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 SREBF2
Basic gene info.Gene symbolSREBF2
Gene namesterol regulatory element binding transcription factor 2
SynonymsSREBP-2|SREBP2|bHLHd2
CytomapUCSC genome browser: 22q13
Genomic locationchr22 :42229105-42302375
Type of geneprotein-coding
RefGenesNM_004599.3,
NR_103834.1,
Ensembl idENSG00000198911
Descriptionclass D basic helix-loop-helix protein 2sterol regulatory element-binding protein 2sterol regulatory element-binding transcription factor 2
Modification date20141207
dbXrefs MIM : 600481
HGNC : HGNC
Ensembl : ENSG00000198911
HPRD : 02726
Vega : OTTHUMG00000151261
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SREBF2
BioGPS: 6721
Gene Expression Atlas: ENSG00000198911
The Human Protein Atlas: ENSG00000198911
PathwayNCI Pathway Interaction Database: SREBF2
KEGG: SREBF2
REACTOME: SREBF2
ConsensusPathDB
Pathway Commons: SREBF2
MetabolismMetaCyc: SREBF2
HUMANCyc: SREBF2
RegulationEnsembl's Regulation: ENSG00000198911
miRBase: chr22 :42,229,105-42,302,375
TargetScan: NM_004599
cisRED: ENSG00000198911
ContextiHOP: SREBF2
cancer metabolism search in PubMed: SREBF2
UCL Cancer Institute: SREBF2
Assigned class in ccmGDBC

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Phenotypic Information for SREBF2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SREBF2
Familial Cancer Database: SREBF2
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SREBF2
MedGen: SREBF2 (Human Medical Genetics with Condition)
ClinVar: SREBF2
PhenotypeMGI: SREBF2 (International Mouse Phenotyping Consortium)
PhenomicDB: SREBF2

Mutations for SREBF2
* 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
breastSREBF2chr224225580142255801SREBF2chr224225737242257372
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 SREBF2 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 1  2   
GAIN (# sample)        1    2   
LOSS (# sample)          1      
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=69)
Stat. for Synonymous SNVs
(# total SNVs=29)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=2)

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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
chr22:42262990-42262990p.G82*3
chr22:42269825-42269825p.T297T3
chr22:42293097-42293097p.S846C2
chr22:42263110-42263110p.P122S2
chr22:42293157-42293158p.S866F2
chr22:42262862-42262862p.V39G2
chr22:42299055-42299055p.V997L2
chr22:42262864-42262864p.G40R2
chr22:42263037-42263037p.L97L2
chr22:42264766-42264766p.T230T2

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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
# sample33 171 3 4 1332 1158115
# mutation33 151 3 4 1332 1159121
nonsynonymous SNV33 61 3 3 1221 167115
synonymous SNV   9    1  111  92 6
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
chr22:42269825p.T297T3
chr22:42263110p.S69G2
chr22:42263193p.F834F2
chr22:42262951p.L97L2
chr22:42293062p.P122S2
chr22:42269956p.R341Q2
chr22:42263037p.T149T2
chr22:42262839p.S752C1
chr22:42269974p.R1060Q1
chr22:42289166p.M31I1

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 SREBF2 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 SREBF2

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

ACO2,EIF4ENIF1,EP300,ST13P4,GTPBP1,L3MBTL2,MAPK1,
MTMR3,NUP50,PACSIN2,PEX26,POLDIP3,MIEF1,SREBF2,
ST13,TCF20,TMEM184B,TNRC6B,XPNPEP3,XRCC6,ZC3H7B
CAD,CD3EAP,CDC42BPG,CELSR2,CGNL1,CHERP,DDR1,
FNDC8,GGT6,GLB1L2,GNG7,KIAA1324,KIAA1522,LIG1,
MYBBP1A,LINC00086,PIGO,PTK7,SIPA1L3,SREBF2,TTC22

ACO2,BRD1,PRR14L,CARD10,DGCR2,DHCR24,FASN,
GRAMD4,GTPBP1,HIRA,KIAA1671,PACSIN2,PEX26,PI4KA,
SBF1,SH3BP1,MIEF1,SREBF2,TCF20,ZBED4,ZC3H7B
PRR14L,CLIP2,EDC4,IGF2R,KIF13B,MAVS,MINK1,
MYH9,MYO18A,PIK3C2B,PLCE1,PLEKHA6,PLEKHM1,PTPRF,
RREB1,SCAP,SIPA1L3,SLC44A2,SLC9A1,SREBF2,TMEM131
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 SREBF2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00363sterol regulatory element binding transcription factor 2approvedClozapine
DB00502sterol regulatory element binding transcription factor 2approvedHaloperidol


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Cross referenced IDs for SREBF2
* 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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