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 PIK3CD
Basic gene info.Gene symbolPIK3CD
Gene namephosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta
SynonymsAPDS|IMD14|P110DELTA|PI3K|p110D
CytomapUCSC genome browser: 1p36.2
Genomic locationchr1 :9711789-9789172
Type of geneprotein-coding
RefGenesNM_005026.3,
Ensembl idENSG00000171608
DescriptionPI3-kinase p110 subunit deltaPI3Kdeltaphosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoformphosphatidylinositol-4,5-bisphosphate 3-kinase 110 kDa catalytic subunit deltaphosphatidylinositol-4,5-bisphosphate 3-kinase catalytic
Modification date20141207
dbXrefs MIM : 602839
HGNC : HGNC
Ensembl : ENSG00000171608
Vega : OTTHUMG00000001450
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PIK3CD
BioGPS: 5293
Gene Expression Atlas: ENSG00000171608
The Human Protein Atlas: ENSG00000171608
PathwayNCI Pathway Interaction Database: PIK3CD
KEGG: PIK3CD
REACTOME: PIK3CD
ConsensusPathDB
Pathway Commons: PIK3CD
MetabolismMetaCyc: PIK3CD
HUMANCyc: PIK3CD
RegulationEnsembl's Regulation: ENSG00000171608
miRBase: chr1 :9,711,789-9,789,172
TargetScan: NM_005026
cisRED: ENSG00000171608
ContextiHOP: PIK3CD
cancer metabolism search in PubMed: PIK3CD
UCL Cancer Institute: PIK3CD
Assigned class in ccmGDBC

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Phenotypic Information for PIK3CD(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PIK3CD
Familial Cancer Database: PIK3CD
* 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
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PIK3CD
MedGen: PIK3CD (Human Medical Genetics with Condition)
ClinVar: PIK3CD
PhenotypeMGI: PIK3CD (International Mouse Phenotyping Consortium)
PhenomicDB: PIK3CD

Mutations for PIK3CD
* 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
breastPIK3CDchr197177199717719chr11228031012280310
ovaryPIK3CDchr197354459735465ERCC6L2chr99869673698696756
ovaryPIK3CDchr197622069762406PIK3CDchr197627139762913
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 PIK3CD related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF926362ZNF8142992195838300458383067PIK3CD83395197720119772324
BI020398PIK3CD118141197842419784264CDS21254232051737325174032
AV739808PIK3CD43435197882709788663PIK3CD429613197881569788348
BE181134SLC35E46314223103299831033308PIK3CD295314197384919738510

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 # sample1                
GAIN (# sample)                 
LOSS (# sample)1                
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=74)
Stat. for Synonymous SNVs
(# total SNVs=28)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted snv.

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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
chr1:9780711-9780711p.E505K3
chr1:9787030-9787030p.E1021K3
chr1:9781596-9781596p.R636W3
chr1:9770571-9770571p.V20I3
chr1:9770629-9770629p.N39S3
chr1:9783245-9783245p.R830H2
chr1:9783259-9783259p.A835T2
chr1:9780836-9780836p.S520A2
chr1:9775698-9775698p.E81K2
chr1:9775719-9775719p.R88C2

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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
# sample342175 4 21 342  714114
# mutation342165 5 21 352  713117
nonsynonymous SNV331112 2 21 242  611 12
synonymous SNV 1153 3    11   1215
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
chr1:9770519p.P2P2
chr1:9778917p.A835T2
chr1:9783259p.A396T2
chr1:9770571p.V20I2
chr1:9777668p.K705E1
chr1:9782153p.S896S1
chr1:9775614p.D91D1
chr1:9780180p.A308V1
chr1:9784049p.N464K1
chr1:9784908p.A723T1

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 PIK3CD 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 PIK3CD

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

AKNA,ARHGAP25,ARHGAP30,ARHGAP9,CARD11,CD6,FAM78A,
FMNL1,IKZF1,IL10RA,JAK3,LCK,MAP4K1,PIK3CD,
PTPN7,SASH3,SNX20,TMC8,TRAF1,UBASH3A,WAS
ACAP1,CARD11,CD6,CORO1A,ITGAL,ITGB7,KIF21B,
LAT,LCK,LIMD2,MAP4K1,MYO1G,PIK3CD,PTPN7,
SEPT1,SPN,TBC1D10C,TMC8,TRAF3IP3,UBASH3A,ZAP70

ARHGAP25,ARHGAP30,ARHGAP9,DOCK2,FAM78A,HCLS1,IKZF1,
IL16,ITGAL,LIMD2,MAP4K1,MYO1G,PIK3CD,PPP1R16B,
PTPRC,RASAL3,RCSD1,SASH3,TRAF3IP3,WAS,WDFY4
AGAP2,APBB1IP,ARHGAP25,ARHGAP30,CORO1A,DOCK2,FAM78A,
GPR18,HVCN1,IKZF1,IL21R,INPP5D,JAK3,LIMD2,
ORAI2,PIK3CD,PPP1R16B,RLTPR,TRAF1,WAS,ZNF831
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 PIK3CD
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB06831phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit deltaexperimental2-((9H-PURIN-6-YLTHIO)METHYL)-5-CHLORO-3-(2-METHOXYPHENYL)QUINAZOLIN-4(3H)-ONE


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Cross referenced IDs for PIK3CD
* 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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