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 FAU

Basic gene info.	Gene symbol	FAU
	Gene name	Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed
	Synonyms	FAU1\|Fub1\|Fubi\|MNSFbeta\|RPS30\|S30\|asr1
	Cytomap	UCSC genome browser: 11q13
	Genomic location	chr11 :64888098-64889672
	Type of gene	protein-coding
	RefGenes	NM_001997.4,
	Ensembl id	ENSG00000149806
	Description	40S ribosomal protein S30FAU-encoded ubiquitin-like proteinFBR-MuSV-associated ubiquitously expressedFinkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived)monoclonal nonspecific suppressor factor betaribosomal prote
	Modification date	20141207
dbXrefs	MIM : 134690
	HGNC : HGNC
	HPRD : 00002
Protein	UniProt: P35544 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FAU
	BioGPS: 2197
	Gene Expression Atlas: ENSG00000149806
	The Human Protein Atlas: ENSG00000149806
Pathway	NCI Pathway Interaction Database: FAU
	KEGG: FAU
	REACTOME: FAU
	ConsensusPathDB
	Pathway Commons: FAU
Metabolism	MetaCyc: FAU
	HUMANCyc: FAU
Regulation	Ensembl's Regulation: ENSG00000149806
	miRBase: chr11 :64,888,098-64,889,672
	TargetScan: NM_001997
	cisRED: ENSG00000149806
Context	iHOP: FAU
	cancer metabolism search in PubMed: FAU
	UCL Cancer Institute: FAU
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: FAU
	Familial Cancer Database: FAU

* 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 REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	134690; gene.
Orphanet
Disease	KEGG Disease: FAU
	MedGen: FAU (Human Medical Genetics with Condition)
	ClinVar: FAU
Phenotype	MGI: FAU (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: FAU

Mutations for FAU

* 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 FAU 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
BG251227	APOL6	1	98	22	36058447	36058545	FAU	98	543	11	64888106	64889283
X75315	FAU	1	64	11	64888171	64888234	MIR5095	57	1434	20	55966720	55983642
BG472330	FAU	20	163	11	64888161	64888479	BAD	164	768	11	64037652	64052162
AJ712941	FAU	9	74	11	64888257	64888496	PLIN3	64	335	19	4838947	4839219
BG479472	FAU	21	165	11	64888161	64888479	BAD	166	617	11	64039085	64052162
AA071465	FAU	22	74	11	64888102	64888154	CNOT2	66	491	12	70747715	70748140
AA469444	PRKDC	14	39	8	48792396	48792421	FAU	37	427	11	64888102	64889225
BG491927	FAU	20	101	11	64888178	64888260	CALR	98	950	19	13050328	13054606
BM990847	FAU	18	86	11	64888102	64888170	MRPL16	78	563	11	59573821	59574306
DR979128	PTPRD	1	89	9	8316051	8316140	FAU	78	152	11	64888106	64888180
CN275873	ANKRD11	6	646	16	89348352	89348995	FAU	633	799	11	64888108	64888275

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=12)	Stat. for Synonymous SNVs (# total SNVs=5)

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
chr11:64888248-64888250	p.K102delK	2
chr11:64888518-64888518	p.?	2
chr11:64888169-64888169	p.P129H	2
chr11:64888211-64888211	p.R115H	1
chr11:64889083-64889083	p.E37*	1
chr11:64888220-64888220	p.Y112C	1
chr11:64889126-64889126	p.?	1
chr11:64889260-64889260	p.E9V	1
chr11:64888252-64888252	p.K101K	1
chr11:64889268-64889268	p.R6R	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	2			2	1				1	1		1						1		2
# mutation	2			2	1				1	1		1						1		2
nonsynonymous SNV	2			2	1				1	1		1								1
synonymous SNV																		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
chr11:64888220	p.Y112C	1
chr11:64888258	p.K99N	1
chr11:64888455	p.K92E	1
chr11:64889007	p.L62P	1
chr11:64889081	p.E37D	1
chr11:64889086	p.P36S	1
chr11:64889260	p.E9V	1
chr11:64889277	p.L3L	1
chr11:64888164	p.A131T	1
chr11:64888175	p.K127M	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 FAU 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 FAU

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


ATP5D,UQCC3,C19orf43,FAU,FKBP2,GADD45GIP1,PRDX5, RPL13,RPL18,RPL28,RPL35,RPL36,RPL37A,RPLP2, RPS15,RPS19,RPS9,TRMT112,UBXN1,ZFPL1,ZNHIT2	C12orf10,EDF1,EEF1D,EIF3G,FAU,NME2,POLR2F, PQBP1,PRDX5,RFXANK,RPL13,RPL18,RPL19,RPL35, RPL36,RPL8,RPS15,RPS16,RPS9,SNRPD2,SURF2

ATP5L,BANF1,C11orf31,UQCC3,C19orf53,COA4,FAU, GADD45GIP1,MRPL11,MRPL21,NDUFA13,NDUFB7,NDUFS3,PFDN5, RPL24,RPS25,RPS3,RPS9,SSSCA1,PAM16,TMEM223	ALKBH2,ANAPC11,C12orf57,C19orf53,FAU,FIS1,HAX1, MRPL40,MRPL43,OST4,PFDN5,RPL24,RPL35,RPL35A, RPL41,RPL5,RPS10,RPS11,RPS13,RPS5,SNRPD2

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 FAU

There's no related Drug.

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Cross referenced IDs for FAU

* 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