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 SRR
Basic gene info.Gene symbolSRR
Gene nameserine racemase
SynonymsILV1|ISO1
CytomapUCSC genome browser: 17p13
Genomic locationchr17 :2207247-2228553
Type of geneprotein-coding
RefGenesNM_021947.1,
Ensembl idENSG00000167720
DescriptionD-serine ammonia-lyaseD-serine dehydrataseL-serine ammonia-lyaseL-serine dehydratase
Modification date20141207
dbXrefs MIM : 606477
HGNC : HGNC
Ensembl : ENSG00000167720
HPRD : 10451
Vega : OTTHUMG00000090583
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SRR
BioGPS: 63826
Gene Expression Atlas: ENSG00000167720
The Human Protein Atlas: ENSG00000167720
PathwayNCI Pathway Interaction Database: SRR
KEGG: SRR
REACTOME: SRR
ConsensusPathDB
Pathway Commons: SRR
MetabolismMetaCyc: SRR
HUMANCyc: SRR
RegulationEnsembl's Regulation: ENSG00000167720
miRBase: chr17 :2,207,247-2,228,553
TargetScan: NM_021947
cisRED: ENSG00000167720
ContextiHOP: SRR
cancer metabolism search in PubMed: SRR
UCL Cancer Institute: SRR
Assigned class in ccmGDBC

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

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

Mutations for SRR
* 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
ovarySRRchr1722196062219626SMG6chr1721301382130158
pancreasSRRchr1722093642209384SRRchr1722111092211129
pancreasSRRchr1722147902214810chr142204382922043849
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 SRR related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN347172SRR15411722268602227400ROMO1539601203428883534288897
AA614279FUS1323163120231431202923SRR3193761722084262208483

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=19)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=1)
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
chr17:2221171-2221171p.G59D3
chr17:2218973-2218973p.R40H2
chr17:2227019-2227019p.A292G2
chr17:2222200-2222200p.V126I1
chr17:2226586-2226586p.I251L1
chr17:2218856-2218856p.M1T1
chr17:2222201-2222201p.V126A1
chr17:2226617-2226617p.T261S1
chr17:2222205-2222205p.Y127Y1
chr17:2226989-2226989p.I282T1

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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
# sample3  3       111   414
# mutation3  3       111   415
nonsynonymous SNV2  3       1 1   414
synonymous SNV1           1      1
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
chr17:2218973p.R40H2
chr17:2224624p.M1T1
chr17:2218856p.I244T1
chr17:2224659p.I282T1
chr17:2224685p.L42I1
chr17:2218978p.S334F1
chr17:2224690p.R58C1
chr17:2221167p.G85G1
chr17:2224836p.P101P1
chr17:2221250p.D112H1

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 SRR 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 SRR

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

C17orf97,CYB5D1,CYB5D2,GLOD4,KIAA0753,LRRC48,MAP2K4,
MED31,METTL16,PIGV,PNPLA4,RABEP1,RBKS,RNF167,
SMG6,SRR,TMEM107,TTC19,YWHAE,ZBTB4,ZNF18
BLZF1,URI1,TRAPPC13,CPD,DHX29,ERGIC2,GOLGA5,
ITFG1,JKAMP,MAP4K3,PIGB,PLA2G12A,RAB5A,RCN2,
RNF141,RNF14,SCARB2,SRR,UBA5,UBE2K,UEVLD

ATPAF2,C17orf49,C17orf85,COPS3,DERL2,EIF4A1,GLOD4,
MED11,MIS12,OVCA2,PEMT,RNF167,RNMTL1,RPA1,
SLC25A11,SRR,STX8,TIMM22,TXNL1,UBE2G1,YWHAE
ARL3,FAM229B,CFAP36,COX7A1,CUEDC2,EIF5A2,FAM195B,
KCNMB2,KIAA0895,MSANTD4,KPNA5,LAYN,NKIRAS1,NME4,
NME5,SNRPN,SRR,TCEAL1,TCEAL7,TCEAL8,TMEM17
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 SRR
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
DB00114serine racemasenutraceuticalPyridoxal Phosphate
DB00133serine racemaseapproved; nutraceuticalL-Serine


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Cross referenced IDs for SRR
* 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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