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 PYGB

Basic gene info.	Gene symbol	PYGB
	Gene name	phosphorylase, glycogen; brain
	Synonyms	GPBB
	Cytomap	UCSC genome browser: 20p11.21
	Genomic location	chr20 :25228705-25278648
	Type of gene	protein-coding
	RefGenes	NM_002862.3,
	Ensembl id	ENSG00000100994
	Description	glycogen phosphorylase Bglycogen phosphorylase, brain form
	Modification date	20141207
dbXrefs	MIM : 138550
	HGNC : HGNC
	Ensembl : ENSG00000100994
	HPRD : 00720
	Vega : OTTHUMG00000032117
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PYGB
	BioGPS: 5834
	Gene Expression Atlas: ENSG00000100994
	The Human Protein Atlas: ENSG00000100994
Pathway	NCI Pathway Interaction Database: PYGB
	KEGG: PYGB
	REACTOME: PYGB
	ConsensusPathDB
	Pathway Commons: PYGB
Metabolism	MetaCyc: PYGB
	HUMANCyc: PYGB
Regulation	Ensembl's Regulation: ENSG00000100994
	miRBase: chr20 :25,228,705-25,278,648
	TargetScan: NM_002862
	cisRED: ENSG00000100994
Context	iHOP: PYGB
	cancer metabolism search in PubMed: PYGB
	UCL Cancer Institute: PYGB
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: PYGB
	Familial Cancer Database: PYGB

* 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_STARCH_AND_SUCROSE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

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

Mutations for PYGB

* 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	PYGB	chr20	25234122	25234142		chr20	24832709	24832729

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 PYGB 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
DA055429	PYGB	1	514	20	25228918	25255316	ACAA1	514	581	3	38168011	38168078
BF088479	LOC100507463	4	88	6	4244041	4244125	PYGB	83	346	20	25277025	25277288
BF764783	CLIP2	1	247	7	73790387	73790631	PYGB	247	383	20	25266898	25267034
BF908082	PYGB	15	162	20	25231048	25231195	PYGB	154	324	20	25231278	25231448
BE696989	PYGB	7	287	20	25266110	25266394	TMEM53	281	332	1	45120425	45120476
Z18966	RPS6KA2	5	139	6	166945316	166945450	PYGB	140	342	20	25277317	25277515

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=70)	Stat. for Synonymous SNVs (# total SNVs=20)

Stat. for Deletions (# total SNVs=4)	Stat. for Insertions (# total SNVs=0)
	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
chr20:25260931-25260931	p.A374A	4
chr20:25239910-25239910	p.R94H	3
chr20:25239951-25239951	p.A108S	3
chr20:25259739-25259739	p.E349V	2
chr20:25259006-25259006	p.A303S	2
chr20:25255239-25255239	p.A180A	2
chr20:25263895-25263895	p.D534D	2
chr20:25261728-25261728	p.S461S	2
chr20:25259702-25259702	p.Q337*	1
chr20:25263913-25263913	p.Q540H	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=3

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	15	2		5		2			3	3	1			8	11	1	13
# mutation		3	1	14	2		5		2			3	3	1			8	14	1	15
nonsynonymous SNV		2	1	13	2		3		2			1	3	1			1	8	1	11
synonymous SNV		1		1			2					2					7	6		4

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
chr20:25239909	p.R94C	2
chr20:25262702	p.R410R	1
chr20:25255237	p.Q540H	1
chr20:25273189	p.C784C	1
chr20:25257951	p.T210S	1
chr20:25261592	p.A416G	1
chr20:25276304	p.L550L	1
chr20:25239910	p.R793W	1
chr20:25262744	p.R94H	1
chr20:25255252	p.P211P	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 PYGB 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 PYGB

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


ACTN4,CHST3,EN1,ENO1,ENTPD6,EPHB3,HRCT1, IL34,ITGB4,KCNN4,LEMD1,LSR,MFI2,MICALL1, PPARGC1A,PYGB,SFRP1,SHC4,SOX6,SOX8,SUN2	ASIC1,ATP6V1B1,C19orf48,CHRM1,DTNB,ENTPD6,EPHB3, ETV3L,FAM3D,FUT6,KCNN4,LOC100127888,NEURL3,NLE1, PODXL2,PPFIA3,PRSS27,PYGB,RASAL1,SOX8,TMCO4

ACSS1,AXIN1,BLCAP,CLCN7,ENTPD6,FN3K,FUK, HOXA2,HOXA3,HS1BP3,LOC25845,MGAT4B,NDRG3,NEU1, OSBPL2,PPDPF,PTK6,PYGB,SNX21,SQSTM1,TFCP2L1	ARRB1,BMP3,CSNK1D,DAB2IP,DGCR2,MVB12B,GPR37L1, IL4R,IP6K1,CIPC,MTMR3,OTUD7B,PYGB,RNF144A, SLC25A23,SSBP3,STIM1,SUN2,TEF,TOM1L2,USP19

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 PYGB

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
DB00114	phosphorylase, glycogen; brain	nutraceutical	Pyridoxal Phosphate

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Cross referenced IDs for PYGB

* 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