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 AAAS

Basic gene info.	Gene symbol	AAAS
	Gene name	achalasia, adrenocortical insufficiency, alacrimia
	Synonyms	AAA\|AAASb\|ADRACALA\|ADRACALIN\|ALADIN
	Cytomap	UCSC genome browser: 12q13
	Genomic location	chr12 :53701239-53715412
	Type of gene	protein-coding
	RefGenes	NM_001173466.1, NM_015665.5,
	Ensembl id	ENSG00000094914
	Description	Allgrove, triple-Aaladin
	Modification date	20141207
dbXrefs	MIM : 605378
	HGNC : HGNC
	Ensembl : ENSG00000094914
	HPRD : 05646
	Vega : OTTHUMG00000169729
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AAAS
	BioGPS: 8086
	Gene Expression Atlas: ENSG00000094914
	The Human Protein Atlas: ENSG00000094914
Pathway	NCI Pathway Interaction Database: AAAS
	KEGG: AAAS
	REACTOME: AAAS
	ConsensusPathDB
	Pathway Commons: AAAS
Metabolism	MetaCyc: AAAS
	HUMANCyc: AAAS
Regulation	Ensembl's Regulation: ENSG00000094914
	miRBase: chr12 :53,701,239-53,715,412
	TargetScan: NM_001173466
	cisRED: ENSG00000094914
Context	iHOP: AAAS
	cancer metabolism search in PubMed: AAAS
	UCL Cancer Institute: AAAS
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: AAAS
	Familial Cancer Database: AAAS

* 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_NON_CODING_RNA REACTOME_METABOLISM_OF_RNA REACTOME_METABOLISM_OF_CARBOHYDRATES

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

Mutations for AAAS

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_b

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows AAAS 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
AW205219	AAAS	17	67	12	53701240	53701290	FKBP6	66	382	7	72738395	72738711
AI755186	AAAS	21	91	12	53701244	53701314	C15orf39	84	406	15	75498882	75499204
AW794716	AAAS	26	324	12	53701363	53701914	MAOB	316	496	X	43626252	43626432
AI523835	AAAS	8	76	12	53701246	53701314	ZNF414	72	491	19	8576625	8577581
BQ301032	AAAS	6	181	12	53714824	53715001	KDM2A	173	519	11	66901279	66901623
BQ327397	ATP2A2	38	216	12	110783843	110784104	AAAS	201	569	12	53702079	53703008

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=37)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=1)

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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
chr12:53702751-53702751	p.R330H	2
chr12:53702114-53702114	p.S401T	2
chr12:53701433-53701433	p.F494C	2
chr12:53703424-53703424	p.R258fs*33	2
chr12:53703435-53703435	p.P254S	2
chr12:53702089-53702090	p.E409fs*17	1
chr12:53708552-53708552	p.R176R	1
chr12:53709211-53709211	p.?	1
chr12:53701431-53701431	p.S495C	1
chr12:53708083-53708083	p.R230*	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		3		4	1		3		3			4	2	1			6	5		6
# mutation		3		4	1		4		3			4	2	1			12	5		6
nonsynonymous SNV		2		3			4		1			3	1				4	4		6
synonymous SNV		1		1	1				2			1	1	1			8	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
chr12:53702751	p.R297H,AAAS	2
chr12:53702559	p.R445Q,AAAS	1
chr12:53708115	p.T258T,AAAS	1
chr12:53701431	p.C80F,AAAS	1
chr12:53709521	p.S438S,AAAS	1
chr12:53702561	p.L206L,AAAS	1
chr12:53708119	p.R66I,AAAS	1
chr12:53701481	p.A435V,AAAS	1
chr12:53714361	p.T196T,AAAS	1
chr12:53702566	p.P58P,AAAS	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 AAAS 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 AAAS

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


AAAS,ANKS3,ATP5G2,BLOC1S1,C12orf10,CCDC101,CCDC24, E4F1,INO80E,MCRS1,NDUFA2,NABP2,OGFOD2,PFDN5, POLL,RHOT2,SMUG1,SPSB3,TARBP2,UBXN11,WIBG	AAAS,CARKD,CCDC22,COQ4,CPSF3L,DDX41,DDX56, DMAP1,DNAJC4,DRG2,ERCC1,HMG20B,NPRL2,POMT1, PTOV1,TMEM161A,TMEM186,WBP1,WRAP53,XAB2,ZFYVE19

AAAS,C12orf10,C17orf53,CNPY2,DDX54,MCRS1,METTL1, NOC4L,NABP2,PA2G4,PCBP2,PUS1,SARS2,SRSF9, SNRPA,SNRPF,TARBP2,TIMELESS,TROAP,TSFM,TUBA1B	AAAS,ACAD9,C17orf53,ARHGEF39,CDH24,CHTF18,EXOSC10, FOXM1,INTS9,KAT2A,KIF18B,MTHFD1,NCAPD3,POLD2, RAD54L,SNRPA,SSRP1,SUV39H1,TARS2,TELO2,TRAP1

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 AAAS

There's no related Drug.

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Cross referenced IDs for AAAS

* 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