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 PGM1

Basic gene info.	Gene symbol	PGM1
	Gene name	phosphoglucomutase 1
	Synonyms	CDG1T\|GSD14
	Cytomap	UCSC genome browser: 1p31
	Genomic location	chr1 :64088886-64125916
	Type of gene	protein-coding
	RefGenes	NM_001172818.1, NM_001172819.1,NM_002633.2,
	Ensembl id	ENSG00000079739
	Description	PGM 1glucose phosphomutase 1phosphoglucomutase-1
	Modification date	20141219
dbXrefs	MIM : 171900
	HGNC : HGNC
	Ensembl : ENSG00000079739
	HPRD : 01389
	Vega : OTTHUMG00000008968
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PGM1
	BioGPS: 5236
	Gene Expression Atlas: ENSG00000079739
	The Human Protein Atlas: ENSG00000079739
Pathway	NCI Pathway Interaction Database: PGM1
	KEGG: PGM1
	REACTOME: PGM1
	ConsensusPathDB
	Pathway Commons: PGM1
Metabolism	MetaCyc: PGM1
	HUMANCyc: PGM1
Regulation	Ensembl's Regulation: ENSG00000079739
	miRBase: chr1 :64,088,886-64,125,916
	TargetScan: NM_001172818
	cisRED: ENSG00000079739
Context	iHOP: PGM1
	cancer metabolism search in PubMed: PGM1
	UCL Cancer Institute: PGM1
Assigned class in ccmGDB	C

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Phenotypic Information for PGM1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PGM1
	Familial Cancer Database: PGM1

* 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_GALACTOSE_METABOLISM KEGG_STARCH_AND_SUCROSE_METABOLISM KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: PGM1
	MedGen: PGM1 (Human Medical Genetics with Condition)
	ClinVar: PGM1
Phenotype	MGI: PGM1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PGM1

Mutations for PGM1

* 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	PGM1	chr1	64125217	64125237	PGM1	chr1	64087200	64087220
pancreas	PGM1	chr1	64103521	64103541	EFCAB7	chr1	64023900	64023920

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 PGM1 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
AI830657	PGM1	1	181	1	64125741	64125974	CPSF2	182	378	14	92628923	92629119
BE836713	XG	52	174	X	2693718	2693841	PGM1	170	343	1	64100606	64101993
AI798979	PGM1	1	71	1	64125276	64125346	PGM1	68	301	1	64125419	64125652

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=49)	Stat. for Synonymous SNVs (# total SNVs=11)

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
chr1:64097432-64097432	p.R221C	3
chr1:64120041-64120041	p.V501V	2
chr1:64059353-64059353	p.F65C	2
chr1:64095098-64095098	p.I83I	2
chr1:64100614-64100614	p.L266H	2
chr1:64095186-64095186	p.I113F	2
chr1:64114301-64114301	p.Y420H	2
chr1:64125315-64125315	p.T553M	2
chr1:64059291-64059291	p.I44M	1
chr1:64101904-64101904	p.?	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	1	1	7	1		1		1	1		5	1	1		1	5	4		8
# mutation	3	1	1	9	1		1		1	1		6	1	1		1	5	4		8
nonsynonymous SNV	2	1	1	8	1		1		1	1		3	1			1	1	2		6
synonymous SNV	1			1								3		1			4	2		2

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
chr1:64095098	p.I101I,PGM1	2
chr1:64059334	p.V59M	1
chr1:64117350	p.V246I,PGM1	1
chr1:64095755	p.E449K,PGM1	1
chr1:64101999	p.T11T	1
chr1:64089164	p.P249P,PGM1	1
chr1:64117371	p.A456T,PGM1	1
chr1:64097386	p.P19S	1
chr1:64102017	p.N264K,PGM1	1
chr1:64089186	p.E464D,PGM1	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 PGM1 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 PGM1

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


CDC20,CMPK1,FAF1,CCDC71L,IFRD1,KTI12,LRP8, LRRC41,LRRC42,MED8,MPP6,MRPL37,NRD1,ORC1, PDIA6,PGM1,RHBDL2,SERBP1,STEAP3,TTC7A,UQCRHL	ACAT1,ACO2,ALPK3,ATP5B,C6orf106,CHCHD3,DLD, ETFDH,HADHB,HOXA10,HSPB6,NRD1,OGDH,OPTN, PGM1,PHYH,SGCG,SLC2A4,SNTA1,SOX6,TBX15

ABCD3,ACADS,ACO2,ADH6,SOWAHB,CPT2,FABP1, GIPC2,HK2,ITM2C,LDHD,NR3C2,P2RY2,PGM1, PIGR,RETSAT,RIMKLA,SLC35A3,UGP2,UGT1A10,UGT2B15	ACOT4,ACSS2,AGFG2,SOWAHB,AP1M2,BDH1,BTBD3, CCNJL,RHOV___CHP1,DTX4,FUT3,IHH,MARVELD3,MYO1D, PFKL,PGM1,PPARG,TNK1,TPRN,TRAF3IP2,WDR78

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 PGM1

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
DB00515	phosphoglucomutase 1	approved	Cisplatin

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Cross referenced IDs for PGM1

* 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