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 F9
Basic gene info.Gene symbolF9
Gene namecoagulation factor IX
SynonymsFIX|HEMB|P19|PTC|THPH8
CytomapUCSC genome browser: Xq27.1-q27.2
Genomic locationchrX :138612894-138645617
Type of geneprotein-coding
RefGenesNM_000133.3,
Ensembl idENSG00000101981
DescriptionChristmas factorF9 p22FIX F9factor 9factor IX F9plasma thromboplastic componentplasma thromboplastin component
Modification date20141219
dbXrefs MIM : 300746
HGNC : HGNC
Ensembl : ENSG00000101981
HPRD : 02385
Vega : OTTHUMG00000022536
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_F9
BioGPS: 2158
Gene Expression Atlas: ENSG00000101981
The Human Protein Atlas: ENSG00000101981
PathwayNCI Pathway Interaction Database: F9
KEGG: F9
REACTOME: F9
ConsensusPathDB
Pathway Commons: F9
MetabolismMetaCyc: F9
HUMANCyc: F9
RegulationEnsembl's Regulation: ENSG00000101981
miRBase: chrX :138,612,894-138,645,617
TargetScan: NM_000133
cisRED: ENSG00000101981
ContextiHOP: F9
cancer metabolism search in PubMed: F9
UCL Cancer Institute: F9
Assigned class in ccmGDBC

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Phenotypic Information for F9(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: F9
Familial Cancer Database: F9
* 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
Orphanet
DiseaseKEGG Disease: F9
MedGen: F9 (Human Medical Genetics with Condition)
ClinVar: F9
PhenotypeMGI: F9 (International Mouse Phenotyping Consortium)
PhenomicDB: F9

Mutations for F9
* 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 F9 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
There's no copy number variation information in COSMIC data for this gene.

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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=95)
Stat. for Synonymous SNVs
(# total SNVs=25)
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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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
chr23:138643994-138643994p.R384*5
chr23:138633258-138633258p.T186T4
chr23:138630596-138630596p.S156T3
chr23:138644029-138644029p.F395L3
chr23:138623283-138623283p.K109R3
chr23:138642945-138642945p.V257I2
chr23:138633376-138633376p.R226R2
chr23:138619310-138619310p.V77A2
chr23:138643870-138643870p.T342T2
chr23:138644105-138644105p.G421R2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 203 5 2  1271  85 9
# mutation 1 163 5 2  1571  95 8
nonsynonymous SNV 1 122 5 2  1251  74 7
synonymous SNV   41      32   21 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])

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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
chrX:138623283p.K109R3
chrX:138643813p.R298Q2
chrX:138644029p.T186T2
chrX:138633258p.E323E2
chrX:138643014p.S156P2
chrX:138630596p.F395L2
chrX:138643737p.G280S2
chrX:138623335p.P414P1
chrX:138630621p.I7M1
chrX:138619222p.E116K1

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 F9 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 F9

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

APCS,APOA2,APOA4,APOC3,ARG1,C8A,C9,
CREB3L3,CRP,F2,F9,FABP1,FGF23,HP,
ITIH1,MT1B,PLG,SERPINA7,SERPINC1,SLC17A2,TM4SF5
ACSL3,ADAM2,ALOX15B,APOD,DHRS2,ENPP3,F9,
GUSB,HAAO,HIST1H2BG,HIST1H4H,NANOG,NAT2,PPEF1,
RNASE12,SERHL2,SERHL,SPINK8,SULT1C3,UGT2B10,UGT2B11

AHSG,ALB,APCS,APOA5,APOC3,C8A,C8B,
C9,CFHR2,CFHR5,CRP,CYP4A11,F9,FGA,
FGG,GDF2,HPX,ITIH1,MBL2,SERPINC1,SPP2
ALB,APCS,APOA2,C3P1,C8A,CFHR2,CFHR5,
CYP4A22,DNAJB8,F13B,F9,FGG,HRG,KIR3DP1,
KRTAP4-11,KRTAP5-3,LECT2,LOC100129935,LINC00160,OR1N1,SLC17A2
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 F9
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00170coagulation factor IXapproved; nutraceuticalMenadione
DB03847coagulation factor IXexperimentalGamma-Carboxy-Glutamic Acid
DB00682coagulation factor IXapprovedWarfarin
DB00668coagulation factor IXapprovedEpinephrine


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Cross referenced IDs for F9
* 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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