Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 ALAS1
Basic gene info.Gene symbolALAS1
Gene name5'-aminolevulinate synthase 1
SynonymsALAS|ALAS3|ALASH|MIG4
CytomapUCSC genome browser: 3p21.1
Genomic locationchr3 :52232098-52248343
Type of geneprotein-coding
RefGenesNM_000688.5,
NM_199166.2,
Ensembl idENSG00000023330
Description5-aminolevulinate synthase, nonspecific, mitochondrial5-aminolevulinic acid synthase 1ALAS-Haminolevulinate, delta-, synthase 1delta-ALA synthase 1delta-aminolevulinate synthase 1migration-inducing protein 4
Modification date20141207
dbXrefs MIM : 125290
HGNC : HGNC
Ensembl : ENSG00000023330
HPRD : 00505
Vega : OTTHUMG00000158108
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALAS1
BioGPS: 211
Gene Expression Atlas: ENSG00000023330
The Human Protein Atlas: ENSG00000023330
PathwayNCI Pathway Interaction Database: ALAS1
KEGG: ALAS1
REACTOME: ALAS1
ConsensusPathDB
Pathway Commons: ALAS1
MetabolismMetaCyc: ALAS1
HUMANCyc: ALAS1
RegulationEnsembl's Regulation: ENSG00000023330
miRBase: chr3 :52,232,098-52,248,343
TargetScan: NM_000688
cisRED: ENSG00000023330
ContextiHOP: ALAS1
cancer metabolism search in PubMed: ALAS1
UCL Cancer Institute: ALAS1
Assigned class in ccmGDBC

Top
Phenotypic Information for ALAS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALAS1
Familial Cancer Database: ALAS1
* 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_GLYCINE_SERINE_AND_THREONINE_METABOLISM
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS
REACTOME_METABOLISM_OF_PORPHYRINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ALAS1
MedGen: ALAS1 (Human Medical Genetics with Condition)
ClinVar: ALAS1
PhenotypeMGI: ALAS1 (International Mouse Phenotyping Consortium)
PhenomicDB: ALAS1

Mutations for ALAS1
* 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 ALAS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN258752ALAS1125335224806252248537ALAS125037035224554952246375
BE826074SRGN4314107085506570855374ALAS130239435224822552248326

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
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)

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=48)
Stat. for Synonymous SNVs
(# total SNVs=17)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=2)

Top
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
chr3:52245521-52245521p.A518G3
chr3:52242102-52242102p.A390V3
chr3:52242218-52242218p.R429W2
chr3:52239985-52239985p.S311P2
chr3:52238038-52238038p.?2
chr3:52239987-52239987p.S311S2
chr3:52233380-52233381p.P43fs*242
chr3:52240628-52240628p.M342I2
chr3:52237970-52237970p.I173I2
chr3:52239907-52239907p.G285R2

Top
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
# sample31 91 1 5  112  27112
# mutation31 81 1 4  112  27113
nonsynonymous SNV3  71   3  111  13 9
synonymous SNV 1 1  1 1    1  1414
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
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
chr3:52242102p.A390V,ALAS13
chr3:52242218p.S311P,ALAS12
chr3:52239907p.S311S,ALAS12
chr3:52239985p.R429W,ALAS12
chr3:52245362p.D159Y,ALAS12
chr3:52237926p.K168N,ALAS12
chr3:52239987p.R465Q,ALAS12
chr3:52237955p.G285R,ALAS12
chr3:52237967p.L27L,ALAS11
chr3:52240616p.G302G,ALAS11

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 ALAS1 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 ALAS1

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))
Top
check002.gifCNV 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
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

ADAMDEC1,ALAS1,THEMIS2,CLEC4E,CTSS,GBP1,GBP5,
HK3,IL4I1,IMMT,LILRB2,LILRB4,LYN,POC1A,
PSMD6,RDX,SIRPB1,SLAMF8,TAP2,TMEM150B,WDR82
AK1,ALAS1,COX7A1,CUTC,DNASE1L1,DUSP3,FHL1,
FHOD1,HSPB7,KLHL30,KLHL31,LMCD1,OGDH,P2RX6,
PINK1,RHOBTB1,RXRG,SCN4A,SIRT2,SNTA1,UBE2D4

ALAS1,ATP5A1,ATP5B,CYSTM1,CCDC68,CDCP1,ERO1L,
GOT1,HK2,LIMA1,ME2,PGAM1,PIGR,PKM,
RNF19B,SCO1,SDHA,SLC16A3,SLC37A1,SQRDL,TNFSF13
ACOX1,ALAS1,ARF3,ATP1B1,CGN,RHOV___CHP1,CORO2A,
CUL3,ABHD17C,ITFG1,KIF16B,MVP,PAPSS2,PDCD6IP,
PIP4K2C,RAB14,RBM47,SFXN1,SLC26A3,UGT1A10,VDAC1
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for ALAS1
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
DB00114aminolevulinate, delta-, synthase 1nutraceuticalPyridoxal Phosphate
DB00145aminolevulinate, delta-, synthase 1approved; nutraceuticalGlycine


Top
Cross referenced IDs for ALAS1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas