Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	SREBF1
	Gene name	sterol regulatory element binding transcription factor 1
	Synonyms	SREBP-1c\|SREBP1\|bHLHd1
	Cytomap	UCSC genome browser: 17p11.2
	Genomic location	chr17 :17714662-17740325
	Type of gene	protein-coding
	RefGenes	NM_001005291.2, NM_004176.4,
	Ensembl id	ENSG00000072310
	Description	SREBP-1class D basic helix-loop-helix protein 1sterol regulatory element-binding protein 1
	Modification date	20141222
dbXrefs	MIM : 184756
	HGNC : HGNC
	Ensembl : ENSG00000072310
	HPRD : 01701
	Vega : OTTHUMG00000059313
Protein	UniProt: P36956 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SREBF1
	BioGPS: 6720
	Gene Expression Atlas: ENSG00000072310
	The Human Protein Atlas: ENSG00000072310
Pathway	NCI Pathway Interaction Database: SREBF1
	KEGG: SREBF1
	REACTOME: SREBF1
	ConsensusPathDB
	Pathway Commons: SREBF1
Metabolism	MetaCyc: SREBF1
	HUMANCyc: SREBF1
Regulation	Ensembl's Regulation: ENSG00000072310
	miRBase: chr17 :17,714,662-17,740,325
	TargetScan: NM_001005291
	cisRED: ENSG00000072310
Context	iHOP: SREBF1
	cancer metabolism search in PubMed: SREBF1
	UCL Cancer Institute: SREBF1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SREBF1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	184756; gene. 184756; gene.
Orphanet
Disease	KEGG Disease: SREBF1
	MedGen: SREBF1 (Human Medical Genetics with Condition)
	ClinVar: SREBF1
Phenotype	MGI: SREBF1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
haematopoietic_and_lymphoid_tissue	SREBF1	chr17	17734394	17734394		chr5	177610246	177610246

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SREBF1 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BG009780	SREBF1	14	135	17	17722426	17722547	C12orf10	135	258	12	53696817	53696940
BM975798	RAI1	12	360	17	17714663	17721040	SREBF1	360	468	17	17720412	17720639
DA092279	UBE2E3	1	385	2	181881546	181881928	SREBF1	381	499	17	17722911	17723029

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr17:17723785-17723785	p.D78Y	3
chr17:17719818-17719818	p.R697Q	2
chr17:17717044-17717044	p.R1011C	2
chr17:17721595-17721595	p.R418C	2
chr17:17726899-17726899	p.G38G	2
chr17:17717999-17717999	p.R919W	2
chr17:17721038-17721038	p.P489H	2
chr17:17719517-17719517	p.?	2
chr17:17722901-17722901	p.T251M	2
chr17:17719811-17719811	p.A699A	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	4	1	2	8	1		3		3	2		4	3	1			8	13	1	3
# mutation	4	1	3	9	1		3		3	2		4	3	1			8	14	1	3
nonsynonymous SNV	4	1	2	8	1		2		1	2		3	3	1			5	9	1	3
synonymous SNV			1	1			1		2			1					3	5

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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr17:17721595	p.R388C,SREBF1	2
chr17:17718174	p.R325L,SREBF1	1
chr17:17722327	p.P76H,SREBF1	1
chr17:17719525	p.P820S,SREBF1	1
chr17:17722985	p.R480R,SREBF1	1
chr17:17723754	p.R321H,SREBF1	1
chr17:17721053	p.P76A,SREBF1	1
chr17:17718184	p.H808Y,SREBF1	1
chr17:17722350	p.P459H,SREBF1	1
chr17:17719921	p.S312G,SREBF1	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA335; -.
Organism-specific databases	PharmGKB	PA335; -.
Organism-specific databases	CTD	6720; -.
Organism-specific databases	CTD	6720; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00363	sterol regulatory element binding transcription factor 1	approved	Clozapine
DB00502	sterol regulatory element binding transcription factor 1	approved	Haloperidol
DB00755	sterol regulatory element binding transcription factor 1	approved; nutraceutical; investigational	Tretinoin
DB00331	sterol regulatory element binding transcription factor 1	approved	Metformin
DB01076	sterol regulatory element binding transcription factor 1	approved	Atorvastatin
DB01095	sterol regulatory element binding transcription factor 1	approved	Fluvastatin
DB00227	sterol regulatory element binding transcription factor 1	approved; investigational	Lovastatin
DB00175	sterol regulatory element binding transcription factor 1	approved	Pravastatin
DB01098	sterol regulatory element binding transcription factor 1	approved	Rosuvastatin
DB00641	sterol regulatory element binding transcription factor 1	approved	Simvastatin

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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