080104156100
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows STAB2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample   1             
GAIN (# sample)   1             
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=12

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=246)
Stat. for Synonymous SNVs
(# total SNVs=114)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr12:104155080-104155080p.T2417T6
chr12:104033936-104033936p.F314F5
chr12:104062457-104062457p.F708V4
chr12:104155079-104155079p.T2417M4
chr12:104118761-104118761p.G1564G3
chr12:104160076-104160076p.R2540W3
chr12:104092978-104092978p.F1229F3
chr12:104129318-104129318p.G1837V3
chr12:104078786-104078786p.S974L3
chr12:104134523-104134523p.R1957Q3

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=13

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample654494 13 8  422812 16825330
# mutation855534 13 8  532912 19536340
nonsynonymous SNV633362 9 6  25198  6328328
synonymous SNV222172 4 2  28104 1328 12
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr12:104155080p.T2417T7
chr12:104155079p.T2417M4
chr12:104077060p.V52A3
chr12:104033936p.T961T3
chr12:103984748p.F314F3
chr12:104118857p.K2508K2
chr12:104048356p.L583I2
chr12:104031812p.D2532N2
chr12:104126850p.F1896F2
chr12:104078786p.G1564D2

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for STAB2 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for STAB2

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

AADAC,MGARP,C7,CYP11A1,CYP17A1,CYP19A1,FSHR,
HPCAL4,HSD11B1,HSD3B1,INSL3,KLHL4,LHCGR,MBOAT4,
MRO,REG3G,STAB2,STAR,TCF21,TCF23,TREML5P
BPIFA4P,C17orf67,C17orf78,TSPEAR,CDH17,DNTT,FCER1A,
GJD3,GPR182,GPR84,KCNIP1,KRTAP12-2,LGSN,MMRN1,
OR4D2,PIM2,PTPRE,SEC14L4,PMEL,SOX21,STAB2

AKT3,ATP8B2,CCDC184,CPE,FLT4,GPR182,TP73-AS1,
MAP3K12,OR1S1,PPFIA2,RELN,RORB,SALL2,SLC22A17,
SLC26A10,SNCA,STAB2,SUSD5,SYNE1,TBX1,THBS3
ABCA2,AQP12B,DGCR2,ECE1,MVB12B,IL4R,KDM4B,
LOC100131193,LOC646627,LRP4,MICAL3,PNPLA7,PTPN21,SCARB1,
SRGAP1,STAB2,STIM1,TNK2,TOM1L2,TSTD2,USP19
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for STAB2


There's no related Drug.
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Cross referenced IDs for STAB2
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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