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 GALM

Basic gene info.	Gene symbol	GALM
	Gene name	galactose mutarotase (aldose 1-epimerase)
	Synonyms	GLAT\|HEL-S-63p\|IBD1
	Cytomap	UCSC genome browser: 2p22.1
	Genomic location	chr2 :38893051-38961909
	Type of gene	protein-coding
	RefGenes	NM_138801.2,
	Ensembl id	ENSG00000143891
	Description	aldose 1-epimeraseepididymis secretory sperm binding protein Li 63pgalactomutarotasegalactose enzyme activator
	Modification date	20141207
dbXrefs	MIM : 137030
	HGNC : HGNC
	Ensembl : ENSG00000143891
	HPRD : 13559
	Vega : OTTHUMG00000102077
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GALM
	BioGPS: 130589
	Gene Expression Atlas: ENSG00000143891
	The Human Protein Atlas: ENSG00000143891
Pathway	NCI Pathway Interaction Database: GALM
	KEGG: GALM
	REACTOME: GALM
	ConsensusPathDB
	Pathway Commons: GALM
Metabolism	MetaCyc: GALM
	HUMANCyc: GALM
Regulation	Ensembl's Regulation: ENSG00000143891
	miRBase: chr2 :38,893,051-38,961,909
	TargetScan: NM_138801
	cisRED: ENSG00000143891
Context	iHOP: GALM
	cancer metabolism search in PubMed: GALM
	UCL Cancer Institute: GALM
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: GALM
	Familial Cancer Database: GALM

* 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

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

Mutations for GALM

* 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

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	GALM	chr2	38944272	38944292	GALM	chr2	38944398	38944418
pancreas	GALM	chr2	38931828	38931848		chr2	38346045	38346065

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 GALM 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
BX107111	GALM	1	170	2	38960844	38961013	SNX14	167	471	6	86216319	86216623
CR997728	GALM	257	751	2	38905701	39308967	ALK	745	796	2	30081615	30081666

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=14)	Stat. for Synonymous SNVs (# total SNVs=6)

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
chr2:38893492-38893492	p.E63D	3
chr2:38960639-38960639	p.P321S	2
chr2:38956797-38956797	p.N245I	1
chr2:38893397-38893397	p.D32N	1
chr2:38908466-38908466	p.S130S	1
chr2:38956810-38956810	p.K249K	1
chr2:38893484-38893484	p.E61*	1
chr2:38908499-38908499	p.P141P	1
chr2:38958889-38958889	p.A263A	1
chr2:38908517-38908517	p.W147*	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	4			2			1		2			3	1				3	2		4
# mutation	5			2			1		2			3	1				3	3		4
nonsynonymous SNV	2			2					2			1					2	3		1
synonymous SNV	3						1					2	1				1			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
chr2:38893363	p.E20E	2
chr2:38903126	p.G92G	1
chr2:38956751	p.P318S	1
chr2:38903134	p.E94K	1
chr2:38956797	p.F320S	1
chr2:38903139	p.A98A	1
chr2:38956810	p.F337F	1
chr2:38903143	p.E102K	1
chr2:38958889	p.V127I	1
chr2:38903157	p.S130S	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 GALM 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 GALM

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


ALOX15B,CASP10,CCRL2,DPEP2,GALM,GGT1,GGT3P, GGTLC1,GM2A,GNGT2,GUCY2D,HAAO,IFI30,MPV17L, MVK,NR1H3,OXER1,SLC26A6,SLED1,SPINK8,IGFLR1	ABCC2,ADAM2,ALOX15B,C6orf223,CLU,DHRS2,DNASE2B, G6PD,GALM,GUSB,HAAO,HPGD,HSD3B2,LST-3TM12, NUDT8,PNLIPRP3,PPAPDC1A,SCP2,SERHL2,SERHL,TARP

ACADS,ACY3,C6orf136,CEP70,CHST4,FAM162A,GALM, IQGAP2,LDHD,LIMA1,LRG1,MMP15,MOB3B,NANS, PIGR,RBM47,SCP2,SDHA,SH3RF2,SULT1C2,TJP3	ACADS,ACSF3,AP1M2,KDF1,C6orf136,CBLC,CYB561A3, DCAF11,ELMO3,EPN1,ESRRA,GALM,MAP2K2,MGAT4B, MTMR14,OVOL1,PFKL,PPAP2C,PRKCZ,TMEM102,ZDHHC12

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 GALM

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB02379	galactose mutarotase (aldose 1-epimerase)	experimental	Beta-D-Glucose
DB03142	galactose mutarotase (aldose 1-epimerase)	experimental	Alpha-L-Arabinose
DB03389	galactose mutarotase (aldose 1-epimerase)	experimental	alpha-D-Xylopyranose
DB03773	galactose mutarotase (aldose 1-epimerase)	experimental	6-Deoxy-Alpha-D-Glucose

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Cross referenced IDs for GALM

* 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