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 SQRDL

Basic gene info.	Gene symbol	SQRDL
	Gene name	sulfide quinone reductase-like (yeast)
	Synonyms	PRO1975\|SQOR
	Cytomap	UCSC genome browser: 15q15
	Genomic location	chr15 :45927255-45983479
	Type of gene	protein-coding
	RefGenes	NM_001271213.1, NM_021199.3,
	Ensembl id	ENSG00000260170
	Description	sulfide dehydrogenase likesulfide:quinone oxidoreductase, mitochondrial
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000137767
	HPRD : 18102
	Vega : OTTHUMG00000131476
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SQRDL
	BioGPS: 58472
	Gene Expression Atlas: ENSG00000260170
	The Human Protein Atlas: ENSG00000260170
Pathway	NCI Pathway Interaction Database: SQRDL
	KEGG: SQRDL
	REACTOME: SQRDL
	ConsensusPathDB
	Pathway Commons: SQRDL
Metabolism	MetaCyc: SQRDL
	HUMANCyc: SQRDL
Regulation	Ensembl's Regulation: ENSG00000260170
	miRBase: chr15 :45,927,255-45,983,479
	TargetScan: NM_001271213
	cisRED: ENSG00000260170
Context	iHOP: SQRDL
	cancer metabolism search in PubMed: SQRDL
	UCL Cancer Institute: SQRDL
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: SQRDL
	Familial Cancer Database: SQRDL

* 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_SULFUR_AMINO_ACID_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for SQRDL

* 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

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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	SQRDL	chr15	45963439	45963459	SQRDL	chr15	45963906	45963926
ovary	SQRDL	chr15	45975836	45975856		chr15	46002144	46002164

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 SQRDL 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
BU581446	NID1	4	299	1	236143879	236148727	SQRDL	300	495	15	45981354	45983304
BU075210	SQRDL	41	401	15	45981354	45983469	NID1	402	583	1	236143879	236145017

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=26)	Stat. for Synonymous SNVs (# total SNVs=9)

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
chr15:45965849-45965849	p.S168S	4
chr15:45981249-45981249	p.T377A	2
chr15:45951155-45951155	p.R12fs*51	2
chr15:45965918-45965918	p.I191M	2
chr15:45968449-45968449	p.D269N	2
chr15:45968487-45968487	p.P281P	2
chr15:45954319-45954319	p.E134G	1
chr15:45965917-45965917	p.I191T	1
chr15:45968423-45968423	p.K260R	1
chr15:45962137-45962137	p.R139R	1

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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=3

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		2		2			3		2			6		1		1	11	1		6
# mutation		2		2			3		2			7		1		1	11	1		6
nonsynonymous SNV		2		2			2		1			6		1			6	1		3
synonymous SNV							1		1			1				1	5			3

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
chr15:45965849	p.S168S,SQRDL	3
chr15:45965844	p.P341S,SQRDL	1
chr15:45968317	p.N169K,SQRDL	1
chr15:45951232	p.T345T,SQRDL	1
chr15:45981368	p.V172L,SQRDL	1
chr15:45968356	p.V382A,SQRDL	1
chr15:45951281	p.F185F,SQRDL	1
chr15:45981393	p.T402T,SQRDL	1
chr15:45965852	p.I191I,SQRDL	1
chr15:45968358	p.P404L,SQRDL	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 SQRDL 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 SQRDL

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


B2M,EMC7,RHOV___CHP1,CYB561D2,CYB5A,DNAJC17,FAH, RMDN3,FTH1,GCHFR,NDUFAF1,PPP1R7,RARRES3,SQRDL, TMEM62,TPST2,TSPAN15,UQCRQ,VPS18,YIPF1,ZFYVE19	ARHGDIB,ARPC3,BCAS4,BRE,CAPZB,CLIC1,GSTO1, JTB,MFSD5,MIF4GD,N6AMT2,NPC2,PRR13,PSMA4, PSMA5,RHOG,RNF181,S100A11,SDHAF2,SQRDL,TM2D2

ACADS,BCL10,GSKIP,C15orf48,CCL28,CIB1,ETFA, ETHE1,F2RL1,FAM118B,GPA33,LDHD,LGALS3,MPDU1, PIGR,RILP,SCO2,SQRDL,TMEM54,TNFSF13,TSPO	ATP5B,MCU,CCL28,CD24,CSTF2,GNG5,HCCS, HDAC1,HPSE,IL18,MAP2K6,MMAA,MYCBP,OSTF1, PSMD3,RAB11A,RTN4IP1,SCO1,SQRDL,TMEM54,TPM3

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 SQRDL

There's no related Drug.

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Cross referenced IDs for SQRDL

* 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