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 FABP6

Basic gene info.	Gene symbol	FABP6
	Gene name	fatty acid binding protein 6, ileal
	Synonyms	I-15P\|I-BABP\|I-BALB\|I-BAP\|ILBP\|ILBP3\|ILLBP
	Cytomap	UCSC genome browser: 5q33.3-q34
	Genomic location	chr5 :159626047-159665729
	Type of gene	protein-coding
	RefGenes	NM_001040442.1, NM_001130958.1,NM_001445.2,
	Ensembl id	ENSG00000170231
	Description	GTgastrotropinileal bile acid binding proteinileal lipid-binding proteinilleal lipid-binding proteinintestinal 15 kDa protein
	Modification date	20141207
dbXrefs	MIM : 600422
	HGNC : HGNC
	Ensembl : ENSG00000170231
	HPRD : 02689
	Vega : OTTHUMG00000130329
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FABP6
	BioGPS: 2172
	Gene Expression Atlas: ENSG00000170231
	The Human Protein Atlas: ENSG00000170231
Pathway	NCI Pathway Interaction Database: FABP6
	KEGG: FABP6
	REACTOME: FABP6
	ConsensusPathDB
	Pathway Commons: FABP6
Metabolism	MetaCyc: FABP6
	HUMANCyc: FABP6
Regulation	Ensembl's Regulation: ENSG00000170231
	miRBase: chr5 :159,626,047-159,665,729
	TargetScan: NM_001040442
	cisRED: ENSG00000170231
Context	iHOP: FABP6
	cancer metabolism search in PubMed: FABP6
	UCL Cancer Institute: FABP6
Assigned class in ccmGDB	C

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Phenotypic Information for FABP6(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: FABP6
	Familial Cancer Database: FABP6

* 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_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: FABP6
	MedGen: FABP6 (Human Medical Genetics with Condition)
	ClinVar: FABP6
Phenotype	MGI: FABP6 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: FABP6

Mutations for FABP6

* 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 FABP6 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

DB067617

FABP6

357

159624751

159640827

CRK

355

507

1340299

1340451

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=16)	Stat. for Synonymous SNVs (# total SNVs=6)

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
chr5:159656585-159656585	p.F7L	3
chr5:159659148-159659148	p.I37I	3
chr5:159661892-159661892	p.E103D	2
chr5:159659203-159659203	p.G56W	2
chr5:159656578-159656578	p.G5D	2
chr5:159661872-159661872	p.N97Y	2
chr5:159659202-159659202	p.S55S	1
chr5:159661895-159661895	p.I104I	1
chr5:159659229-159659229	p.F64F	1
chr5:159665643-159665643	p.R122S	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		1		4	1		1		1			2	2				3	4		3
# mutation		1		4	1		1		1			2	2				3	4		3
nonsynonymous SNV		1		2	1		1		1			1	1					3		2
synonymous SNV				2								1	1				3	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])

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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
chr5:159656578	p.E103E,FABP6	2
chr5:159661892	p.G5D,FABP6	2
chr5:159659125	p.S51Y,FABP6	1
chr5:159665630	p.G56R,FABP6	1
chr5:159659135	p.F64F,FABP6	1
chr5:159659148	p.K68E,FABP6	1
chr5:159640748	p.G89G,FABP6	1
chr5:159659189	p.F95F,FABP6	1
chr5:159640768	p.L19L,FABP6	1
chr5:159659203	p.C26Y,FABP6	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 FABP6 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 FABP6

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


AADAT,ABCC12,ACE2,ANKRD26P1,C2orf83,CELP,CKMT2, CSAG1,CSTB,FABP6,GGT1,GGTLC1,GGTLC2,H2AFB1, H2BFWT,LCN15,LYZL4,PLA2G4E,SLED1,SSX4,SSX6	ADH7,CLPSL2,CALML3,DLX1,DNAJB3,ETNK2,FABP6, FAM81B,HMGB4,KRT13,KRTAP15-1,LOC286359,MRFAP1,OR10G8, OR4P4,PNMT,PTHLH,SLC18A3,SLC39A11,TNFSF11,TSPAN1

C12orf45,MAPKAPK5-AS1,C12orf73,SWSAP1,SMIM15,CCNH,FABP6, MED7,METTL5,MFF,MTERF2,NACA,NDUFAF2,PDCD5, POC5,QTRT1,TAF7,TBCA,TTC1,ZNF443,ZNF799	AADAC,APOA1,APOA4,APOC3,C17orf78,CRISP1,FABP6, FAM99A,FAM99B,GSTA5,KCNJ13,LCE3E,LOC388428,MOS, ONECUT3,OR10H1,OR10H5,OR4N5,PWAR4___F2RL3___PAWR,SLC2A2,SPANXN3

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 FABP6

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB02659	fatty acid binding protein 6, ileal	experimental	Cholic Acid
DB02691	fatty acid binding protein 6, ileal	experimental	N-Cholylglycine
DB04348	fatty acid binding protein 6, ileal	experimental	Taurocholic Acid
DB00145	fatty acid binding protein 6, ileal	approved; nutraceutical	Glycine

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Cross referenced IDs for FABP6

* 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