Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 HIF1A

Basic gene info.	Gene symbol	HIF1A
	Gene name	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)
	Synonyms	HIF-1A\|HIF-1alpha\|HIF1\|HIF1-ALPHA\|MOP1\|PASD8\|bHLHe78
	Cytomap	UCSC genome browser: 14q23.2
	Genomic location	chr14 :62162118-62214977
	Type of gene	protein-coding
	RefGenes	NM_001243084.1, NM_001530.3,NM_181054.2,
	Ensembl id	ENSG00000100644
	Description	ARNT interacting proteinARNT-interacting proteinHIF-1-alphaPAS domain-containing protein 8basic-helix-loop-helix-PAS protein MOP1class E basic helix-loop-helix protein 78hypoxia-inducible factor 1 alpha isoform I.3hypoxia-inducible factor 1, alpha
	Modification date	20141222
dbXrefs	MIM : 603348
	HGNC : HGNC
	Ensembl : ENSG00000100644
	HPRD : 04517
	Vega : OTTHUMG00000140344
Protein	UniProt: Q16665 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HIF1A
	BioGPS: 3091
	Gene Expression Atlas: ENSG00000100644
	The Human Protein Atlas: ENSG00000100644
Pathway	NCI Pathway Interaction Database: HIF1A
	KEGG: HIF1A
	REACTOME: HIF1A
	ConsensusPathDB
	Pathway Commons: HIF1A
Metabolism	MetaCyc: HIF1A
	HUMANCyc: HIF1A
Regulation	Ensembl's Regulation: ENSG00000100644
	miRBase: chr14 :62,162,118-62,214,977
	TargetScan: NM_001243084
	cisRED: ENSG00000100644
Context	iHOP: HIF1A
	cancer metabolism search in PubMed: HIF1A
	UCL Cancer Institute: HIF1A
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of HIF1A in cancer cell metabolism	1. Maiso P, Huynh D, Moschetta M, Sacco A, Aljawai Y, et al. (2015) Metabolic signature identifies novel targets for drug resistance in multiple myeloma. Cancer Res 75: 2071-2082. doi: 10.1158/0008-5472.CAN-14-3400. pmid: 4433568. go to article 2. Zhdanov AV, Waters AH, Golubeva AV, Papkovsky DB (2015) Differential contribution of key metabolic substrates and cellular oxygen in HIF signalling. Exp Cell Res 330: 13-28. doi: 10.1016/j.yexcr.2014.10.005. go to article

Top

Phenotypic Information for HIF1A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: HIF1A
	Familial Cancer Database: HIF1A

* 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
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145

Others
OMIM	603348; gene.
Orphanet
Disease	KEGG Disease: HIF1A
	MedGen: HIF1A (Human Medical Genetics with Condition)
	ClinVar: HIF1A
Phenotype	MGI: HIF1A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: HIF1A

Mutations for HIF1A

* 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

Top

- 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
ovary	HIF1A	chr14	62181961	62181981	HIF1A	chr14	62200896	62200916
pancreas	HIF1A	chr14	62205083	62205103	GPHN	chr14	67138032	67138052

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 HIF1A 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
DB202604	HIF1A	1	321	14	62162238	62162558	PRKCH	321	578	14	61952220	61995895
BE545257	HIF1A	1	81	14	62207490	62207571	ROMO1	80	131	20	34288850	34288902
BP330336	HIF1A	1	403	14	62162236	62187177	CD63	402	582	12	56121079	56122794
BE767238	MXI1	2	76	10	112038977	112039052	HIF1A	69	365	14	62207754	62212443
CD656091	HIF1A	12	312	14	62212132	62212432	OFD1	305	825	X	13755171	13755695
DA461349	HIF1A	1	474	14	62162238	62187250	NRP1	474	576	10	33467838	33467940

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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=27

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=117)	Stat. for Synonymous SNVs (# total SNVs=14)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=1)

Top

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
chr14:62194237-62194237	p.K213Q	27
chr14:62194312-62194312	p.D238N	11
chr14:62207881-62207881	p.V690M	3
chr14:62200959-62200959	p.K328N	3
chr14:62213745-62213745	p.G808V	2
chr14:62207902-62207902	p.Q697E	2
chr14:62204876-62204876	p.E441K	2
chr14:62207327-62207327	p.K547N	2
chr14:62193462-62193462	p.S166R	2
chr14:62199167-62199167	p.E269*	2

Top

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		14			3		1				1				6	7		13
# mutation	1	3		14			3		1				1				6	7		20
nonsynonymous SNV		1		10			2		1				1				4	4		14
synonymous SNV	1	2		4			1										2	3		6

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])

Top

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
chr14:62207881	p.V714M,HIF1A	2
chr14:62200959	p.K352K,HIF1A	2
chr14:62211508	p.S751P,HIF1A	2
chr14:62188359	p.N713N,HIF1A	1
chr14:62207737	p.L199L,HIF1A	1
chr14:62213704	p.K501T,HIF1A	1
chr14:62203609	p.R269Q,HIF1A	1
chr14:62187113	p.T514A,HIF1A	1
chr14:62205061	p.A718T,HIF1A	1
chr14:62188501	p.L286S,HIF1A	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 HIF1A 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]

Top

Gene Expression for HIF1A

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


ACTR2,ACTR3,ASCC3,ATP2A2,BACH1,CCNYL1,CORO1C, ERO1L,EXOC5,FNDC3B,HIF1A,HIVEP2,LIMS1,LOC284441, PANX1,PHACTR2,PPP2R5E,RDX,RNF145,RNF217,SNAPC1	AHR,BAZ1A,CTBS,DNAJC3,ENAH,FAM91A1,GCH1, HIF1A,LRRC8B,MAGT1,MAPK6,PDE12,SEC23IP,SEC24A, SLC30A7,STARD4,TLR7,TNFRSF10B,UBA6,UGCG,ZFYVE16

ALPK2,CLMP,CALU,CD93,CHST15,CHSY1,DOCK4, ELK3,FCGR2A,FPR1,FUT11,GFPT2,HIF1A,HS3ST3B1, IKBIP,KCNJ15,LOX,NRP1,OSMR,SRGN,WISP1	DNAJB11,DNAJC10,GARS,GTPBP4,HIF1A,HSP90B1,HSPA5, HYOU1,CEMIP,LRP8,MTHFD1L,NAA15,PA2G4P4,PDIA4, RPN2,SRSF1,SLC7A5,SLCO4A1,SSR1,SYNCRIP,YARS

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for HIF1A

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q16665; -.
Chemistry	ChEMBL	CHEMBL2221345; -.
Organism-specific databases	PharmGKB	PA29283; -.
Organism-specific databases	CTD	3091; -.

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
DB08687	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	experimental	N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE
DB00171	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	approved; nutraceutical	Adenosine triphosphate
DB00119	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	approved; nutraceutical	Pyruvic acid
DB00694	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	approved	Daunorubicin
DB00997	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	approved; investigational	Doxorubicin
DB00773	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	approved	Etoposide
DB01204	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	approved; investigational	Mitoxantrone
DB00155	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	approved; nutraceutical	L-Citrulline
DB00125	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	approved; nutraceutical	L-Arginine
DB00435	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	approved	Nitric Oxide

Top

Cross referenced IDs for HIF1A

* 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