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 MCFD2

Basic gene info.	Gene symbol	MCFD2
	Gene name	multiple coagulation factor deficiency 2
	Synonyms	F5F8D\|F5F8D2\|LMAN1IP\|SDNSF
	Cytomap	UCSC genome browser: 2p21
	Genomic location	chr2 :47129008-47143007
	Type of gene	protein-coding
	RefGenes	NM_001171506.2, NM_001171507.2,NM_001171508.2,NM_001171509.2,NM_001171510.2, NM_001171511.2,NM_139279.5,
	Ensembl id	ENSG00000180398
	Description	multiple coagulation factor deficiency protein 2neural stem cell-derived neuronal survival protein
	Modification date	20141207
dbXrefs	MIM : 607788
	HGNC : HGNC
	Ensembl : ENSG00000180398
	HPRD : 09693
	Vega : OTTHUMG00000153100
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MCFD2
	BioGPS: 90411
	Gene Expression Atlas: ENSG00000180398
	The Human Protein Atlas: ENSG00000180398
Pathway	NCI Pathway Interaction Database: MCFD2
	KEGG: MCFD2
	REACTOME: MCFD2
	ConsensusPathDB
	Pathway Commons: MCFD2
Metabolism	MetaCyc: MCFD2
	HUMANCyc: MCFD2
Regulation	Ensembl's Regulation: ENSG00000180398
	miRBase: chr2 :47,129,008-47,143,007
	TargetScan: NM_001171506
	cisRED: ENSG00000180398
Context	iHOP: MCFD2
	cancer metabolism search in PubMed: MCFD2
	UCL Cancer Institute: MCFD2
Assigned class in ccmGDB	C

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Phenotypic Information for MCFD2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MCFD2
	Familial Cancer Database: MCFD2

* 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
Orphanet
Disease	KEGG Disease: MCFD2
	MedGen: MCFD2 (Human Medical Genetics with Condition)
	ClinVar: MCFD2
Phenotype	MGI: MCFD2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MCFD2

Mutations for MCFD2

* 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 MCFD2 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
BC047709	MCFD2	1	2204	2	47168414	47277164	CD37	2199	2417	19	49843645	49843863
CA308526	JAZF1	18	454	7	27872120	27872556	MCFD2	446	643	2	47136175	47142917

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

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

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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=10)	Stat. for Synonymous SNVs (# total SNVs=7)

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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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
chr2:47135054-47135054	p.S68S	2
chr2:47135080-47135080	p.I60V	2
chr2:47135052-47135052	p.P69L	1
chr2:47136246-47136246	p.P22L	1
chr2:47136283-47136283	p.P10A	1
chr2:47135055-47135055	p.S68L	1
chr2:47136304-47136304	p.M3L	1
chr2:47135063-47135063	p.A65A	1
chr2:47135071-47135071	p.P63A	1
chr2:47132679-47132679	p.D122Y	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				3			1					2	1	1				1		3
# mutation				3			1					2	1	1				1		3
nonsynonymous SNV				3			1					2	1	1
synonymous SNV																		1		3

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
chr2:47135054	p.S16S,MCFD2	2
chr2:47135071	p.E27K,MCFD2	1
chr2:47136169	p.P22L,MCFD2	1
chr2:47136209	p.P10A,MCFD2	1
chr2:47136232	p.D70Y,MCFD2	1
chr2:47136246	p.D29V,MCFD2	1
chr2:47136283	p.P17L,MCFD2	1
chr2:47132679	p.A13A,MCFD2	1
chr2:47135016	p.P11A,MCFD2	1
chr2:47135052	p.D48H,MCFD2	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 MCFD2 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 MCFD2

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


AAK1,ADAM17,ASXL2,BIRC6,EXOC6B,FBXO11,FNDC3B, LOC284441,MAP3K2,MCFD2,NCKAP1,RANBP2,ROCK2,SLC30A6, SMEK2,SOCS5,STRN,TRIP12,USP34,VPS54,ZBTB38	CHM,DIS3,FAM8A1,FBXW11,HIPK1,ITCH,EFCAB14, TRAPPC8,LOC647979,MCFD2,NCKAP1,OSBPL8,PAFAH1B1,PJA2, RBL2,SEPT10,TOR1AIP1,UBE4A,UBL3,ZBTB38,ZFP91

ADAM17,ALS2,CALU,COPS8,EXOC6B,GPR180,ITGB1, KDELC1,LIMS1,LMO7,MCFD2,PAPOLG,PPP3R1,RALB, RNGTT,SAMD8,SGTB,SOCS5,UBXN2A,UGCG,WWC2	CTF1,DEGS1,DNAJC18,FEZ1,KCNJ8,KLHL5,KPNA5, LOC283856,LOC644538,MCFD2,PRDM8,RAB34,RAMP1,RGN, RHOQ,RPS6KC1,SEC22C,TCEA2,TCEAL3,TMEM55A,ZNF25

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 MCFD2

There's no related Drug.

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Cross referenced IDs for MCFD2

* 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