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 SREBF1
Basic gene info.Gene symbolSREBF1
Gene namesterol regulatory element binding transcription factor 1
SynonymsSREBP-1c|SREBP1|bHLHd1
CytomapUCSC genome browser: 17p11.2
Genomic locationchr17 :17714662-17740325
Type of geneprotein-coding
RefGenesNM_001005291.2,
NM_004176.4,
Ensembl idENSG00000072310
DescriptionSREBP-1class D basic helix-loop-helix protein 1sterol regulatory element-binding protein 1
Modification date20141222
dbXrefs MIM : 184756
HGNC : HGNC
Ensembl : ENSG00000072310
HPRD : 01701
Vega : OTTHUMG00000059313
ProteinUniProt: P36956
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SREBF1
BioGPS: 6720
Gene Expression Atlas: ENSG00000072310
The Human Protein Atlas: ENSG00000072310
PathwayNCI Pathway Interaction Database: SREBF1
KEGG: SREBF1
REACTOME: SREBF1
ConsensusPathDB
Pathway Commons: SREBF1
MetabolismMetaCyc: SREBF1
HUMANCyc: SREBF1
RegulationEnsembl's Regulation: ENSG00000072310
miRBase: chr17 :17,714,662-17,740,325
TargetScan: NM_001005291
cisRED: ENSG00000072310
ContextiHOP: SREBF1
cancer metabolism search in PubMed: SREBF1
UCL Cancer Institute: SREBF1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SREBF1 in cancer cell metabolism1. Luckert C, Hessel S, Lenze D, Lampen A (2015) Disturbance of gene expression in primary human hepatocytes by hepatotoxic pyrrolizidine alkaloids: A whole genome transcriptome analysis. Toxicology in Vitro 29: 1669-1682. go to article

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Phenotypic Information for SREBF1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SREBF1
Familial Cancer Database: SREBF1
* 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 184756; gene.
184756; gene.
Orphanet
DiseaseKEGG Disease: SREBF1
MedGen: SREBF1 (Human Medical Genetics with Condition)
ClinVar: SREBF1
PhenotypeMGI: SREBF1 (International Mouse Phenotyping Consortium)
PhenomicDB: SREBF1

Mutations for SREBF1
* 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
haematopoietic_and_lymphoid_tissueSREBF1chr171773439417734394chr5177610246177610246
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 SREBF1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG009780SREBF114135171772242617722547C12orf10135258125369681753696940
BM975798RAI112360171771466317721040SREBF1360468171772041217720639
DA092279UBE2E313852181881546181881928SREBF1381499171772291117723029

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 # sample1             1  
GAIN (# sample)1             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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=55)
Stat. for Synonymous SNVs
(# total SNVs=16)
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
chr17:17723785-17723785p.D78Y3
chr17:17721595-17721595p.R418C2
chr17:17726899-17726899p.G38G2
chr17:17717999-17717999p.R919W2
chr17:17721038-17721038p.P489H2
chr17:17719517-17719517p.?2
chr17:17722901-17722901p.T251M2
chr17:17719811-17719811p.A699A2
chr17:17719818-17719818p.R697Q2
chr17:17717044-17717044p.R1011C2

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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
# sample41281 3 32 431  81313
# mutation41391 3 32 431  81413
nonsynonymous SNV41281 2 12 331  5913
synonymous SNV  11  1 2  1    35  
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
chr17:17721595p.R388C,SREBF12
chr17:17719921p.G58D,SREBF11
chr17:17723446p.V795L,SREBF11
chr17:17721064p.G454D,SREBF11
chr17:17718242p.S312G,SREBF11
chr17:17722368p.S778S,SREBF11
chr17:17719999p.S450S,SREBF11
chr17:17723486p.S231L,SREBF11
chr17:17716007p.R1125G,SREBF11
chr17:17721087p.A759A,SREBF11

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 SREBF1 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 SREBF1

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

ABCA3,APEH,ATPAF2,LINC00263,CYB561D2,DALRD3,FASN,
IVD,MFSD7,MYO1C,NPRL2,P4HTM,RAI1,RTN4RL1,
SCD,MIEF2,SREBF1,TMEM25,TNK1,TOM1L2,TTC36
ACAT2,ARHGEF16,CTNNBIP1,CYB561,CYB561D2,EBP,FDPS,
FIBCD1,G6PD,GMPPB,IGSF8,IVD,MMAB,MVD,
MVK,NUDT8,PEX10,REEP6,SREBF1,TMEM63B,TOLLIP

ATP5A1,CDC42EP1,COX10,CTDNEP1,ELAC2,FLII,GEMIN4,
CLUH,LPIN1,MINK1,PCSK9,RAI1,RNMTL1,SCO1,
SREBF1,TMEM102,TNFSF13,TNK1,TRIM16,USP43,WRAP53
ACLY,ALDH16A1,CDC42BPB,CDRT15P1,DAZAP1,DDX54,DOT1L,
EVPL,HTT,KLF16,TONSL,NUDT16,PCLO,PCSK5,
PHRF1,PTGER1,SLC38A10,SMAD6,SREBF1,TTLL4,ZNF598
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 SREBF1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA335; -.
Organism-specific databasesPharmGKB PA335; -.
Organism-specific databasesCTD 6720; -.
Organism-specific databasesCTD 6720; -.

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 1approvedClozapine
DB00502sterol regulatory element binding transcription factor 1approvedHaloperidol
DB00755sterol regulatory element binding transcription factor 1approved; nutraceutical; investigationalTretinoin
DB00331sterol regulatory element binding transcription factor 1approvedMetformin
DB01076sterol regulatory element binding transcription factor 1approvedAtorvastatin
DB01095sterol regulatory element binding transcription factor 1approvedFluvastatin
DB00227sterol regulatory element binding transcription factor 1approved; investigationalLovastatin
DB00175sterol regulatory element binding transcription factor 1approvedPravastatin
DB01098sterol regulatory element binding transcription factor 1approvedRosuvastatin
DB00641sterol regulatory element binding transcription factor 1approvedSimvastatin


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Cross referenced IDs for SREBF1
* 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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