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 ALDOC

Basic gene info.	Gene symbol	ALDOC
	Gene name	aldolase C, fructose-bisphosphate
	Synonyms	ALDC
	Cytomap	UCSC genome browser: 17cen-q12
	Genomic location	chr17 :26900132-26903951
	Type of gene	protein-coding
	RefGenes	NM_005165.2,
	Ensembl id	ENSG00000109107
	Description	aldolase 3brain-type aldolasefructoaldolase Cfructose-1,6-biphosphate triosephosphate lyasefructose-bisphosphate aldolase C
	Modification date	20141207
dbXrefs	MIM : 103870
	HGNC : HGNC
	Ensembl : ENSG00000109107
	HPRD : 02386
	Vega : OTTHUMG00000132605
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ALDOC
	BioGPS: 230
	Gene Expression Atlas: ENSG00000109107
	The Human Protein Atlas: ENSG00000109107
Pathway	NCI Pathway Interaction Database: ALDOC
	KEGG: ALDOC
	REACTOME: ALDOC
	ConsensusPathDB
	Pathway Commons: ALDOC
Metabolism	MetaCyc: ALDOC
	HUMANCyc: ALDOC
Regulation	Ensembl's Regulation: ENSG00000109107
	miRBase: chr17 :26,900,132-26,903,951
	TargetScan: NM_005165
	cisRED: ENSG00000109107
Context	iHOP: ALDOC
	cancer metabolism search in PubMed: ALDOC
	UCL Cancer Institute: ALDOC
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: ALDOC
	Familial Cancer Database: ALDOC

* 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
KEGG_GLYCOLYSIS_GLUCONEOGENESIS KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

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

Mutations for ALDOC

* 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 ALDOC 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
DA078791	GAD1	1	274	2	171673400	171675153	ALDOC	274	581	17	26901972	26902481
AI193580	SYN1	1	136	X	47446055	47446190	ALDOC	128	718	17	26900382	26901220
BE070871	TRAK1	17	140	3	42245638	42245761	ALDOC	126	278	17	26900278	26900430
AI308067	MARK2	1	152	11	63676897	63677048	ALDOC	151	275	17	26900284	26900408
DA088736	WNK1	1	199	12	971381	987436	ALDOC	198	572	17	26902165	26903883

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=18)	Stat. for Synonymous SNVs (# total SNVs=8)

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
chr17:26901115-26901115	p.L257L	6
chr17:26901108-26901108	p.R259H	2
chr17:26901111-26901111	p.R258H	2
chr17:26902486-26902486	p.R22Q	2
chr17:26901545-26901545	p.H197H	2
chr17:26901099-26901099	p.P262H	1
chr17:26902013-26902013	p.G112G	1
chr17:26900833-26900833	p.Q307K	1
chr17:26902186-26902186	p.P93P	1
chr17:26900838-26900838	p.A305V	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		1		3	1		3					2	2	1		1	3	6		4
# mutation		1		3	1		3					2	2	1		1	3	6		4
nonsynonymous SNV		1		3			1					2	1	1		1	2	4		3
synonymous SNV					1		2						1				1	2		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
chr17:26901108	p.R259H	2
chr17:26901211	p.Y358Y	1
chr17:26902474	p.H197H	1
chr17:26900833	p.L311F	1
chr17:26901251	p.R173C	1
chr17:26902486	p.Q307K	1
chr17:26900841	p.P93P	1
chr17:26901258	p.R304H	1
chr17:26902512	p.G91V	1
chr17:26900842	p.R304C	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 ALDOC 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 ALDOC

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


ALDOC,DNLZ,ERAL1,FLOT2,GAPDH,IFT20,LOC389458, MRPS24,PIGS,PLAC8L1,POLD2,POLDIP2,RPL23A,SCT, SDF2,SPAG4,TBRG4,TLCD1,TMEM199,TRAF4,UNC119	ABCD2,ADIPOR2,AIFM2,ALDOC,CALB2,CPA2,DGAT1, DGAT2,EPHX1,FADS3,FMOD,GDPD5,GLYAT,GPAM, HSPA12A,SLC25A51,MRAP,PDXK,RASGRF2,RPS2P32,TK2

ACAT2,ALDOA,ALDOC,C14orf1,C6orf223,CYP51A1,DHCR7, GPI,HMGCS1,INSIG1,LDHA,MVD,NARF,P4HA1, PCSK9,PLA2G3,PRR15L,MSMO1,TFRC,TMEM97,WDR45B	ALDOC,ALPI,SLC25A47,C9orf24,CCDC108,CREB3L3,CRIP1, DNASE1,FADS6,FAM151A,MLXIPL,NAALADL1,PFKFB4,PLB1, PNLIPRP2,PRODH,SI,SLC15A1,TM4SF5,UGT2B7,VNN1

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 ALDOC

There's no related Drug.

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Cross referenced IDs for ALDOC

* 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