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 AASS
Basic gene info.Gene symbolAASS
Gene nameaminoadipate-semialdehyde synthase
SynonymsLKR/SDH|LKRSDH|LORSDH
CytomapUCSC genome browser: 7q31.3
Genomic locationchr7 :121713597-121784344
Type of geneprotein-coding
RefGenesNM_005763.3,
Ensembl idENSG00000008311
Descriptionalpha-aminoadipate semialdehyde synthasealpha-aminoadipic semialdehyde synthase, mitochondrialaminoadipic semialdehyde synthaselysine-2-oxoglutarate reductaselysine-ketoglutarate reductase /saccharopine dehydrogenase
Modification date20141207
dbXrefs MIM : 605113
HGNC : HGNC
HPRD : 05489
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AASS
BioGPS: 10157
Gene Expression Atlas: ENSG00000008311
The Human Protein Atlas: ENSG00000008311
PathwayNCI Pathway Interaction Database: AASS
KEGG: AASS
REACTOME: AASS
ConsensusPathDB
Pathway Commons: AASS
MetabolismMetaCyc: AASS
HUMANCyc: AASS
RegulationEnsembl's Regulation: ENSG00000008311
miRBase: chr7 :121,713,597-121,784,344
TargetScan: NM_005763
cisRED: ENSG00000008311
ContextiHOP: AASS
cancer metabolism search in PubMed: AASS
UCL Cancer Institute: AASS
Assigned class in ccmGDBC

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

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

Mutations for AASS
* 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
There's no inter-chromosomal structural variation.
- 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
pancreasAASSchr7121721988121722008AASSchr7121725577121725597
pancreasAASSchr7121725032121725052AASSchr7121732575121732595
pancreasAASSchr7121742818121742838AASSchr7121732586121732606
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 AASS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
H48691TLR8-AS112122X1293933412939444AASS1164237121715791121716095
H65666TLR8-AS11110X1293933512939444AASS1044277121715774121716095
BX282586TLR8-AS11111X1293933412939444AASS1054877121715713121716095

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
GAIN (# sample)          1     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)

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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=109)
Stat. for Synonymous SNVs
(# total SNVs=32)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr7:121758477-121758477p.S191C3
chr7:121766507-121766507p.R132C3
chr7:121756793-121756793p.T263M3
chr7:121773699-121773699p.V28I3
chr7:121738539-121738539p.L540L2
chr7:121773726-121773726p.G19S2
chr7:121717989-121717989p.T855T2
chr7:121726159-121726159p.L697F2
chr7:121769560-121769560p.E81V2
chr7:121721588-121721588p.P749H2

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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
# sample42 132 2 2  15103  67 16
# mutation42 132 2 2  16123  68 17
nonsynonymous SNV32 81   2  11103  46 11
synonymous SNV1  51 2    52   22 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
chr7:121758477p.S191G3
chr7:121738539p.T263M2
chr7:121773576p.D69N2
chr7:121718988p.L540L2
chr7:121756793p.D805N2
chr7:121766507p.R132C2
chr7:121756943p.L419F1
chr7:121738533p.L271V1
chr7:121741719p.N119D1
chr7:121769442p.G10D1

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 AASS 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 AASS

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

AASS,ABCA10,C20orf194,CALCOCO1,CDC14B,CLCN6,CLK4,
MICU3,GPRASP1,INTU,LAMA2,LCA5,LHFP,LOC286367,
NPHP3,PLSCR4,RBM5,RHOJ,SPARCL1,TSHZ2,TTC28
AASS,AGPAT9,ALDH6A1,BCKDHB,C6,CALCRL,DNAH9,
FAM161A,GMCL1,GYS2,LOC100190938,LPIN1,MAP3K5,MOGAT1,
MPDZ,PLCXD1,PRKAG2,RNF125,RORB,ST3GAL6,STOX1

AASS,CBX7,CLSTN3,CRTC3,CRYBG3,CYP46A1,DYNC2H1,
GLRB,ITPR1,KLF15,POU6F1,PRKCH,RFTN2,RHOQ,
SEMA6C,TCEAL3,THSD1,TSPYL5,TTBK2,TTC28,USP51
AASS,ABLIM3,ADAM33,LINC00472,CHRD,COL16A1,COL27A1,
COL5A2,GPR116,GPR133,GPR135,HIP1,MN1,MTR,
PCDHGB3,PDZD2,PTPN13,REV3L,SASH1,STXBP1,TTC28
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 AASS
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
DB00142aminoadipate-semialdehyde synthaseapproved; nutraceuticalL-Glutamic Acid
DB00157aminoadipate-semialdehyde synthaseapproved; nutraceuticalNADH
DB02338aminoadipate-semialdehyde synthaseexperimentalNadph Dihydro-Nicotinamide-Adenine-Dinucleotidephosphate
DB04207aminoadipate-semialdehyde synthaseexperimentalN-(5-Amino-5-Carboxypentyl)Glutamic Acid
DB00123aminoadipate-semialdehyde synthaseapproved; nutraceuticalL-Lysine


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Cross referenced IDs for AASS
* 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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