Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolHSPA9
Gene nameheat shock 70kDa protein 9 (mortalin)
SynonymsCRP40|CSA|GRP-75|GRP75|HEL-S-124m|HSPA9B|MOT|MOT2|MTHSP75|PBP74
CytomapUCSC genome browser: 5q31.1
Genomic locationchr5 :137890570-137911318
Type of geneprotein-coding
RefGenesNM_004134.6,
Ensembl idENSG00000113013
Description75 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 date20141222
dbXrefs MIM : 600548
HGNC : HGNC
Ensembl : ENSG00000113013
HPRD : 02770
Vega : OTTHUMG00000129206
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HSPA9
BioGPS: 3313
Gene Expression Atlas: ENSG00000113013
The Human Protein Atlas: ENSG00000113013
PathwayNCI Pathway Interaction Database: HSPA9
KEGG: HSPA9
REACTOME: HSPA9
ConsensusPathDB
Pathway Commons: HSPA9
MetabolismMetaCyc: HSPA9
HUMANCyc: HSPA9
RegulationEnsembl's Regulation: ENSG00000113013
miRBase: chr5 :137,890,570-137,911,318
TargetScan: NM_004134
cisRED: ENSG00000113013
ContextiHOP: HSPA9
cancer metabolism search in PubMed: HSPA9
UCL Cancer Institute: HSPA9
Assigned class in ccmGDBC

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Phenotypic Information for HSPA9(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HSPA9
MedGen: HSPA9 (Human Medical Genetics with Condition)
ClinVar: HSPA9
PhenotypeMGI: HSPA9 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HSPA9 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA499861HSPA91625137896734137896795NEFL5855882481363124814131
BG876899HSPA971685137906742137909524HSPA91602135137906680137906733
BM835588HSPA911035137893155137893629SLC35A2104631X4876269848768953
DA922289MARCH6119851035400410378944HSPA91995625137902388137903411
BM818077HSPA911165137902738137902852RPS2010851085698572356987059
BM722787INA152710105049348105049874HSPA95235935137891576137891646
BG993754ZRANB12124210126656048126656269HSPA92404955137899374137899629

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      
GAIN (# sample)          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=3

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check002.gifSomatic 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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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
chr5:137894317-137894317p.T480T3
chr5:137892170-137892170p.L645L2
chr5:137893676-137893676p.?2
chr5:137895585-137895585p.R460R2
chr5:137909762-137909762p.D45E2
chr5:137895590-137895590p.I458T2
chr5:137906735-137906735p.Q108Q1
chr5:137895598-137895598p.T455T1
chr5:137902369-137902369p.Q306H1
chr5:137910939-137910939p.A23A1

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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
# sample11 9  1 5  45   27 6
# mutation11 9  1 5  45   28 7
nonsynonymous SNV11 6    3  34   16 6
synonymous SNV   3  1 2  11   12 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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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
chr5:137894317p.T480T2
chr5:137902719p.M392V1
chr5:137906735p.Q108Q1
chr5:137892185p.L640V1
chr5:137895576p.G353W1
chr5:137902767p.T87T1
chr5:137906798p.S638T1
chr5:137892191p.A311G1
chr5:137895598p.A84S1
chr5:137903145p.S616S1

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 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

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

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
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 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



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