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 STARD5
Basic gene info.Gene symbolSTARD5
Gene nameStAR-related lipid transfer (START) domain containing 5
Synonyms-
CytomapUCSC genome browser: 15q26
Genomic locationchr15 :81605006-81616524
Type of geneprotein-coding
RefGenesNM_030574.2,
NM_181900.2,
Ensembl idENSG00000172345
DescriptionSTART domain containing 5START domain-containing protein 5stAR-related lipid transfer protein 5
Modification date20141207
dbXrefs MIM : 607050
HGNC : HGNC
HPRD : 09517
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_STARD5
BioGPS: 80765
Gene Expression Atlas: ENSG00000172345
The Human Protein Atlas: ENSG00000172345
PathwayNCI Pathway Interaction Database: STARD5
KEGG: STARD5
REACTOME: STARD5
ConsensusPathDB
Pathway Commons: STARD5
MetabolismMetaCyc: STARD5
HUMANCyc: STARD5
RegulationEnsembl's Regulation: ENSG00000172345
miRBase: chr15 :81,605,006-81,616,524
TargetScan: NM_030574
cisRED: ENSG00000172345
ContextiHOP: STARD5
cancer metabolism search in PubMed: STARD5
UCL Cancer Institute: STARD5
Assigned class in ccmGDBC

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Phenotypic Information for STARD5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: STARD5
Familial Cancer Database: STARD5
* 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: STARD5
MedGen: STARD5 (Human Medical Genetics with Condition)
ClinVar: STARD5
PhenotypeMGI: STARD5 (International Mouse Phenotyping Consortium)
PhenomicDB: STARD5

Mutations for STARD5
* 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
* 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
ovarySTARD5chr158161542881615448TMC3chr158162520181625221
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 STARD5 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=8)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr15:81605711-81605711p.F176F2
chr15:81615245-81615245p.G48G2
chr15:81610812-81610812p.P144P2
chr15:81611670-81611670p.?2
chr15:81611689-81611689p.S131G2
chr15:81605706-81605706p.T178I1
chr15:81611704-81611704p.E126Q1
chr15:81605707-81605707p.T178A1
chr15:81611720-81611720p.V120V1
chr15:81605709-81605709p.H177R1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  6  1    3 1  11 3
# mutation2  7  1    3 1  11 3
nonsynonymous SNV2  3       1        
synonymous SNV   4  1    2 1  11 3
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
chr15:81605711p.F176L2
chr15:81610812p.P144P2
chr15:81605706p.H177R1
chr15:81615284p.P162P1
chr15:81605707p.F159F1
chr15:81616399p.V120V1
chr15:81605709p.D66D1
chr15:81610758p.E62D1
chr15:81610767p.G48G1
chr15:81605606p.F211F1

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 STARD5 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 STARD5

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

ABCD4,FAM212A,CAPNS2,CIRBP,CTDSP1,DEF6,DNAJC17,
ELMOD3,FLT3LG,GLTSCR2,JMJD7-PLA2G4B,KANK3,KRT10,LIME1,
LYL1,MMP28,MXD4,STARD5,SYTL1,TNFRSF14,TNFSF12
ARHGDIB,ATP8B3,B3GNT9,C17orf62,CNPY3,CTSH,EDEM2,
GBA,GBAP1,IFI27L2,MANF,NAGA,PTPN6,RAET1G,
RNASET2,SDF2,SERPINA1,SSR4,STARD5,TIMP1,TMEM91

ABHD3,ACADS,ADH6,BAIAP2L2,GDPGP1,CALML4,CASP7,
CES3,CIB1,COX5A,LGALS4,LPCAT4,LRRIQ4,MARVELD3,
RETSAT,RPS27L,SCAMP2,STARD5,TNFSF13,TP53I3,TSPO
AP1G2,AP1M2,ARHGEF16,HMGN2P46,CLN3,COMMD4,ELMO3,
GALM,LLGL2,MTMR14,MXD3,OGFOD2,PLEKHJ1,RABGGTA,
RAD9A,RASSF7,STARD5,STXBP2,TNFRSF14,TOR2A,TXNDC11
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 STARD5


There's no related Drug.
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Cross referenced IDs for STARD5
* 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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