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 STARD4
Basic gene info.Gene symbolSTARD4
Gene nameStAR-related lipid transfer (START) domain containing 4
Synonyms-
CytomapUCSC genome browser: 5q22.1
Genomic locationchr5 :110834021-110848157
Type of geneprotein-coding
RefGenesNM_139164.1,
Ensembl idENSG00000164211
DescriptionSTART domain containing 4 sterol-regulatedSTART domain containing 4, sterol regulatedSTART domain-containing protein 4stAR-related lipid transfer protein 4
Modification date20141207
dbXrefs MIM : 607049
HGNC : HGNC
Ensembl : ENSG00000164211
HPRD : 06133
Vega : OTTHUMG00000128793
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_STARD4
BioGPS: 134429
Gene Expression Atlas: ENSG00000164211
The Human Protein Atlas: ENSG00000164211
PathwayNCI Pathway Interaction Database: STARD4
KEGG: STARD4
REACTOME: STARD4
ConsensusPathDB
Pathway Commons: STARD4
MetabolismMetaCyc: STARD4
HUMANCyc: STARD4
RegulationEnsembl's Regulation: ENSG00000164211
miRBase: chr5 :110,834,021-110,848,157
TargetScan: NM_139164
cisRED: ENSG00000164211
ContextiHOP: STARD4
cancer metabolism search in PubMed: STARD4
UCL Cancer Institute: STARD4
Assigned class in ccmGDBC

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Phenotypic Information for STARD4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: STARD4
Familial Cancer Database: STARD4
* 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: STARD4
MedGen: STARD4 (Human Medical Genetics with Condition)
ClinVar: STARD4
PhenotypeMGI: STARD4 (International Mouse Phenotyping Consortium)
PhenomicDB: STARD4

Mutations for STARD4
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovarySTARD4chr5110842441110842461chr65873815558738175
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 STARD4 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=30)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr5:110835763-110835763p.R147*4
chr5:110835597-110835597p.R202Q3
chr5:110835774-110835774p.P143L2
chr5:110835665-110835665p.G179G2
chr5:110842033-110842033p.G50G2
chr5:110836754-110836754p.E115*2
chr5:110835631-110835631p.A191T2
chr5:110837699-110837699p.S81R1
chr5:110843031-110843031p.K34T1
chr5:110835658-110835658p.P182S1

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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
# sample12141 2 2  132  9  3
# mutation12141 2 2  132  8  3
nonsynonymous SNV1214  2 1  122  7  2
synonymous SNV    1   1   1   1  1
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
chr5:110835597p.R202Q3
chr5:110835665p.G179G2
chr5:110835631p.A191T2
chr5:110843034p.G73G1
chr5:110835662p.M180I1
chr5:110836745p.A55S1
chr5:110843054p.G50G1
chr5:110836762p.R178S1
chr5:110843058p.W41L1
chr5:110835670p.I173V1

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 STARD4 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 STARD4

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

ACSL4,ADAM19,AIM2,ARSB,MB21D1,CCDC102B,CFLAR,
CHST11,DSE,EGFL6,FAS,GLIPR1,HIVEP2,ITGA5,
KCNJ15,LIMS1,RDX,RNF145,ST8SIA4,STARD4,ZEB2
ABCC2,ABCC4,ADD3,C6orf223,CCDC15,HIF1A,HMGCR,
HMGCS1,HPGD,KIAA1919,LONP2,PNLIPRP3,PPAPDC1A,SLC41A2,
SLC5A11,ST6GAL1,STARD4,TARP,TLR7,UGT2B28,ZNF518B

CLINT1,DNAJC22,FAM118B,FDFT1,FEM1C,HMGCR,HMGCS1,
IDI1,KIF2A,MAN2A1,MOB1A,PANK3,PCSK9,PGGT1B,
MSMO1,SEC24A,SLC25A46,SLC31A1,STARD4,TFRC,TMED7
BATF3,C6orf223,CCL2,FDPS,HSD17B7,IDI1,INSIG1,
MMAB,MVK,NSDHL,PAQR9,PLA2G2A,PLA2G3,PPA1,
RARRES1,RDH11,MSMO1,SC5D,STARD4,TEAD4,TMPRSS11F
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 STARD4


There's no related Drug.
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Cross referenced IDs for STARD4
* 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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