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 PIK3CD

Basic gene info.	Gene symbol	PIK3CD
	Gene name	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta
	Synonyms	APDS\|IMD14\|P110DELTA\|PI3K\|p110D
	Cytomap	UCSC genome browser: 1p36.2
	Genomic location	chr1 :9711789-9789172
	Type of gene	protein-coding
	RefGenes	NM_005026.3,
	Ensembl id	ENSG00000171608
	Description	PI3-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 date	20141207
dbXrefs	MIM : 602839
	HGNC : HGNC
	Ensembl : ENSG00000171608
	Vega : OTTHUMG00000001450
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PIK3CD
	BioGPS: 5293
	Gene Expression Atlas: ENSG00000171608
	The Human Protein Atlas: ENSG00000171608
Pathway	NCI Pathway Interaction Database: PIK3CD
	KEGG: PIK3CD
	REACTOME: PIK3CD
	ConsensusPathDB
	Pathway Commons: PIK3CD
Metabolism	MetaCyc: PIK3CD
	HUMANCyc: PIK3CD
Regulation	Ensembl's Regulation: ENSG00000171608
	miRBase: chr1 :9,711,789-9,789,172
	TargetScan: NM_005026
	cisRED: ENSG00000171608
Context	iHOP: PIK3CD
	cancer metabolism search in PubMed: PIK3CD
	UCL Cancer Institute: PIK3CD
Assigned class in ccmGDB	C

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Phenotypic Information for PIK3CD(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PIK3CD
	MedGen: PIK3CD (Human Medical Genetics with Condition)
	ClinVar: PIK3CD
Phenotype	MGI: PIK3CD (International Mouse Phenotyping Consortium)
Phenotype	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.

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

* 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
breast	PIK3CD	chr1	9717719	9717719		chr1	12280310	12280310
ovary	PIK3CD	chr1	9735445	9735465	ERCC6L2	chr9	98696736	98696756
ovary	PIK3CD	chr1	9762206	9762406	PIK3CD	chr1	9762713	9762913

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 PIK3CD 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
BF926362	ZNF814	29	92	19	58383004	58383067	PIK3CD	83	395	1	9772011	9772324
BI020398	PIK3CD	118	141	1	9784241	9784264	CDS2	125	423	20	5173732	5174032
AV739808	PIK3CD	43	435	1	9788270	9788663	PIK3CD	429	613	1	9788156	9788348
BE181134	SLC35E4	6	314	22	31032998	31033308	PIK3CD	295	314	1	9738491	9738510

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=3

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Somatic 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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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
chr1:9780711-9780711	p.E505K	3
chr1:9787030-9787030	p.E1021K	3
chr1:9781596-9781596	p.R636W	3
chr1:9770571-9770571	p.V20I	3
chr1:9770629-9770629	p.N39S	3
chr1:9780836-9780836	p.S520A	2
chr1:9783259-9783259	p.A835T	2
chr1:9775698-9775698	p.E81K	2
chr1:9775719-9775719	p.R88C	2
chr1:9780202-9780202	p.T458S	2

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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	3	4	2	17	5		4		2	1		3	4	2			7	14	1	14
# mutation	3	4	2	16	5		5		2	1		3	5	2			7	13	1	17
nonsynonymous SNV	3	3	1	11	2		2		2	1		2	4	2			6	11		12
synonymous SNV		1	1	5	3		3					1	1				1	2	1	5

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
chr1:9770519	p.P2P	2
chr1:9778917	p.A396T	2
chr1:9783259	p.A835T	2
chr1:9770571	p.V20I	2
chr1:9781280	p.I325M	1
chr1:9784908	p.S467S	1
chr1:9776604	p.A723T	1
chr1:9777681	p.E903K	1
chr1:9782591	p.I113M	1
chr1:9780197	p.A335V	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 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

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


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

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 PIK3CD

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
DB06831	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	experimental	2-((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