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 F7

Basic gene info.	Gene symbol	F7
	Gene name	coagulation factor VII (serum prothrombin conversion accelerator)
	Synonyms	SPCA
	Cytomap	UCSC genome browser: 13q34
	Genomic location	chr13 :113760104-113774995
	Type of gene	protein-coding
	RefGenes	NM_000131.4, NM_001267554.1,NM_019616.3,NR_051961.1,
	Ensembl id	ENSG00000057593
	Description	FVII coagulation proteincoagulation factor VIIeptacog alfaproconvertin
	Modification date	20141207
dbXrefs	MIM : 613878
	HGNC : HGNC
	Ensembl : ENSG00000057593
	HPRD : 01965
	Vega : OTTHUMG00000017373
Protein	UniProt: P08709 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_F7
	BioGPS: 2155
	Gene Expression Atlas: ENSG00000057593
	The Human Protein Atlas: ENSG00000057593
Pathway	NCI Pathway Interaction Database: F7
	KEGG: F7
	REACTOME: F7
	ConsensusPathDB
	Pathway Commons: F7
Metabolism	MetaCyc: F7
	HUMANCyc: F7
Regulation	Ensembl's Regulation: ENSG00000057593
	miRBase: chr13 :113,760,104-113,774,995
	TargetScan: NM_000131
	cisRED: ENSG00000057593
Context	iHOP: F7
	cancer metabolism search in PubMed: F7
	UCL Cancer Institute: F7
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for F7(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: F7
	Familial Cancer Database: F7

* 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_PROTEINS

Others
OMIM	227500; phenotype. 613878; gene.
Orphanet	327; Congenital factor VII deficiency.
Disease	KEGG Disease: F7
	MedGen: F7 (Human Medical Genetics with Condition)
	ClinVar: F7
Phenotype	MGI: F7 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: F7

Mutations for F7

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows F7 related fusion information.

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

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=30)	Stat. for Synonymous SNVs (# total SNVs=17)

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
chr13:113768163-113768163	p.G107R	3
chr13:113773099-113773099	p.S393L	2
chr13:113771901-113771901	p.A266T	2
chr13:113760170-113760170	p.A5A	2
chr13:113768231-113768231	p.I129I	2
chr13:113771902-113771902	p.A266V	2
chr13:113770093-113770093	p.G184R	2
chr13:113773001-113773001	p.L360L	2
chr13:113768272-113768272	p.T143M	2
chr13:113773011-113773011	p.R364W	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		7	1		3					8	3	1			10	10	1	6
# mutation		3		6	1		4					9	3	1			10	11	1	6
nonsynonymous SNV		1		5			2					5	2	1			7	9	1	2
synonymous SNV		2		2	1		2					4	1				3	2		4

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
chr13:113771857	p.R280W,F7	2
chr13:113773011	p.E241K,F7	2
chr13:113772894	p.F78F,F7	2
chr13:113771901	p.A167E,F7	2
chr13:113768074	p.I45I,F7	2
chr13:113768231	p.A182T,F7	2
chr13:113772771	p.N69N,F7	1
chr13:113768272	p.A182V,F7	1
chr13:113772926	p.G72D,F7	1
chr13:113771834	p.L189F,F7	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 F7 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 F7

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


BLID,FAM228A,CARKD,CARS2,CHIA,CSAD,D2HGDH, F7,GRTP1,IGSF21,KRT86,LCN9,MLPH,PCID2, PCSK4,SHROOM1,SLC10A2,TMEM27,TNFRSF10D,TRAF5,ZNF385A	ABAT,AGR2,AGR3,ARMC3,CLGN,F7,GOLM1, KIAA1257,MAGED2,MUC1,NAT1,NBPF4,PRR15,SHROOM1, SIAH2,SLC9A3R1,SPATA17,SPEF1,TFF1,ZNF552,ZYG11A

ABCC2,AGT,ARL11,ASB18,TSPEAR,CST9,HOGA1, F10,F7,FARP1,FATE1,GCM1,GPR113,GRIN2C, IL34,LDHAL6A,DNMBP-AS1,PER4,SLC5A6,STRA6,XPNPEP2	ABCC2,ACE,AGXT2,ASPDH,ERICH4,F7,GALNT14, GGN,GLTPD2,GPR112,GSTA1,HAPLN4,HTR1D,KCNH6, LOC285733,MME,MRO,PDZD7,RBP3,SLC5A4,TMEM213

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 F7

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P08709; -.
Chemistry	ChEMBL	CHEMBL2111412; -.
Chemistry	GuidetoPHARMACOLOGY	2363; -.
Organism-specific databases	PharmGKB	PA160; -.
Organism-specific databases	CTD	2155; -.

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
DB00170	coagulation factor VII (serum prothrombin conversion accelerator)	approved; nutraceutical	Menadione
DB04590	coagulation factor VII (serum prothrombin conversion accelerator)	experimental	(2R)-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO){5-ETHOXY-2-FLUORO-3-[(3R)-TETRAHYDROFURAN-3-YLOXY]PHENYL}ACETICACID
DB04593	coagulation factor VII (serum prothrombin conversion accelerator)	experimental	3-({1-[3-CARBAMIMIDOYL-1-(4-CARBAMIMIDOYL-BENZYLCARBAMOYL)-PROPYLCARBAMOYL]-2-METHYL-BUTYLSULFAMOYL}-METHYL)-BENZOIC ACID
DB04606	coagulation factor VII (serum prothrombin conversion accelerator)	experimental	2-[2-ETHANESULFONYLAMINO-3-(5-PROPOXY-1H-INDOL-3-YL)-PROPIONYLAMINO]-PENTANEDIOIC ACID 5-AMIDE 1-(4-CARBAMIMIDOYL-BENZYLAMIDE)
DB04758	coagulation factor VII (serum prothrombin conversion accelerator)	experimental	2-[2-ETHANESULFONYLAMINO-3-(1H-INDOL-3-YL)-PROPIONYLAMINO]-PENTANEDIOIC ACID 5-AMIDE 1-(4-CARBAMIM IDOYL-BENZYLAMIDE)
DB04767	coagulation factor VII (serum prothrombin conversion accelerator)	experimental	N-[1-(4-CARBAMIMIDOYL-BENZYLCARBAMOYL)-3-METHYLSULFANYL-PROPYL]-3-HYDROXY-2-PROPOXYAMINO-BUTYRAMID
DB07207	coagulation factor VII (serum prothrombin conversion accelerator)	experimental	2-(4-HYDROXY-5-PHENYL-1H-PYRAZOL-3-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE
DB07247	coagulation factor VII (serum prothrombin conversion accelerator)	experimental	[2'-HYDROXY-3'-(1H-PYRROLO[3,2-C]PYRIDIN-2-YL)-BIPHENYL-3-YLMETHYL]-UREA
DB07376	coagulation factor VII (serum prothrombin conversion accelerator)	experimental	5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID)
DB08232	coagulation factor VII (serum prothrombin conversion accelerator)	experimental	{5-(5-AMINO-1H-PYRROLO[3,2-B]PYRIDIN-2-YL)-6-HYDROXY-3'-NITRO-BIPHENYL-3-YL]-ACETIC ACID
DB00175	coagulation factor VII (serum prothrombin conversion accelerator)	approved	Pravastatin
DB00682	coagulation factor VII (serum prothrombin conversion accelerator)	approved	Warfarin

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Cross referenced IDs for F7

* 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