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 PIK3C3
Basic gene info.Gene symbolPIK3C3
Gene namephosphatidylinositol 3-kinase, catalytic subunit type 3
SynonymsVPS34|hVps34
CytomapUCSC genome browser: 18q12.3
Genomic locationchr18 :39535198-39661446
Type of geneprotein-coding
RefGenesNM_002647.2,
Ensembl idENSG00000078142
DescriptionPI3-kinase type 3PI3K type 3PtdIns-3-kinase type 3phosphatidylinositol 3-kinase catalytic subunit type 3phosphatidylinositol 3-kinase p100 subunitphosphoinositide-3-kinase, class 3
Modification date20141207
dbXrefs MIM : 602609
HGNC : HGNC
HPRD : 04009
ProteinUniProt: Q8NEB9
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PIK3C3
BioGPS: 5289
Gene Expression Atlas: ENSG00000078142
The Human Protein Atlas: ENSG00000078142
PathwayNCI Pathway Interaction Database: PIK3C3
KEGG: PIK3C3
REACTOME: PIK3C3
ConsensusPathDB
Pathway Commons: PIK3C3
MetabolismMetaCyc: PIK3C3
HUMANCyc: PIK3C3
RegulationEnsembl's Regulation: ENSG00000078142
miRBase: chr18 :39,535,198-39,661,446
TargetScan: NM_002647
cisRED: ENSG00000078142
ContextiHOP: PIK3C3
cancer metabolism search in PubMed: PIK3C3
UCL Cancer Institute: PIK3C3
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PIK3C3 in cancer cell metabolism1. Zhao X-J, Zhuo H (2014) ECR-MAPK Regulation in Liver Early Development. BioMed research international. go to article

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Phenotypic Information for PIK3C3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PIK3C3
Familial Cancer Database: PIK3C3
* 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
KEGG_INOSITOL_PHOSPHATE_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 602609; gene.
Orphanet
DiseaseKEGG Disease: PIK3C3
MedGen: PIK3C3 (Human Medical Genetics with Condition)
ClinVar: PIK3C3
PhenotypeMGI: PIK3C3 (International Mouse Phenotyping Consortium)
PhenomicDB: PIK3C3

Mutations for PIK3C3
* 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
* 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
NSPIK3C3chr183963339239633392TLR2chr4154611152154611152
pancreasPIK3C3chr183960423039604250LOC643542chr186543848365438503
pancreasPIK3C3chr183964953239649552chr136264116362641183
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 PIK3C3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DW414072PIK3C318210183953522739542478DAB220631753937514539376168
CB124531PIK3C330630183963790939661363LOC100132273624692224250484642504914

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   1  
GAIN (# sample)          1   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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=97)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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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
chr18:39570422-39570422p.?21
chr18:39620697-39620697p.S699G4
chr18:39623726-39623726p.E711D3
chr18:39567803-39567803p.M187L3
chr18:39567804-39567804p.M187T2
chr18:39567805-39567805p.M187I2
chr18:39620662-39620662p.S687L2
chr18:39647367-39647367p.R847C2
chr18:39584325-39584325p.L330F2
chr18:39637947-39637947p.G788G2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample522274 2 3  1233  58 11
# mutation522234 2 3  1333  510 16
nonsynonymous SNV522203 2 3  1032  39 14
synonymous SNV   31      3 1  21 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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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
chr18:39620697p.S699G4
chr18:39575890p.R275R3
chr18:39637995p.T804T2
chr18:39567805p.E406D2
chr18:39576652p.D314D2
chr18:39593453p.M187I2
chr18:39575919p.T625T1
chr18:39609346p.R768W1
chr18:39584404p.L193R1
chr18:39617750p.V337I1

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 PIK3C3 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 PIK3C3

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

ADNP2,C18orf25,DYM,HDHD2,TRAPPC8,KIAA1328,KIAA1468,
EPG5,LMAN1,MIB1,NARS,PIAS2,PIGN,PIK3C3,
RPRD1A,SMAD2,SMAD4,VPS4B,ZNF24,ZNF271P,ZNF397
AFF4,BIRC6,TRAPPC11,ERCC6L2,CASP8AP2,KDM5A,GLTSCR1L,
KIAA0586,KIAA2026,LATS1,NIPBL,NUP153,PIAS1,PIK3C3,
RANBP2,RIF1,LTN1,SF3B1,SCAF11,THOC2,WAPAL

C18orf25,DYM,ELP2,ESCO1,TRAPPC8,KIAA1328,EPG5,
MBD1,MEX3C,PIK3C3,ROCK1,RPRD1A,SLC39A6,SMAD2,
SMAD4,SMCHD1,VPS4B,WDR7,ZNF24,ZNF271P,ZNF397
ATAD1,ATE1,TBC1D32,GPATCH11,CTDSPL2,DNAJB14,FBXO38,
HDAC9,HDHD2,MAPK14,PDCL,PHAX,PIK3C3,RAB30,
RBBP5,SIKE1,SP3,USP8,VPS41,ZNF19,ZNF41
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 PIK3C3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q8NEB9; -.
ChemistryChEMBL CHEMBL1075165; -.
Organism-specific databasesPharmGKB PA33307; -.
Organism-specific databasesCTD 5289; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB06836phosphatidylinositol 3-kinase, catalytic subunit type 3experimentalN-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE


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Cross referenced IDs for PIK3C3
* 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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