Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolF7
Gene namecoagulation factor VII (serum prothrombin conversion accelerator)
SynonymsSPCA
CytomapUCSC genome browser: 13q34
Genomic locationchr13 :113760104-113774995
Type of geneprotein-coding
RefGenesNM_000131.4,
NM_001267554.1,NM_019616.3,NR_051961.1,
Ensembl idENSG00000057593
DescriptionFVII coagulation proteincoagulation factor VIIeptacog alfaproconvertin
Modification date20141207
dbXrefs MIM : 613878
HGNC : HGNC
Ensembl : ENSG00000057593
HPRD : 01965
Vega : OTTHUMG00000017373
ProteinUniProt: P08709
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_F7
BioGPS: 2155
Gene Expression Atlas: ENSG00000057593
The Human Protein Atlas: ENSG00000057593
PathwayNCI Pathway Interaction Database: F7
KEGG: F7
REACTOME: F7
ConsensusPathDB
Pathway Commons: F7
MetabolismMetaCyc: F7
HUMANCyc: F7
RegulationEnsembl's Regulation: ENSG00000057593
miRBase: chr13 :113,760,104-113,774,995
TargetScan: NM_000131
cisRED: ENSG00000057593
ContextiHOP: F7
cancer metabolism search in PubMed: F7
UCL Cancer Institute: F7
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for F7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM 227500; phenotype.
613878; gene.
Orphanet 327; Congenital factor VII deficiency.
DiseaseKEGG Disease: F7
MedGen: F7 (Human Medical Genetics with Condition)
ClinVar: F7
PhenotypeMGI: F7 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows F7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
GAIN (# sample)1                
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr13:113768163-113768163p.G107R3
chr13:113773011-113773011p.R364W2
chr13:113771857-113771857p.A251V2
chr13:113772894-113772894p.E325K2
chr13:113773099-113773099p.S393L2
chr13:113771901-113771901p.A266T2
chr13:113760170-113760170p.A5A2
chr13:113768231-113768231p.I129I2
chr13:113771902-113771902p.A266V2
chr13:113770093-113770093p.G184R2

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample 3 71 3    831  101016
# mutation 3 61 4    931  101116
nonsynonymous SNV 1 5  2    521  7912
synonymous SNV 2 21 2    41   32 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr13:113771901p.E241K,F72
chr13:113768074p.F78F,F72
chr13:113768231p.A167E,F72
chr13:113771857p.I45I,F72
chr13:113773011p.A182T,F72
chr13:113772894p.R280W,F72
chr13:113772905p.G30R1
chr13:113770093p.G138E,F71
chr13:113773108p.D232H,F71
chr13:113771902p.H324Y,F71

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P08709; -.
ChemistryChEMBL CHEMBL2111412; -.
ChemistryGuidetoPHARMACOLOGY 2363; -.
Organism-specific databasesPharmGKB PA160; -.
Organism-specific databasesCTD 2155; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00170coagulation factor VII (serum prothrombin conversion accelerator)approved; nutraceuticalMenadione
DB04590coagulation 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
DB04593coagulation factor VII (serum prothrombin conversion accelerator)experimental3-({1-[3-CARBAMIMIDOYL-1-(4-CARBAMIMIDOYL-BENZYLCARBAMOYL)-PROPYLCARBAMOYL]-2-METHYL-BUTYLSULFAMOYL}-METHYL)-BENZOIC ACID
DB04606coagulation factor VII (serum prothrombin conversion accelerator)experimental2-[2-ETHANESULFONYLAMINO-3-(5-PROPOXY-1H-INDOL-3-YL)-PROPIONYLAMINO]-PENTANEDIOIC ACID 5-AMIDE 1-(4-CARBAMIMIDOYL-BENZYLAMIDE)
DB04758coagulation factor VII (serum prothrombin conversion accelerator)experimental2-[2-ETHANESULFONYLAMINO-3-(1H-INDOL-3-YL)-PROPIONYLAMINO]-PENTANEDIOIC ACID 5-AMIDE 1-(4-CARBAMIM IDOYL-BENZYLAMIDE)
DB04767coagulation factor VII (serum prothrombin conversion accelerator)experimentalN-[1-(4-CARBAMIMIDOYL-BENZYLCARBAMOYL)-3-METHYLSULFANYL-PROPYL]-3-HYDROXY-2-PROPOXYAMINO-BUTYRAMID
DB07207coagulation factor VII (serum prothrombin conversion accelerator)experimental2-(4-HYDROXY-5-PHENYL-1H-PYRAZOL-3-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE
DB07247coagulation factor VII (serum prothrombin conversion accelerator)experimental[2'-HYDROXY-3'-(1H-PYRROLO[3,2-C]PYRIDIN-2-YL)-BIPHENYL-3-YLMETHYL]-UREA
DB07376coagulation factor VII (serum prothrombin conversion accelerator)experimental5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID)
DB08232coagulation 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
DB00175coagulation factor VII (serum prothrombin conversion accelerator)approvedPravastatin
DB00682coagulation factor VII (serum prothrombin conversion accelerator)approvedWarfarin


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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



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