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 HSPB1

Basic gene info.	Gene symbol	HSPB1
	Gene name	heat shock 27kDa protein 1
	Synonyms	CMT2F\|HEL-S-102\|HMN2B\|HS.76067\|HSP27\|HSP28\|Hsp25\|SRP27
	Cytomap	UCSC genome browser: 7q11.23
	Genomic location	chr7 :75931874-75933614
	Type of gene	protein-coding
	RefGenes	NM_001540.3,
	Ensembl id	ENSG00000106211
	Description	28 kDa heat shock proteinHSP 27epididymis secretory protein Li 102estrogen-regulated 24 kDa proteinheat shock 27 kDa proteinheat shock 27kD protein 1heat shock protein beta-1stress-responsive protein 27
	Modification date	20141219
dbXrefs	MIM : 602195
	HGNC : HGNC
	Ensembl : ENSG00000106211
	HPRD : 09076
	Vega : OTTHUMG00000023228
Protein	UniProt: P04792 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HSPB1
	BioGPS: 3315
	Gene Expression Atlas: ENSG00000106211
	The Human Protein Atlas: ENSG00000106211
Pathway	NCI Pathway Interaction Database: HSPB1
	KEGG: HSPB1
	REACTOME: HSPB1
	ConsensusPathDB
	Pathway Commons: HSPB1
Metabolism	MetaCyc: HSPB1
	HUMANCyc: HSPB1
Regulation	Ensembl's Regulation: ENSG00000106211
	miRBase: chr7 :75,931,874-75,933,614
	TargetScan: NM_001540
	cisRED: ENSG00000106211
Context	iHOP: HSPB1
	cancer metabolism search in PubMed: HSPB1
	UCL Cancer Institute: HSPB1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of HSPB1 in cancer cell metabolism	1. Sun X, Ou Z, Xie M, Kang R, Fan Y, et al. (2015) HSPB1 as a novel regulator of ferroptotic cancer cell death. Oncogene. doi: 10.1038/onc.2015.32. go to article

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Phenotypic Information for HSPB1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: HSPB1
	Familial Cancer Database: HSPB1

* 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_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	602195; gene. 602195; gene. 606595; phenotype. 606595; phenotype. 608634; phenotype. 608634; phenotype.
Orphanet	139525; Distal hereditary motor neuropathy type 2. 139525; Distal hereditary motor neuropathy type 2. 99940; Autosomal dominant Charcot-Marie-Tooth disease type 2F. 99940; Autosomal dominant Charcot-Marie-Tooth disease type 2F.
Disease	KEGG Disease: HSPB1
	MedGen: HSPB1 (Human Medical Genetics with Condition)
	ClinVar: HSPB1
Phenotype	MGI: HSPB1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: HSPB1

Mutations for HSPB1

* 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 HSPB1 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
AA903814	HSPB1	1	85	7	75933533	75933895	EGR1	77	212	5	137801706	137802528
AJ710478	SKP1	2	257	5	133496716	133509692	HSPB1	257	365	7	75932016	75932124
BU737515	HSPB1	19	94	7	75933537	75933612	STXBP1	89	413	9	130454104	130454428
DA893722	TNNC2	1	173	20	44453224	44455951	HSPB1	172	475	7	75932242	75933388
CD387519	HSPB1	24	228	7	75931990	75932194	UBE2M	226	934	19	59067367	59069801
DA283619	HSPB1	1	113	7	75931992	75932104	RAPGEF5	112	575	7	22159500	22159963
N36356	RMRP	2	252	9	35657753	35658003	HSPB1	249	529	7	75932236	75933353
AI470274	HSPB1	8	65	7	75933548	75933605	FARP2	58	202	2	242382597	242382741
R77849	GJC1	1	224	17	42878774	42878996	HSPB1	220	298	7	75933535	75933612
Z23090	XPO5	460	484	6	43506601	43506625	HSPB1	478	1231	7	75932016	75933612
AI609727	HSPB1	1	417	7	75932066	75933611	HSPB1	412	459	7	75933328	75933375
BU631277	HSPB1	25	94	7	75933535	75933603	WASF1	87	586	6	110423249	110426758
DA537518	HSPB1	1	99	7	75931994	75932092	OBSL1	84	540	2	220432891	220435250
AI123558	HSPB1	4	69	7	75933544	75933609	DDX17	57	418	22	38884189	38884549
AI801539	HSPB1	24	169	7	75933457	75933602	HSPB1	165	488	7	75932071	75932394
CA336509	HSPB1	2	78	7	75932992	75933068	KRT19	74	186	17	39679869	39679981

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

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

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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=1

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=6)	Stat. for Synonymous SNVs (# total SNVs=2)

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
chr7:75932376-75932376	p.G116V	1
chr7:75933134-75933134	p.R127Q	1
chr7:75933348-75933348	p.P159H	1
chr7:75933373-75933373	p.A167A	1
chr7:75933408-75933408	p.I179N	1
chr7:75933416-75933416	p.P182S	1
chr7:75933446-75933446	p.G192W	1
chr7:75932036-75932036	p.E3Q	1
chr7:75933484-75933484	p.A204A	1
chr7:75932058-75932058	p.L10H	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=1

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				2								1	2	1			2	1
# mutation				2								1	2	1			2	1
nonsynonymous SNV				1								1		1			2
synonymous SNV				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
chr7:75933382	p.P182S	1
chr7:75933408	p.G192W	1
chr7:75933416	p.A204A	1
chr7:75933446	p.L10H	1
chr7:75933484	p.Q31Q	1
chr7:75932058	p.L81I	1
chr7:75932122	p.A167A	1
chr7:75932270	p.P170P	1
chr7:75933373	p.I179N	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 HSPB1 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 HSPB1

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


BLOC1S1,BOLA2,C12orf10,IFT43,C16orf13,TSR3,ECI1, MZT2B,FAM173A,FAM195A,HSPB1,JOSD2,MRPL28,MRPS34, NDUFA2,NDUFB10,NOSIP,NUBP2,TCEB2,PAM16,ZNHIT1	ARAF,COX17,COX8A,DEXI,ENDOG,HCFC1R1,HSPB1, LSM10,LINC00116,NDUFB10,NDUFB2,NDUFS7,NDUFS8,PGP, PHPT1,SEPW1,SLC16A3,SLC25A11,EMC6,UBAC1,UQCR10

C7orf61,CDKN2A,DHDH,FLJ25758,IZUMO1R,GAGE12D,GAGE4, HIST1H2BI,HSPB1,LOC728392,LRRC7,MS4A13,OXT,PFN3, RHBDD2,SEPW1,SSX2,TMEM88,TUBG2,VAT1,ZFAND2A	ACTG2,CCDC136,CNN1,CTNNA3,CTXN1,DES,DMPK, DNAJB5,FAM46B,FLNA,FLNC,HSPB1,HSPB7,ILDR2, KY,LDB3,PDLIM7,PYGM,SLC2A4,SMTN,TAGLN

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 HSPB1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P04792; -.
Chemistry	ChEMBL	CHEMBL5976; -.
Chemistry	BindingDB	P04792; -.
Chemistry	ChEMBL	CHEMBL5976; -.
Organism-specific databases	PharmGKB	PA29511; -.
Organism-specific databases	PharmGKB	PA29511; -.
Organism-specific databases	CTD	3315; -.
Organism-specific databases	CTD	3315; -.

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
DB00125	heat shock 27kDa protein 1	approved; nutraceutical	L-Arginine
DB00435	heat shock 27kDa protein 1	approved	Nitric Oxide
DB00269	heat shock 27kDa protein 1	approved	Chlorotrianisene
DB00286	heat shock 27kDa protein 1	approved	Conjugated Estrogens
DB00890	heat shock 27kDa protein 1	approved	Dienestrol
DB00255	heat shock 27kDa protein 1	approved	Diethylstilbestrol
DB00783	heat shock 27kDa protein 1	approved; investigational	Estradiol
DB00655	heat shock 27kDa protein 1	approved	Estrone
DB00977	heat shock 27kDa protein 1	approved	Ethinyl Estradiol
DB00143	heat shock 27kDa protein 1	approved; nutraceutical	Glutathione

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Cross referenced IDs for HSPB1

* 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