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 DDX6

Basic gene info.	Gene symbol	DDX6
	Gene name	DEAD (Asp-Glu-Ala-Asp) box helicase 6
	Synonyms	HLR2\|P54\|RCK
	Cytomap	UCSC genome browser: 11q23.3
	Genomic location	chr11 :118618472-118661972
	Type of gene	protein-coding
	RefGenes	NM_001257191.2, NM_004397.5,
	Ensembl id	ENSG00000269612
	Description	ATP-dependent RNA helicase p54DEAD (Asp-Glu-Ala-Asp) box polypeptide 6DEAD box protein 6DEAD box-6DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 6 (RNA helicase, 54kD)oncogene RCKprobable ATP-dependent RNA helicase DDX6
	Modification date	20141207
dbXrefs	MIM : 600326
	HGNC : HGNC
	Ensembl : ENSG00000110367
	HPRD : 02638
Protein	UniProt: P26196 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DDX6
	BioGPS: 1656
	Gene Expression Atlas: ENSG00000269612
	The Human Protein Atlas: ENSG00000269612
Pathway	NCI Pathway Interaction Database: DDX6
	KEGG: DDX6
	REACTOME: DDX6
	ConsensusPathDB
	Pathway Commons: DDX6
Metabolism	MetaCyc: DDX6
	HUMANCyc: DDX6
Regulation	Ensembl's Regulation: ENSG00000269612
	miRBase: chr11 :118,618,472-118,661,972
	TargetScan: NM_001257191
	cisRED: ENSG00000269612
Context	iHOP: DDX6
	cancer metabolism search in PubMed: DDX6
	UCL Cancer Institute: DDX6
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DDX6 in cancer cell metabolism	1. Iio A, Takagi T, Miki K, Naoe T, Nakayama A, et al. (2013) DDX6 post-transcriptionally down-regulates miR-143/145 expression through host gene NCR143/145 in cancer cells. Biochim Biophys Acta 1829: 1102-1110. doi: 10.1016/j.bbagrm.2013.07.010. go to article

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Phenotypic Information for DDX6(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: DDX6
	Familial Cancer Database: DDX6

* 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_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	600326; gene.
Orphanet
Disease	KEGG Disease: DDX6
	MedGen: DDX6 (Human Medical Genetics with Condition)
	ClinVar: DDX6
Phenotype	MGI: DDX6 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DDX6

Mutations for DDX6

* 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
ovary	DDX6	chr11	118652817	118652837	LNX2	chr13	28120237	28120257

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 DDX6 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
BC065007	DDX6	25	2515	11	118622042	118657228	RAB7A	2506	2568	3	128533579	128533641
BF085678	DDX6	6	429	11	118635822	118636246	C14orf37	424	576	14	58760276	58760429
BF356738	DDX6	1	157	11	118647776	118647931	FGD4	153	431	12	32699487	32699765
BE934709	DDX6	1	163	11	118622197	118622362	DDX6	158	230	11	118618929	118619001
DN997510	DDX6	8	457	11	118656818	118661846	ROBO1	438	457	3	78766603	78766622

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=27)	Stat. for Synonymous SNVs (# total SNVs=9)

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
chr11:118626197-118626197	p.G386D	3
chr11:118627889-118627889	p.K356K	2
chr11:118626210-118626210	p.L382M	2
chr11:118630698-118630698	p.T255M	2
chr11:118627025-118627025	p.R362Q	2
chr11:118627886-118627886	p.M357I	1
chr11:118633939-118633939	p.Q230H	1
chr11:118625502-118625502	p.I446I	1
chr11:118650341-118650341	p.Q112Q	1
chr11:118633946-118633946	p.H228R	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=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	1	2		8	1		3		4			1	1	1			1	3		5
# mutation	1	2		7	1		3		4			1	1	1			1	3		6
nonsynonymous SNV	1	2		5	1		2		2				1	1				1		4
synonymous SNV				2			1		2			1					1	2		2

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
chr11:118626210	p.L393L,DDX6	2
chr11:118627889	p.K367K,DDX6	2
chr11:118627891	p.I400L,DDX6	1
chr11:118638975	p.R157W,DDX6	1
chr11:118625487	p.I152S,DDX6	1
chr11:118627953	p.G397D,DDX6	1
chr11:118639000	p.T144A,DDX6	1
chr11:118625512	p.Q123Q,DDX6	1
chr11:118629524	p.N387D,DDX6	1
chr11:118650341	p.K104K,DDX6	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 DDX6 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 DDX6

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


ARCN1,ARHGEF12,ATM,BCLAF1,CCDC186,C11orf57,CBL, CREB1,CUL5,DDX6,DLAT,MGA,KMT2A,NPAT, PAFAH1B2,PRDM10,RBM7,TBCEL,UBE4A,USP28,ZW10	ARIH1,ASH1L,BTBD7,BROX,DDX6,GSK3B,IPO8, KIAA0430,NR2C2,NUCKS1,PREPL,RAB3GAP2,TAB2,TMEM184C, TNKS,USP34,USP48,XPO7,ZFX,ZMYM4,ZNF510

ARCN1,ARHGEF12,C11orf30,CBL,DDX6,HIPK3,KDM2A, KIAA0430,KMT2A,NPAT,PICALM,PRDM10,REV3L,RNF169, RSF1,SON,SOS1,TRIP11,UBE4A,USP34,ZBTB44	ARID2,COL4A3BP,DDX6,DYNLL2,DYRK1A,FBXO11,FBXW11, GLG1,HNRNPUL2,IPO8,JAK1,KIF1B,MAPK1,PAFAH1B1, PHF3,PIK3R4,SEL1L,SMG7,TNRC6B,USP9X,ZC3HAV1

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 DDX6

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA27229; -.
Organism-specific databases	CTD	1656; -.

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
DB01694	DEAD (Asp-Glu-Ala-Asp) box helicase 6	experimental	D-tartaric acid

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Cross referenced IDs for DDX6

* 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