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 STARD6
Basic gene info.Gene symbolSTARD6
Gene nameStAR-related lipid transfer (START) domain containing 6
Synonyms-
CytomapUCSC genome browser: 18q21.2
Genomic locationchr18 :51851061-51880943
Type of geneprotein-coding
RefGenesNM_139171.1,
Ensembl idENSG00000174448
DescriptionSTART domain containing 6START domain-containing protein 6stAR-related lipid transfer protein 6
Modification date20141207
dbXrefs MIM : 607051
HGNC : HGNC
Ensembl : ENSG00000174448
HPRD : 09518
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_STARD6
BioGPS: 147323
Gene Expression Atlas: ENSG00000174448
The Human Protein Atlas: ENSG00000174448
PathwayNCI Pathway Interaction Database: STARD6
KEGG: STARD6
REACTOME: STARD6
ConsensusPathDB
Pathway Commons: STARD6
MetabolismMetaCyc: STARD6
HUMANCyc: STARD6
RegulationEnsembl's Regulation: ENSG00000174448
miRBase: chr18 :51,851,061-51,880,943
TargetScan: NM_139171
cisRED: ENSG00000174448
ContextiHOP: STARD6
cancer metabolism search in PubMed: STARD6
UCL Cancer Institute: STARD6
Assigned class in ccmGDBC

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Phenotypic Information for STARD6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: STARD6
Familial Cancer Database: STARD6
* 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_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: STARD6
MedGen: STARD6 (Human Medical Genetics with Condition)
ClinVar: STARD6
PhenotypeMGI: STARD6 (International Mouse Phenotyping Consortium)
PhenomicDB: STARD6

Mutations for STARD6
* 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
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 STARD6 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
There's no copy number variation information in COSMIC data for this gene.

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=20)
Stat. for Synonymous SNVs
(# total SNVs=2)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr18:51863496-51863496p.S89L2
chr18:51851219-51851219p.M169T2
chr18:51863577-51863577p.S62Y2
chr18:51851242-51851242p.N161N2
chr18:51855760-51855760p.G146C2
chr18:51858192-51858192p.A102V1
chr18:51851088-51851088p.G213R1
chr18:51863622-51863622p.?1
chr18:51855767-51855767p.Y143*1
chr18:51851121-51851121p.G202R1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   6  1 1  211  106 4
# mutation   5  1 1  211  106 4
nonsynonymous SNV   5  1 1  111  94 4
synonymous SNV   1       1    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
chr18:51863496p.M169T2
chr18:51851219p.L167L2
chr18:51851226p.S89L2
chr18:51851242p.N161K2
chr18:51851088p.F195L1
chr18:51855788p.R109Q1
chr18:51863545p.E185K1
chr18:51851142p.S107S1
chr18:51855808p.S107F1
chr18:51863546p.V168A1

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 STARD6 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 STARD6

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

C18orf54,C1orf94,ADTRP,CCKBR,CD70,DCBLD1,ELOVL4,
FAM19A3,FAM81A,FETUB,H2BFXP,LRRC8D,LINC00092,PCBP4,
RSPO4,SOAT2,STARD6,TLX1NB,TUBB2B,UNC93A,WBSCR28
BCAN,C1QTNF4,C8orf74,CCDC70,DPPA2,FLJ46361,GJA10,
GLT6D1,KCNK4,KRTAP4-2,KRTAP9-4,MGC16703,LINC00029,NTRK3,
OR2T2,OR4A5,OR5F1,OR8H2,OR9G9,PIWIL3,PLA2G1B,
RAB9BP1,SNORA32,STARD6,

ADAM3A,CT47A1,CYP3A4,DKK4,GCG,ITGA2B,KRTAP19-8,
MBD3L1,C7orf62,MOG,MT1F,MT1G,MT1H,MYOZ2,
NKX2-6,NRG1,CFAP221,SNORA14A,STARD6,TMPRSS11BNL,XAGE2
C11orf40,CGB7,HHLA1,HORMAD2,IQCA1,LOC145474,OR11H12,
OR1B1,OR2AK2,PPP3R2,RDH8,SNORA54,SNORA5B,SPINK9,
SSX3,STARD6,TAS2R41,TAS
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 STARD6


There's no related Drug.
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Cross referenced IDs for STARD6
* 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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