Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolPAX6
Gene namepaired box 6
SynonymsAN|AN2|D11S812E|FVH1|MGDA|WAGR
CytomapUCSC genome browser: 11p13
Genomic locationchr11 :31806339-31832879
Type of geneprotein-coding
RefGenesNM_000280.4,
NM_001127612.1,NM_001258462.1,NM_001258463.1,NM_001258464.1,
NM_001258465.1,NM_001604.5,
Ensembl idENSG00000007372
Descriptionaniridia type II proteinoculorhombinpaired box homeotic gene-6paired box protein Pax-6
Modification date20141222
dbXrefs MIM : 607108
HGNC : HGNC
Ensembl : ENSG00000007372
HPRD : 06167
Vega : OTTHUMG00000041447
ProteinUniProt: P26367
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PAX6
BioGPS: 5080
Gene Expression Atlas: ENSG00000007372
The Human Protein Atlas: ENSG00000007372
PathwayNCI Pathway Interaction Database: PAX6
KEGG: PAX6
REACTOME: PAX6
ConsensusPathDB
Pathway Commons: PAX6
MetabolismMetaCyc: PAX6
HUMANCyc: PAX6
RegulationEnsembl's Regulation: ENSG00000007372
miRBase: chr11 :31,806,339-31,832,879
TargetScan: NM_000280
cisRED: ENSG00000007372
ContextiHOP: PAX6
cancer metabolism search in PubMed: PAX6
UCL Cancer Institute: PAX6
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PAX6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
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.
DiseaseKEGG Disease: PAX6
MedGen: PAX6 (Human Medical Genetics with Condition)
ClinVar: PAX6
PhenotypeMGI: PAX6 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PAX6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
M86017PAX61119113181105931811177CTNNA11203115138124956138125147
W21798PAX665240113183269531832870PAX6232464113182839731832531
EB361003PAX61391113181146531815220PAX6387681113181093831811232

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1        
GAIN (# sample)        1        
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr11:31812317-31812317p.P389fs*76
chr11:31822286-31822286p.R173H2
chr11:31812409-31812409p.?2
chr11:31812316-31812317p.H390fs*362
chr11:31823109-31823109p.S133S2
chr11:31823266-31823266p.R81I2
chr11:31812352-31812352p.S377S2
chr11:31815103-31815103p.?2
chr11:31816302-31816302p.N200K1
chr11:31823152-31823152p.R119I1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample11 141 3 1  1333  510 8
# mutation11 151 3 1  1433  511 10
nonsynonymous SNV   111 2    812  57 7
synonymous SNV11 4  1 1  621   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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr11:31823109p.S119S,PAX63
chr11:31812352p.S363S,PAX62
chr11:31816281p.G141S,PAX62
chr11:31822341p.N193N,PAX62
chr11:31822358p.E185E,PAX61
chr11:31815010p.R125I,PAX61
chr11:31823241p.L32P,PAX61
chr11:31815586p.T323P,PAX61
chr11:31816308p.E185E,PAX61
chr11:31824340p.R19L,PAX61

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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