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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 SDC4

Basic gene info.	Gene symbol	SDC4
	Gene name	syndecan 4
	Synonyms	SYND4
	Cytomap	UCSC genome browser: 20q12
	Genomic location	chr20 :43953928-43977064
	Type of gene	protein-coding
	RefGenes	NM_002999.3,
	Ensembl id	ENSG00000124145
	Description	amphiglycanryudocan amphiglycanryudocan core proteinsyndecan 4 (amphiglycan, ryudocan)syndecan proteoglycan 4syndecan-4
	Modification date	20141207
dbXrefs	MIM : 600017
	HGNC : HGNC
	Ensembl : ENSG00000124145
	HPRD : 08366
	Vega : OTTHUMG00000033083
Protein	UniProt: P31431 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SDC4
	BioGPS: 6385
	Gene Expression Atlas: ENSG00000124145
	The Human Protein Atlas: ENSG00000124145
Pathway	NCI Pathway Interaction Database: SDC4
	KEGG: SDC4
	REACTOME: SDC4
	ConsensusPathDB
	Pathway Commons: SDC4
Metabolism	MetaCyc: SDC4
	HUMANCyc: SDC4
Regulation	Ensembl's Regulation: ENSG00000124145
	miRBase: chr20 :43,953,928-43,977,064
	TargetScan: NM_002999
	cisRED: ENSG00000124145
Context	iHOP: SDC4
	cancer metabolism search in PubMed: SDC4
	UCL Cancer Institute: SDC4
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

Top

Phenotypic Information for SDC4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SDC4
	Familial Cancer Database: SDC4

* 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_CARBOHYDRATES

Others
OMIM	600017; gene.
Orphanet
Disease	KEGG Disease: SDC4
	MedGen: SDC4 (Human Medical Genetics with Condition)
	ClinVar: SDC4
Phenotype	MGI: SDC4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SDC4

Mutations for SDC4

* 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

Top

- 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
breast	SDC4	chr20	43961670	43961670		chr20	44111689	44111689
pancreas	SDC4	chr20	43969216	43969236	SDC4	chr20	43969756	43969776

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 SDC4 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
CB136042	SDC4	1	490	20	43954796	43955290	BIN1	481	537	2	127805626	127805682
BE177716	MLL5	16	394	7	104717430	104719333	SDC4	391	714	20	43955050	43955376
AW850072	ARHGEF3	49	68	3	56819238	56819257	SDC4	69	259	20	43954446	43954636
BF768117	SDC4	18	184	20	43967860	43968026	SDC4	174	272	20	43968032	43968130
BQ312086	SDC4	1	124	20	43955655	43955781	SDC4	123	180	20	43955777	43955834

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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=6

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=17)	Stat. for Synonymous SNVs (# total SNVs=4)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

Top

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
chr20:43976991-43976991	p.F12L	6
chr20:43964515-43964515	p.R36*	3
chr20:43955949-43955949	p.K184N	2
chr20:43977004-43977004	p.F7F	2
chr20:43959164-43959164	p.G96V	2
chr20:43959038-43959038	p.S138N	1
chr20:43964440-43964440	p.S61T	1
chr20:43959044-43959044	p.Q136R	1
chr20:43964457-43964457	p.S55F	1
chr20:43959090-43959090	p.E121K	1

Top

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				2			1					1					4	1	1	3
# mutation				2			1					1					5	1	1	4
nonsynonymous SNV				1								1					4	1	1	4
synonymous SNV				1			1										1

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])

Top

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
chr20:43964468	p.P51P	2
chr20:43959123	p.D44E	1
chr20:43959164	p.F196L	1
chr20:43959189	p.K184N	1
chr20:43955913	p.D181Y	1
chr20:43961686	p.S179G	1
chr20:43955949	p.L164M	1
chr20:43955960	p.L159L	1
chr20:43964489	p.Q136R	1
chr20:43955966	p.P118L	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 SDC4 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]

Top

Gene Expression for SDC4

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


OSER1,CDH1,CDS2,CGN,DBNDD2,MAGED2,KAT6B, NECAB3,NEDD4L,OSBPL2,PCIF1,PIGT,RIMS4,RP1, SDC4,SLC26A11,SYS1,TMEM150C,TP53RK,PLEKHD1,ZSWIM1	AK5,SOWAHB,CD9,CDS1,CGN,EZR,FAAH2, GNB5,HHAT,IRF6,LIPH,LRRC8E,MAP7,PIP4K2C, PRRG4,RBM23,SDC4,TACSTD2,TMEM30B,UBXN10,VAV3

ACOT8,ATP9A,BCL2L1,RTFDC1,CHMP4B,DBNDD2,DNTTIP1, DYNLRB1,HNF4A,ITCH,OSBPL2,PCIF1,PMEPA1,RAB22A, SDC4,SERINC3,SLC35C2,STAU1,SULF2,SYS1,YWHAB	CACFD1,CAMK2N1,CTSA,FAM134A,IFNGR2,KIAA0195,LCMT1, LRP4,MPND,MUC20,NMT2,PIGZ,PINK1,PRDX6, PTTG1IP,SDC4,SERINC2,STAP2,TMC4,TSPAN7,TUFT1

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for SDC4

There's no related Drug.

Top

Cross referenced IDs for SDC4

* 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