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 PSMD8

Basic gene info.	Gene symbol	PSMD8
	Gene name	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8
	Synonyms	HEL-S-91n\|HIP6\|HYPF\|Nin1p\|Rpn12\|S14\|p31
	Cytomap	UCSC genome browser: 19q13.2
	Genomic location	chr19 :38865189-38874464
	Type of gene	protein-coding
	RefGenes	NM_002812.4,
	Ensembl id	ENSG00000099341
	Description	26S proteasome non-ATPase regulatory subunit 826S proteasome regulatory subunit RPN1226S proteasome regulatory subunit S1426S proteasome regulatory subunit p31epididymis secretory sperm binding protein Li 91n
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000099341
	HPRD : 10171
	Vega : OTTHUMG00000150691
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMD8
	BioGPS: 5714
	Gene Expression Atlas: ENSG00000099341
	The Human Protein Atlas: ENSG00000099341
Pathway	NCI Pathway Interaction Database: PSMD8
	KEGG: PSMD8
	REACTOME: PSMD8
	ConsensusPathDB
	Pathway Commons: PSMD8
Metabolism	MetaCyc: PSMD8
	HUMANCyc: PSMD8
Regulation	Ensembl's Regulation: ENSG00000099341
	miRBase: chr19 :38,865,189-38,874,464
	TargetScan: NM_002812
	cisRED: ENSG00000099341
Context	iHOP: PSMD8
	cancer metabolism search in PubMed: PSMD8
	UCL Cancer Institute: PSMD8
Assigned class in ccmGDB	C

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Phenotypic Information for PSMD8(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMD8
	Familial Cancer Database: PSMD8

* 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_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: PSMD8
	MedGen: PSMD8 (Human Medical Genetics with Condition)
	ClinVar: PSMD8
Phenotype	MGI: PSMD8 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMD8

Mutations for PSMD8

* 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

There's no inter-chromosomal structural variation.

- 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
ovary	PSMD8	chr19	38870129	38870149	PSMD8	chr19	38872296	38872316

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 PSMD8 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
DW427896	PSMD8	17	109	19	38866836	38867047	HDLBP	110	277	2	242195674	242196041
AA437370	PSMD8	1	63	19	38874402	38874464	SLC35B2	53	445	6	44222415	44222808
BF093758	ITGAL	1	412	16	30518119	30525166	PSMD8	410	497	19	38866122	38866209
AX794816	ITGAL	1	412	16	30518119	30525166	PSMD8	410	497	19	38866122	38866209
BC071826	ELF2	45	447	4	140035878	140036280	PSMD8	448	1392	19	38865435	38874115

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=10)	Stat. for Synonymous SNVs (# total SNVs=9)

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
chr19:38871622-38871622	p.I169I	2
chr19:38866832-38866832	p.T38T	1
chr19:38866844-38866844	p.K42N	1
chr19:38871643-38871643	p.?	1
chr19:38867066-38867067	p.Q77fs*8	1
chr19:38872778-38872778	p.I182I	1
chr19:38869925-38869925	p.L101L	1
chr19:38872859-38872859	p.Y209Y	1
chr19:38869929-38869929	p.L103I	1
chr19:38872860-38872860	p.A210T	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		3			1			1								3		3
# mutation		1		2			1			1								3		3
nonsynonymous SNV		1		1						1								2		1
synonymous SNV				1			1											1		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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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
chr19:38869973	p.T210T	2
chr19:38871607	p.L194L	1
chr19:38872859	p.L196I	1
chr19:38872860	p.T257T	1
chr19:38873894	p.Y302Y	1
chr19:38873943	p.A303T	1
chr19:38874011	p.R306Q	1
chr19:38865566	p.Q322Q	1
chr19:38866844	p.Q345R	1
chr19:38869925	p.L109I	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 PSMD8 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 PSMD8

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


ACTN4,C19orf47,ECH1,EID2,EIF3K,FAM98C,FBL, MRPS12,PAF1,POLR2I,PSMC4,PSMD8,RPS16,SARS2, SHKBP1,SIRT2,SPINT2,SUPT5H,TIMM50,TMEM147,YIF1B	CNPPD1,GPX4,HINT2,LOC729991,MRPL24,MRPL46,MRPS11, MRPS15,NDUFAF3,NDUFB8,PARK7,POLR2E,POLR2L,PSMA7, PSMD8,SLC2A4RG,SOD1,TALDO1,TESK1,TST,UROD

AP2S1,ATP5SL,COX6B1,EIF3K,GEMIN7,MED31,MRPL54, MRPS12,NDUFB7,NOSIP,OAZ1,POLR2I,PRMT1,PSMC4, PSMD8,RPS16,RPS5,SDHAF1,SNRPD2,TIMM50,YIF1B	CHCHD2,CKLF,DAD1,HAX1,LAMTOR5,MRPL22,MRPL52, MYEOV2,NDUFA6,NDUFA7,NDUFB4,NDUFB6,PHF5A,POLR2F, PSMA7,PSMD8,PSMD9,RBX1,STOML2,TIMM8B,UFD1L

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 PSMD8

There's no related Drug.

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Cross referenced IDs for PSMD8

* 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