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 ALAD
Basic gene info.Gene symbolALAD
Gene nameaminolevulinate dehydratase
SynonymsALADH|PBGS
CytomapUCSC genome browser: 9q33.1
Genomic locationchr9 :116148591-116163618
Type of geneprotein-coding
RefGenesNM_000031.5,
NM_001003945.1,
Ensembl idENSG00000148218
Descriptionaminolevulinate, delta-, dehydratasedelta-aminolevulinic acid dehydrataseporphobilinogen synthase
Modification date20141207
dbXrefs MIM : 125270
HGNC : HGNC
Ensembl : ENSG00000148218
HPRD : 00504
Vega : OTTHUMG00000020522
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALAD
BioGPS: 210
Gene Expression Atlas: ENSG00000148218
The Human Protein Atlas: ENSG00000148218
PathwayNCI Pathway Interaction Database: ALAD
KEGG: ALAD
REACTOME: ALAD
ConsensusPathDB
Pathway Commons: ALAD
MetabolismMetaCyc: ALAD
HUMANCyc: ALAD
RegulationEnsembl's Regulation: ENSG00000148218
miRBase: chr9 :116,148,591-116,163,618
TargetScan: NM_000031
cisRED: ENSG00000148218
ContextiHOP: ALAD
cancer metabolism search in PubMed: ALAD
UCL Cancer Institute: ALAD
Assigned class in ccmGDBC

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Phenotypic Information for ALAD(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALAD
Familial Cancer Database: ALAD
* 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
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM
REACTOME_METABOLISM_OF_PORPHYRINS

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

Mutations for ALAD
* 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 ALAD related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC009172ALAD12519116155725116163552ESRP22372321166826330568266732
BE563268ALAD12329116155725116163533ESRP2218740166826570768266732

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

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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=15)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr9:116151291-116151291p.A328A4
chr9:116151917-116151917p.L255L2
chr9:116153104-116153104p.C153Y2
chr9:116151918-116151918p.Q254H2
chr9:116152053-116152053p.R238Q2
chr9:116151266-116151266p.R337S2
chr9:116152082-116152082p.K228K2
chr9:116151366-116151366p.A303A2
chr9:116153891-116153891p.K88N2
chr9:116153900-116153900p.Y85Y2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 2  3 11 3    68 3
# mutation 1 2  3 11 3    68 3
nonsynonymous SNV   1  2    2    45 3
synonymous SNV 1 1  1 11 1    23  
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
chr9:116151291p.A299A3
chr9:116150638p.A312D2
chr9:116154442p.P321P1
chr9:116152751p.E89G1
chr9:116155727p.E70K1
chr9:116150607p.R308S1
chr9:116152888p.I47I1
chr9:116155760p.P41S1
chr9:116150610p.D259D1
chr9:116152945p.T38M1

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 ALAD 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 ALAD

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

ALAD,AUH,BSPRY,C9orf156,AK8,CALCOCO1,CASZ1,
CRY2,FAM120AOS,FKBP15,KIAA0141,KIF13B,NINJ1,NTN4,
PHF2,RXRA,TBC1D13,TENC1,TIGD6,TMEM25,ZER1
ALAD,BCL2L2,BHMT2,DHDDS,EPB41L1,GCOM1,GLYAT,
GPD1,ITPK1,KANK1,CTIF,LEP,MCAM,MYO1C,
PLIN4,PYGL,RETSAT,TBC1D9B,TFE3,TNIP1,TNS1

ALAD,BRD3,FKBP15,GOLGA1,GOLGA2,IL11RA,LOC100272217,
LOC253039,PHF2,PNPLA7,RABGAP1,RALGPS1,RNF20,RNF38,
SLC25A42,SNX30,TBC1D13,TSC1,USP20,ZER1,ZNF782
ALAD,ATG9A,CTDSP1,EIF4EBP2,FAM63A,ARHGAP35,H1F0,
HECA,IQSEC2,LOC283267,LOC90110,NAIF1,NBR1,P4HA2,
PINK1,SLC25A23,TADA2B,TLE3,ZFYVE1,ZNF768,ZNF821
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 ALAD
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00855aminolevulinate dehydrataseapprovedAminolevulinic acid
DB02068aminolevulinate dehydrataseexperimentalDelta-Amino Valeric Acid
DB02239aminolevulinate dehydrataseexperimentalLaevulinic Acid
DB02260aminolevulinate dehydrataseexperimental4-Oxosebacic Acid
DB02272aminolevulinate dehydrataseexperimentalPorphobilinogen
DB02878aminolevulinate dehydrataseexperimental3-(2-Aminoethyl)-4-(Aminomethyl)Heptanedioic Acid
DB04560aminolevulinate dehydrataseexperimental4,7-Dioxosebacic Acid
DB04781aminolevulinate dehydrataseexperimental5-hydroxyvaleric acid
DB01942aminolevulinate dehydrataseexperimentalFormic Acid
DB02828aminolevulinate dehydrataseexperimental5-Fluorolevulinic Acid
DB04530aminolevulinate dehydrataseexperimentalS,S-(2-Hydroxyethyl)Thiocysteine
DB00145aminolevulinate dehydrataseapproved; nutraceuticalGlycine


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Cross referenced IDs for ALAD
* 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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