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 HIF1A
Basic gene info.Gene symbolHIF1A
Gene namehypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)
SynonymsHIF-1A|HIF-1alpha|HIF1|HIF1-ALPHA|MOP1|PASD8|bHLHe78
CytomapUCSC genome browser: 14q23.2
Genomic locationchr14 :62162118-62214977
Type of geneprotein-coding
RefGenesNM_001243084.1,
NM_001530.3,NM_181054.2,
Ensembl idENSG00000100644
DescriptionARNT 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 date20141222
dbXrefs MIM : 603348
HGNC : HGNC
Ensembl : ENSG00000100644
HPRD : 04517
Vega : OTTHUMG00000140344
ProteinUniProt: Q16665
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HIF1A
BioGPS: 3091
Gene Expression Atlas: ENSG00000100644
The Human Protein Atlas: ENSG00000100644
PathwayNCI Pathway Interaction Database: HIF1A
KEGG: HIF1A
REACTOME: HIF1A
ConsensusPathDB
Pathway Commons: HIF1A
MetabolismMetaCyc: HIF1A
HUMANCyc: HIF1A
RegulationEnsembl's Regulation: ENSG00000100644
miRBase: chr14 :62,162,118-62,214,977
TargetScan: NM_001243084
cisRED: ENSG00000100644
ContextiHOP: HIF1A
cancer metabolism search in PubMed: HIF1A
UCL Cancer Institute: HIF1A
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of HIF1A in cancer cell metabolism1. 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

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Phenotypic Information for HIF1A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145

check002.gifOthers
OMIM 603348; gene.
Orphanet
DiseaseKEGG Disease: HIF1A
MedGen: HIF1A (Human Medical Genetics with Condition)
ClinVar: HIF1A
PhenotypeMGI: HIF1A (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryHIF1Achr146218196162181981HIF1Achr146220089662200916
pancreasHIF1Achr146220508362205103GPHNchr146713803267138052
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HIF1A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB202604HIF1A1321146216223862162558PRKCH321578146195222061995895
BE545257HIF1A181146220749062207571ROMO180131203428885034288902
BP330336HIF1A1403146216223662187177CD63402582125612107956122794
BE767238MXI127610112038977112039052HIF1A69365146220775462212443
CD656091HIF1A12312146221213262212432OFD1305825X1375517113755695
DA461349HIF1A1474146216223862187250NRP1474576103346783833467940

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 1  1   
GAIN (# sample)        1        
LOSS (# sample)          1  1   
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=27

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check002.gifSomatic 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)

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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
chr14:62194237-62194237p.K213Q27
chr14:62194312-62194312p.D238N11
chr14:62207881-62207881p.V690M3
chr14:62200959-62200959p.K328N3
chr14:62193462-62193462p.S166R2
chr14:62199167-62199167p.E269*2
chr14:62207856-62207856p.E681D2
chr14:62211508-62211508p.S727P2
chr14:62207575-62207575p.A588P2
chr14:62187153-62187153p.R30Q2

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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
# sample13 14  3 1   1   67 13
# mutation13 14  3 1   1   67 20
nonsynonymous SNV 1 10  2 1   1   44 14
synonymous SNV12 4  1         23 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])

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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
chr14:62207881p.K352K,HIF1A2
chr14:62200959p.S751P,HIF1A2
chr14:62211508p.V714M,HIF1A2
chr14:62193473p.P540P,HIF1A1
chr14:62207856p.K745N,HIF1A1
chr14:62203800p.R42Q,HIF1A1
chr14:62207257p.P356P,HIF1A1
chr14:62187119p.D548G,HIF1A1
chr14:62193491p.K43Q,HIF1A1
chr14:62207880p.I359I,HIF1A1

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 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]

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Gene Expression for HIF1A

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

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
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 HIF1A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q16665; -.
ChemistryChEMBL CHEMBL2221345; -.
Organism-specific databasesPharmGKB PA29283; -.
Organism-specific databasesCTD 3091; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB08687hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)experimentalN-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE
DB00171hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)approved; nutraceuticalAdenosine triphosphate
DB00119hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)approved; nutraceuticalPyruvic acid
DB00694hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)approvedDaunorubicin
DB00997hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)approved; investigationalDoxorubicin
DB00773hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)approvedEtoposide
DB01204hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)approved; investigationalMitoxantrone
DB00155hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)approved; nutraceuticalL-Citrulline
DB00125hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)approved; nutraceuticalL-Arginine
DB00435hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)approvedNitric Oxide


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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



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