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 ALB

Basic gene info.	Gene symbol	ALB
	Gene name	albumin
	Synonyms	ANALBA\|FDAH\|PRO0883\|PRO0903\|PRO1341
	Cytomap	UCSC genome browser: 4q13.3
	Genomic location	chr4 :74269971-74287129
	Type of gene	protein-coding
	RefGenes	NM_000477.5,
	Ensembl id	ENSG00000163631
	Description	albumin (32 AA)albumin (AA 34)cell growth inhibiting protein 42growth-inhibiting protein 20serum albumin
	Modification date	20141207
dbXrefs	MIM : 103600
	HGNC : HGNC
	Ensembl : ENSG00000163631
	HPRD : 00062
	Vega : OTTHUMG00000129919
Protein	UniProt: P02768 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ALB
	BioGPS: 213
	Gene Expression Atlas: ENSG00000163631
	The Human Protein Atlas: ENSG00000163631
Pathway	NCI Pathway Interaction Database: ALB
	KEGG: ALB
	REACTOME: ALB
	ConsensusPathDB
	Pathway Commons: ALB
Metabolism	MetaCyc: ALB
	HUMANCyc: ALB
Regulation	Ensembl's Regulation: ENSG00000163631
	miRBase: chr4 :74,269,971-74,287,129
	TargetScan: NM_000477
	cisRED: ENSG00000163631
Context	iHOP: ALB
	cancer metabolism search in PubMed: ALB
	UCL Cancer Institute: ALB
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ALB in cancer cell metabolism	1. Kamphorst JJ, Nofal M, Commisso C, Hackett SR, Lu W, et al. (2015) Human pancreatic cancer tumors are nutrient poor and tumor cells actively scavenge extracellular protein. Cancer Res 75: 544-553. doi: 10.1158/0008-5472.CAN-14-2211. pmid: 4316379. go to article

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

Cancer Description
Cancer	CGAP: ALB
	Familial Cancer Database: ALB

* 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 REACTOME_LIPOPROTEIN_METABOLISM

Others
OMIM	103600; gene. 103600; gene. 615999; phenotype. 615999; phenotype.
Orphanet	276271; Familial dysalbuminemic hyperthyroxinemia. 276271; Familial dysalbuminemic hyperthyroxinemia. 86816; Congenital analbuminemia. 86816; Congenital analbuminemia.
Disease	KEGG Disease: ALB
	MedGen: ALB (Human Medical Genetics with Condition)
	ClinVar: ALB
Phenotype	MGI: ALB (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ALB

Mutations for ALB

* 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 ALB 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
BP294362	ALB	1	475	4	74270006	74274476	SERPING1	475	582	11	57381845	57381951
BG562874	APOB	1	367	2	21227268	21228146	ALB	359	660	4	74279174	74280877
DA643030	EBNA1BP2	2	413	1	43680937	43713713	ALB	412	590	4	74270084	74272426
AI133546	ALB	10	564	4	74283248	74286029	ZDHHC2	557	638	8	17078894	17078975
AI114516	STK38L	1	194	12	27476070	27476263	ALB	188	767	4	74279302	74283959
AV653907	AOX1	1	364	2	201534428	201535676	ALB	362	706	4	74283944	74286870
AF119890	GABPA	1	354	21	27141926	27142279	ALB	350	1598	4	74277769	74286973
AW072570	ALB	1	158	4	74286814	74286971	APP	159	498	21	27354655	27394191
AF119840	CMAS	1	647	12	22215302	22215952	ALB	641	2699	4	74270004	74286973
AF118090	ZNF536	1	697	19	30863628	30864332	ALB	692	1690	4	74279313	74286973
AI174891	ACTR3	2	489	2	114677181	114677671	ALB	483	758	4	74270078	74274349
AF116711	ALB	167	274	4	74281996	74283280	RPS4Y1	268	1144	Y	2709643	2734997
AI064841	RABGAP1L	13	211	1	174189320	174189518	ALB	208	654	4	74283248	74285307
AI114561	MSL3	19	341	X	11777779	11778966	ALB	337	680	4	74283960	74286879
AI207561	ALAS2	20	340	X	55035491	55039953	ALB	338	642	4	74285286	74286973
W86731	ALB	1	93	4	74279196	74279288	VPS13B	84	452	8	100222381	100222742
AI065112	ALB	1	544	4	74283820	74286942	TF	539	641	3	133497528	133497630
AI305112	C3	1	387	19	6678438	6682029	ALB	379	612	4	74270017	74272414
BG545312	ALB	2	400	4	74270004	74274400	MALAT1	388	714	11	65267378	65267699
AF116645	TF	1	240	3	133490670	133490909	ALB	234	1242	4	74279289	74286959
AI114654	ALB	8	218	4	74283921	74285332	ALB	216	744	4	74279251	74283862
AI174917	ALB	167	274	4	74281996	74283280	RPS4Y1	268	691	Y	2709643	2722681
AI133207	SASH3	1	58	X	128929090	128929147	ALB	50	699	4	74270004	74275197
AV654807	ABLIM3	1	128	5	148534150	148534277	ALB	129	393	4	74270030	74272458
AA884347	ALB	1	158	4	74286814	74286971	APP	159	459	21	27354655	27372495
AI064877	ALB	1	51	4	74282020	74282070	ALB	48	444	4	74283298	74285307
AF116688	MATR3	5	1032	5	138631171	138632200	ALB	1029	1124	4	74287034	74287129
AI110818	ALB	1	466	4	74280850	74284021	ALB	455	636	4	74279160	74279341
DA640348	KNG1	4	317	3	186435149	186435462	ALB	318	545	4	74270004	74272395
AI174759	AHSG	1	163	3	186338913	186339075	ALB	154	609	4	74270015	74274466
AF075316	ALB	1	466	4	74280850	74284021	ALB	455	636	4	74279160	74279341
BG563936	MYO18A	2	363	17	27405532	27405893	ALB	359	685	4	74280437	74280766
DQ145726	TXNL4B	46	876	16	72094073	72094903	ALB	863	1070	4	74285996	74286973
AI133116	TF	1	240	3	133490670	133490909	ALB	234	582	4	74279289	74283301
AU120466	ARID4B	329	349	1	235456198	235456218	ALB	331	790	4	74270005	74274461
BG564023	MYO18A	2	363	17	27405532	27405893	ALB	359	683	4	74280437	74280763
AI207513	ALB	1	154	4	74270006	74270868	SETD4	148	652	21	37444788	37445291

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=77)	Stat. for Synonymous SNVs (# total SNVs=26)

Stat. for Deletions (# total SNVs=25)	Stat. for Insertions (# total SNVs=3)

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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
chr4:74281975-74281975	p.F398F	6
chr4:74279174-74279174	p.S294L	4
chr4:74283258-74283258	p.R434C	4
chr4:74280861-74280861	p.P390S	4
chr4:74276115-74276115	p.A234A	4
chr4:74276060-74276060	p.S216L	3
chr4:74270067-74270067	p.S8F	3
chr4:74285296-74285296	p.F575F	3
chr4:74270047-74270047	p.M1I	2
chr4:74285285-74285288	p.D573fs*6	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=6

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	4			16	4		5		2	1		6	4	4			25	5	1	11
# mutation	4			13	4		5		2	1		6	5	4			29	7	1	11
nonsynonymous SNV	2			8	4		4		2	1		5	4	3			19	5	1	8
synonymous SNV	2			5			1					1	1	1			10	2		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
chr4:74281975	p.F398F	5
chr4:74276115	p.A234A	4
chr4:74283258	p.S294L	3
chr4:74279174	p.R434C	3
chr4:74280861	p.R210W	2
chr4:74283322	p.P390S	2
chr4:74276114	p.H312R	2
chr4:74279228	p.G455E	2
chr4:74276041	p.F575F	2
chr4:74285296	p.A234V	2

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 ALB 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 ALB

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


AFP,ALB,CACNG1,CHD1,GABRB3,GLDN,HTR7P1, ITPR2,KCNC1,KIAA1467,LOC285401,MOCS1,NAPB,NELL1, PAQR5,PCSK2,PVALB,RASSF6,SEMA5A,SNAP25,WBP11	AFP,ALB,ANGPTL3,BCO1,HNF1A-AS1,SMCO3,LINC00470___CHMP1B, HABP2,HNF1A,KCNH6,KIF12,MIA2,MTNR1B,PKHD1, POTED,SCARNA15,TMED6,TTLL6,UGT2B15,UTS2,ZNF385B

AHSG,ALB,APCS,APOC3,C8A,C8B,C9, CFHR2,CFHR5,CRP,F9,FGA,FGG,GDF2, HFE2,HPX,HRG,ITIH1,SERPINC1,SPP2,VTN	ALB,APCS,APOA2,C3P1,C8A,CFHR2,CFHR5, CYP4A22,DNAJB8,F13B,F9,FGG,HRG,KIR3DP1, KRTAP4-11,KRTAP5-3,LECT2,LOC100129935,LINC00160,OR1N1,SLC17A2

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 ALB

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P02768; -.
Chemistry	ChEMBL	CHEMBL3253; -.
Chemistry	BindingDB	P02768; -.
Chemistry	ChEMBL	CHEMBL3253; -.
Organism-specific databases	PharmGKB	PA24690; -.
Organism-specific databases	PharmGKB	PA24690; -.
Organism-specific databases	CTD	213; -.
Organism-specific databases	CTD	213; -.

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
DB00145	albumin	approved; nutraceutical	Glycine

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Cross referenced IDs for ALB

* 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