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 PAX6

Basic gene info.	Gene symbol	PAX6
	Gene name	paired box 6
	Synonyms	AN\|AN2\|D11S812E\|FVH1\|MGDA\|WAGR
	Cytomap	UCSC genome browser: 11p13
	Genomic location	chr11 :31806339-31832879
	Type of gene	protein-coding
	RefGenes	NM_000280.4, NM_001127612.1,NM_001258462.1,NM_001258463.1,NM_001258464.1, NM_001258465.1,NM_001604.5,
	Ensembl id	ENSG00000007372
	Description	aniridia type II proteinoculorhombinpaired box homeotic gene-6paired box protein Pax-6
	Modification date	20141222
dbXrefs	MIM : 607108
	HGNC : HGNC
	Ensembl : ENSG00000007372
	HPRD : 06167
	Vega : OTTHUMG00000041447
Protein	UniProt: P26367 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PAX6
	BioGPS: 5080
	Gene Expression Atlas: ENSG00000007372
	The Human Protein Atlas: ENSG00000007372
Pathway	NCI Pathway Interaction Database: PAX6
	KEGG: PAX6
	REACTOME: PAX6
	ConsensusPathDB
	Pathway Commons: PAX6
Metabolism	MetaCyc: PAX6
	HUMANCyc: PAX6
Regulation	Ensembl's Regulation: ENSG00000007372
	miRBase: chr11 :31,806,339-31,832,879
	TargetScan: NM_000280
	cisRED: ENSG00000007372
Context	iHOP: PAX6
	cancer metabolism search in PubMed: PAX6
	UCL Cancer Institute: PAX6
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PAX6(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PAX6
	Familial Cancer Database: PAX6

* 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_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM	106210; phenotype. 120200; phenotype. 120430; phenotype. 136520; phenotype. 148190; phenotype. 165550; phenotype. 206700; phenotype. 604229; phenotype. 607108; gene.
Orphanet	1065; Aniridia - cerebellar ataxia - intellectual disability. 137902; Isolated optic nerve hypoplasia. 194; Ocular coloboma. 2253; Foveal hypoplasia - presenile cataract. 2334; Autosomal dominant keratitis. 250923; Isolated aniridia. 35737; Morning glory syndrome. 708; Peters anomaly. 893; WAGR syndrome.
Disease	KEGG Disease: PAX6
	MedGen: PAX6 (Human Medical Genetics with Condition)
	ClinVar: PAX6
Phenotype	MGI: PAX6 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PAX6

Mutations for PAX6

* 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 PAX6 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
M86017	PAX6	1	119	11	31811059	31811177	CTNNA1	120	311	5	138124956	138125147
W21798	PAX6	65	240	11	31832695	31832870	PAX6	232	464	11	31828397	31832531
EB361003	PAX6	1	391	11	31811465	31815220	PAX6	387	681	11	31810938	31811232

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=45)	Stat. for Synonymous SNVs (# total SNVs=20)

Stat. for Deletions (# total SNVs=6)	Stat. for Insertions (# total SNVs=4)

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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
chr11:31812317-31812317	p.P389fs*7	6
chr11:31812409-31812409	p.?	2
chr11:31812316-31812317	p.H390fs*36	2
chr11:31823109-31823109	p.S133S	2
chr11:31823266-31823266	p.R81I	2
chr11:31812352-31812352	p.S377S	2
chr11:31815103-31815103	p.?	2
chr11:31822286-31822286	p.R173H	2
chr11:31816307-31816307	p.E199Q	1
chr11:31823185-31823185	p.C108Y	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	1		14	1		3		1			13	3	3			5	10		8
# mutation	1	1		15	1		3		1			14	3	3			5	11		10
nonsynonymous SNV				11	1		2					8	1	2			5	7		7
synonymous SNV	1	1		4			1		1			6	2	1				4		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
chr11:31823109	p.S119S,PAX6	3
chr11:31812352	p.S363S,PAX6	2
chr11:31816281	p.G141S,PAX6	2
chr11:31822341	p.N193N,PAX6	2
chr11:31822365	p.T173M,PAX6	1
chr11:31815029	p.V84L,PAX6	1
chr11:31823250	p.G387D,PAX6	1
chr11:31815651	p.R275I,PAX6	1
chr11:31816333	p.G165V,PAX6	1
chr11:31812271	p.E82K,PAX6	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 PAX6 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 PAX6

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


ABTB2,CRLF1,DCLRE1B,DENND2C,FOXC1,GPR64,KCNK10, LOC100127888,MAPRE2,NRAS,OR8S1,OTX1,OTX2,PAX6, POU3F4,RGS20,SFRP1,SHISA3,SNAR-E,TRIM2,TRIM33	ABHD13,AEBP2,GPBP1,HNRNPLL,IKZF5,LEMD3,LIN7C, MAP4K5,LAMTOR3,MARCH7,MED21,NUDT21,ORC4,PAX6, PCNP,RCHY1,SMAD4,TMEM168,TWISTNB,WASL,ZRANB2

ACTR6,BUB3,CFAP46,C9orf116,CEP55,CPSF6,CRYZL1, HJURP,LOC100130238,LOC144438,METTL10,NACA,NACAP1,PA2G4, PAX6,PLA2G3,PTGES3,RACGAP1,SPINK2,TROAP,WIBG	AEBP2,ARID5B,ACKR3,ELFN2,FAM155A,GNRHR2,GPR125, HGSNAT,KLHL15,LINC00312,LTBP4,MOB1B,HNRNPU-AS1,PAN3, PAX6,PGAP1,PPIL6,TMEM8B,TROVE2,ZNF793,ZNF805

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 PAX6

There's no related Drug.

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Cross referenced IDs for PAX6

* 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