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 FABP4

Basic gene info.	Gene symbol	FABP4
	Gene name	fatty acid binding protein 4, adipocyte
	Synonyms	A-FABP\|AFABP\|ALBP\|HEL-S-104\|aP2
	Cytomap	UCSC genome browser: 8q21
	Genomic location	chr8 :82390731-82395473
	Type of gene	protein-coding
	RefGenes	NM_001442.2,
	Ensembl id	ENSG00000170323
	Description	adipocyte lipid-binding proteinadipocyte-type fatty acid-binding proteinepididymis secretory protein Li 104fatty acid-binding protein 4fatty acid-binding protein, adipocyte
	Modification date	20141222
dbXrefs	MIM : 600434
	HGNC : HGNC
	Ensembl : ENSG00000170323
	HPRD : 02698
	Vega : OTTHUMG00000164602
Protein	UniProt: P15090 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FABP4
	BioGPS: 2167
	Gene Expression Atlas: ENSG00000170323
	The Human Protein Atlas: ENSG00000170323
Pathway	NCI Pathway Interaction Database: FABP4
	KEGG: FABP4
	REACTOME: FABP4
	ConsensusPathDB
	Pathway Commons: FABP4
Metabolism	MetaCyc: FABP4
	HUMANCyc: FABP4
Regulation	Ensembl's Regulation: ENSG00000170323
	miRBase: chr8 :82,390,731-82,395,473
	TargetScan: NM_001442
	cisRED: ENSG00000170323
Context	iHOP: FABP4
	cancer metabolism search in PubMed: FABP4
	UCL Cancer Institute: FABP4
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of FABP4 in cancer cell metabolism	1. Uehara H, Takahashi T, Oha M, Ogawa H, Izumi K (2014) Exogenous fatty acid binding protein 4 promotes human prostate cancer cell progression. Int J Cancer 135: 2558-2568. doi: 10.1002/ijc.28903. go to article 2. Harjes U, Bridges E, McIntyre A, Fielding BA, Harris AL (2014) Fatty acid-binding protein 4, a point of convergence for angiogenic and metabolic signaling pathways in endothelial cells. J Biol Chem 289: 23168-23176. doi: 10.1074/jbc.M114.576512. pmid: 4132814. go to article 3. Hu J, Liu Z, Wang X (2013) Does TP53 mutation promote ovarian cancer metastasis to omentum by regulating lipid metabolism? Med Hypotheses 81: 515-520. doi: 10.1016/j.mehy.2013.06.009. go to article

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Phenotypic Information for FABP4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: FABP4
	Familial Cancer Database: FABP4

* 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	600434; gene.
Orphanet
Disease	KEGG Disease: FABP4
	MedGen: FABP4 (Human Medical Genetics with Condition)
	ClinVar: FABP4
Phenotype	MGI: FABP4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: FABP4

Mutations for FABP4

* 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 FABP4 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
BP317019	FABP4	1	390	8	82391673	82395468	PMP22	390	516	17	15143726	15143852
BG290021	FABP4	11	258	8	82390927	82391672	SEMA3C	259	359	7	80371856	80371956
BG992392	METTL17	1	105	14	21464814	21464977	FABP4	99	560	8	82391102	82395468

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=13)	Stat. for Synonymous SNVs (# total SNVs=2)

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
chr8:82392794-82392794	p.K38T	2
chr8:82392828-82392828	p.G27S	1
chr8:82391652-82391652	p.V115V	1
chr8:82395328-82395328	p.?	1
chr8:82391672-82391672	p.R109*	1
chr8:82395334-82395334	p.E23D	1
chr8:82391709-82391709	p.Q96H	1
chr8:82395335-82395335	p.E23G	1
chr8:82391717-82391717	p.H94N	1
chr8:82395335-82395346	p.D19_K22delDYMK	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=1

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		3			2							1			1			1
# mutation		1		3			2							1			1			1
nonsynonymous SNV		1		3			2							1			1			1
synonymous SNV

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
chr8:82391709	p.A76S	1
chr8:82392681	p.M41I	1
chr8:82392784	p.A37T	1
chr8:82392798	p.G27R	1
chr8:82392828	p.E23G	1
chr8:82395335	p.A4D	1
chr8:82395392	p.T126M	1
chr8:82391122	p.V119I	1
chr8:82391144	p.Q96H	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 FABP4 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 FABP4

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


ADH1B,ADIPOQ,AOC3,AQP7,AQP7P1,C14orf180,CIDEC, FABP4,FHL1,GLYAT,GPD1,GPX3,ITIH5,KCNIP2, LIPE,NPR1,PDE1B,PLIN1,PLIN4,RDH5,TMEM37	AOC3,FAM213A,CD36,CIDEC,CPM,ESYT1,FABP4, FBXO27,GABRE,GNAI1,GYG2,HRASLS5,KCNIP2,PDE8A, PEX19,PLIN1,PPARG,SH3KBP1,SLC35G2,TYRO3,VEGFB

ACSM5,ADH1B,ADIPOQ,AQP7,CD300LG,CD36,CIDEA, FABP4,GLYAT,HEPACAM,KCNIP2,LBP,LEP,LGALS12, LIPE,LOC339524,MRAP,PLIN1,PLIN4,SCN4A,TUSC5	ADIPOQ,AQP7P1,CD300LG,CD36,CIDEA,DEFB132,DGAT2, FABP4,G0S2,GPAM,KCNIP2,LGALS12,LIPE,LOC283392, LPL,MRAP,PLIN1,RBP7,SLC7A10,THRSP,TUSC5

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 FABP4

There's no related Drug.

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Cross referenced IDs for FABP4

* 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