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 FABP1

Basic gene info.	Gene symbol	FABP1
	Gene name	fatty acid binding protein 1, liver
	Synonyms	FABPL\|L-FABP
	Cytomap	UCSC genome browser: 2p11
	Genomic location	chr2 :88422507-88427650
	Type of gene	protein-coding
	RefGenes	NM_001443.2,
	Ensembl id	ENSG00000163586
	Description	fatty acid-binding protein 1fatty acid-binding protein, liverliver-type fatty acid-binding protein
	Modification date	20141207
dbXrefs	MIM : 134650
	HGNC : HGNC
	Ensembl : ENSG00000163586
	HPRD : 00612
	Vega : OTTHUMG00000130312
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FABP1
	BioGPS: 2168
	Gene Expression Atlas: ENSG00000163586
	The Human Protein Atlas: ENSG00000163586
Pathway	NCI Pathway Interaction Database: FABP1
	KEGG: FABP1
	REACTOME: FABP1
	ConsensusPathDB
	Pathway Commons: FABP1
Metabolism	MetaCyc: FABP1
	HUMANCyc: FABP1
Regulation	Ensembl's Regulation: ENSG00000163586
	miRBase: chr2 :88,422,507-88,427,650
	TargetScan: NM_001443
	cisRED: ENSG00000163586
Context	iHOP: FABP1
	cancer metabolism search in PubMed: FABP1
	UCL Cancer Institute: FABP1
Assigned class in ccmGDB	C

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Phenotypic Information for FABP1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: FABP1
	Familial Cancer Database: FABP1

* 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: FABP1
	MedGen: FABP1 (Human Medical Genetics with Condition)
	ClinVar: FABP1
Phenotype	MGI: FABP1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: FABP1

Mutations for FABP1

* 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 FABP1 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
AK000234	PRDM10	1	2619	11	129772259	129812485	FABP1	2613	2916	2	88422501	88425782
AI114691	GOT1	30	319	10	101180445	101190377	FABP1	304	643	2	88424050	88427579
CB163566	FABP1	1	407	2	88427067	88427473	FABP1	400	650	2	88422552	88425780

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=25)	Stat. for Synonymous SNVs (# total SNVs=7)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr2:88425751-88425751	p.E62K	5
chr2:88425826-88425826	p.G37R	4
chr2:88425757-88425757	p.Q60E	2
chr2:88425708-88425708	p.G76E	2
chr2:88427470-88427470	p.G23S	2
chr2:88425812-88425812	p.I41I	2
chr2:88422621-88422621	p.T112T	2
chr2:88427491-88427491	p.E16K	2
chr2:88427523-88427523	p.G5D	2
chr2:88425847-88425847	p.Q30E	2

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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=3

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	1		2	1		2		2			4	1				9	1		3
# mutation	1	1		2	1		2		2			4	1				7	1		3
nonsynonymous SNV		1		2	1		1		1				1				4			3
synonymous SNV	1						1		1			4					3	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
chr2:88425751	p.E62K	3
chr2:88424070	p.E68K	1
chr2:88425812	p.E16E	1
chr2:88424078	p.S4F	1
chr2:88425819	p.E67D	1
chr2:88425708	p.G66G	1
chr2:88425824	p.V65V	1
chr2:88425733	p.Q60E	1
chr2:88425840	p.G55G	1
chr2:88425734	p.T53T	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 FABP1 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 FABP1

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


APCS,APOA2,APOA4,APOB,APOC3,ARG1,C8A, C9,CREB3L3,CRP,F2,FABP1,FGF23,HP, ITIH1,MT1B,PLG,SERPINA7,SERPINC1,SLC17A2,TM4SF5	ANXA10,CCL14-CCL15,CDH17,DCT,FABP1,FAM71B,GPR101, GUCA1C,HSFY1P1,IFNA2,LGALS4,MUC17,NKX6-2,OPTC, OR10K1,OR52B2,OR52E4,OR5AS1,OR6S1,PRAMEF6,WIF1

ABCC13,AXDND1,EPCAM,FABP1,FER1L4,GPR39,HHLA2, KRT20,NAT2,P2RY2,PDE6A,PDZD3,PIGZ,PLCE1, PPARG,PPP1R14C,PPP1R14D,PRELID2,SFXN5,SGK2,UGP2	ABHD3,ACOX1,CXorf56,EPCAM,FABP1,GRAMD3,JOSD1, MGLL,OPN3,PDCD6IP,PKIB,PLOD2,PPARG,PPP1R14C, PTPRR,RNF103,SGK2,TGFA,TMEM171,TMEM65,VDAC1

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 FABP1

There's no related Drug.

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Cross referenced IDs for FABP1

* 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