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 HSPA9

Basic gene info.	Gene symbol	HSPA9
	Gene name	heat shock 70kDa protein 9 (mortalin)
	Synonyms	CRP40\|CSA\|GRP-75\|GRP75\|HEL-S-124m\|HSPA9B\|MOT\|MOT2\|MTHSP75\|PBP74
	Cytomap	UCSC genome browser: 5q31.1
	Genomic location	chr5 :137890570-137911318
	Type of gene	protein-coding
	RefGenes	NM_004134.6,
	Ensembl id	ENSG00000113013
	Description	75 kDa glucose-regulated proteincatecholamine-regulated protein 40epididymis secretory sperm binding protein Li 124mheat shock 70kD protein 9Bmortalin, perinuclearmortalin-2p66-mortalinpeptide-binding protein 74stress-70 protein, mitochondrial
	Modification date	20141222
dbXrefs	MIM : 600548
	HGNC : HGNC
	Ensembl : ENSG00000113013
	HPRD : 02770
	Vega : OTTHUMG00000129206
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HSPA9
	BioGPS: 3313
	Gene Expression Atlas: ENSG00000113013
	The Human Protein Atlas: ENSG00000113013
Pathway	NCI Pathway Interaction Database: HSPA9
	KEGG: HSPA9
	REACTOME: HSPA9
	ConsensusPathDB
	Pathway Commons: HSPA9
Metabolism	MetaCyc: HSPA9
	HUMANCyc: HSPA9
Regulation	Ensembl's Regulation: ENSG00000113013
	miRBase: chr5 :137,890,570-137,911,318
	TargetScan: NM_004134
	cisRED: ENSG00000113013
Context	iHOP: HSPA9
	cancer metabolism search in PubMed: HSPA9
	UCL Cancer Institute: HSPA9
Assigned class in ccmGDB	C

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Phenotypic Information for HSPA9(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: HSPA9
	Familial Cancer Database: HSPA9

* 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_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: HSPA9
	MedGen: HSPA9 (Human Medical Genetics with Condition)
	ClinVar: HSPA9
Phenotype	MGI: HSPA9 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: HSPA9

Mutations for HSPA9

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HSPA9 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
DA499861	HSPA9	1	62	5	137896734	137896795	NEFL	58	558	8	24813631	24814131
BG876899	HSPA9	7	168	5	137906742	137909524	HSPA9	160	213	5	137906680	137906733
BM835588	HSPA9	1	103	5	137893155	137893629	SLC35A2	104	631	X	48762698	48768953
DA922289	MARCH6	1	198	5	10354004	10378944	HSPA9	199	562	5	137902388	137903411
BM818077	HSPA9	1	116	5	137902738	137902852	RPS20	108	510	8	56985723	56987059
BM722787	INA	1	527	10	105049348	105049874	HSPA9	523	593	5	137891576	137891646
BG993754	ZRANB1	21	242	10	126656048	126656269	HSPA9	240	495	5	137899374	137899629

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=41)	Stat. for Synonymous SNVs (# total SNVs=15)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted 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
chr5:137894317-137894317	p.T480T	3
chr5:137892170-137892170	p.L645L	2
chr5:137893676-137893676	p.?	2
chr5:137895585-137895585	p.R460R	2
chr5:137909762-137909762	p.D45E	2
chr5:137895590-137895590	p.I458T	2
chr5:137906735-137906735	p.Q108Q	1
chr5:137895598-137895598	p.T455T	1
chr5:137902369-137902369	p.Q306H	1
chr5:137910939-137910939	p.A23A	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	1		9			1		5			4	5				2	7		6
# mutation	1	1		9			1		5			4	5				2	8		7
nonsynonymous SNV	1	1		6					3			3	4				1	6		6
synonymous SNV				3			1		2			1	1				1	2		1

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
chr5:137894317	p.T480T	2
chr5:137902719	p.M392V	1
chr5:137906735	p.Q108Q	1
chr5:137892185	p.L640V	1
chr5:137895576	p.G353W	1
chr5:137902767	p.T87T	1
chr5:137906798	p.S638T	1
chr5:137892191	p.A311G	1
chr5:137895598	p.A84S	1
chr5:137903145	p.S616S	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 HSPA9 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 HSPA9

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


CANX,CDC23,ETF1,FAF2,GFM2,GRPEL2,HARS2, HSPA4,HSPA9,LARP1,LARS,PAIP2,PHAX,PPP2CA, RAD50,RARS,RNF14,RRN3,SAR1B,SKP1,VDAC1	AFG3L2,ATP5A1,BZW2,CACNG6,CUL4A,DNAJA3,DNAJA4, FAF1,FASTKD5,GOT1,GOT2,HSPA2,HSPA9,IDH2, MDH2,NEURL1,PPM1J,PREP,RBM20,TNP1,VDAC1

CDC23,CHCHD4,COX7C,DLAT,ETF1,GEMIN5,HARS, HSPA4,HSPA9,HSPD1,IMMT,LARS,MCCC2,MRPS27, NPM1,RARS,TAF9,TBCA,UBE2D2,UTP15,VDAC1	CDC25A,DARS2,DLAT,FUBP1,G3BP1,GAR1,HSPA9, HSPD1,LRPPRC,MCCC2,MCM4,MIPEP,NARS,NOL10, NOP14,PAICS,SFPQ,SRSF1,SLC5A6,SRPK1,STT3B

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 HSPA9

There's no related Drug.

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Cross referenced IDs for HSPA9

* 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