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 LSS

Basic gene info.	Gene symbol	LSS
	Gene name	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)
	Synonyms	OSC
	Cytomap	UCSC genome browser: 21q22.3
	Genomic location	chr21 :47608359-47648738
	Type of gene	protein-coding
	RefGenes	NM_001001438.2, NM_001145436.1,NM_001145437.1,NM_002340.5,
	Ensembl id	ENSG00000160285
	Description	2,3-epoxysqualene--lanosterol cyclase2,3-epoxysqualene-lanosterol cyclasehOSClanosterol synthaseoxidosqualene--lanosterol cyclase
	Modification date	20141207
dbXrefs	MIM : 600909
	HGNC : HGNC
	Ensembl : ENSG00000160285
	HPRD : 02945
	Vega : OTTHUMG00000090633
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_LSS
	BioGPS: 4047
	Gene Expression Atlas: ENSG00000160285
	The Human Protein Atlas: ENSG00000160285
Pathway	NCI Pathway Interaction Database: LSS
	KEGG: LSS
	REACTOME: LSS
	ConsensusPathDB
	Pathway Commons: LSS
Metabolism	MetaCyc: LSS
	HUMANCyc: LSS
Regulation	Ensembl's Regulation: ENSG00000160285
	miRBase: chr21 :47,608,359-47,648,738
	TargetScan: NM_001001438
	cisRED: ENSG00000160285
Context	iHOP: LSS
	cancer metabolism search in PubMed: LSS
	UCL Cancer Institute: LSS
Assigned class in ccmGDB	C

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Phenotypic Information for LSS(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: LSS
	Familial Cancer Database: LSS

* 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
Orphanet
Disease	KEGG Disease: LSS
	MedGen: LSS (Human Medical Genetics with Condition)
	ClinVar: LSS
Phenotype	MGI: LSS (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: LSS

Mutations for LSS

* 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

* 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	LSS	chr21	47626204	47626224	RASA3	chr13	114892263	114892283
pancreas	LSS	chr21	47624725	47624745	MCM3AP-AS1	chr21	47650566	47650586
pancreas	LSS	chr21	47644418	47644438	MCM3AP-AS1	chr21	47650575	47650595

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 LSS 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
BE827726	NDE1	2	311	16	15812243	15814046	LSS	304	556	21	47635094	47636327
BI055158	C9orf3	11	349	9	97848810	97849148	LSS	341	411	21	47609069	47609139

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=50)	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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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
chr21:47614469-47614469	p.L642V	3
chr21:47611069-47611069	p.L716L	2
chr21:47635627-47635627	p.P288P	2
chr21:47615617-47615617	p.A597V	2
chr21:47647529-47647529	p.G86W	2
chr21:47633708-47633708	p.D351D	2
chr21:47648371-47648371	p.A53T	2
chr21:47614443-47614443	p.H650H	2
chr21:47635176-47635176	p.H310R	2
chr21:47635593-47635593	p.?	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	3		1	5			3		2	1		7	2	1	1		3	8		11
# mutation	3		1	5			3		2	1		7	2	1	1		3	8		12
nonsynonymous SNV	3			4			2		2	1		5	2	1			2	6		6
synonymous SNV			1	1			1					2			1		1	2		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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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
chr21:47642638	p.D271D,LSS	2
chr21:47633708	p.C32S,LSS	2
chr21:47641783	p.A334G,LSS	1
chr21:47611134	p.S69Y,LSS	1
chr21:47648502	p.A581D,LSS	1
chr21:47626638	p.F311F,LSS	1
chr21:47633740	p.R52W,LSS	1
chr21:47641853	p.M577I,LSS	1
chr21:47611873	p.Y288C,LSS	1
chr21:47627345	p.R49Q,LSS	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 LSS 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 LSS

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


AGPAT3,C21orf33,C21orf58,FAM207A,DIP2A,LSS,MCM3AP, MCM3AP-AS1,MVD,PCNT,PDXK,PFKL,PRMT2,PWP2, RANGAP1,RRP1,SLC19A1,SUMO3,U2AF1,UBE2G2,WDR4	ABCD1,ACACA,ACOT2,ACSS2,AGPAT2,APMAP,CKB, CYB5A,FASN,IDH1,LETM1,LSS,MCCC1,ME1, PC,PGD,SLC25A1,SLC25A18,TKT,TSKU,ZP1

ACAT2,ACSS2,AGPAT3,CC2D1A,CYP51A1,DHCR24,DHCR7, FASN,FDPS,HMGCR,HMGCS1,IDI1,INSIG1,LSS, MVD,MVK,PCSK9,PDXK,PFKL,PWP2,SLC19A1	ACACA,ACSL1,ACSL3,C6orf223,CYP51A1,DHCR7,DUXA, FASN,FLRT2,LSS,MUC5B,NAV1,PCSK9,PTPRG, SCD,SQLE,TANC1,THSD7A,TRIP11,USP32,VPS13D

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 LSS

There's no related Drug.

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Cross referenced IDs for LSS

* 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