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 SRP72
Basic gene info.Gene symbolSRP72
Gene namesignal recognition particle 72kDa
SynonymsBMFF|BMFS1|HEL103
CytomapUCSC genome browser: 4q11
Genomic locationchr4 :57333761-57369847
Type of geneprotein-coding
RefGenesNM_001267722.1,
NM_006947.3,
Ensembl idENSG00000174780
Descriptionepididymis luminal protein 103signal recognition particle 72 kDa proteinsignal recognition particle 72kDsignal recognition particle subunit SRP72
Modification date20141207
dbXrefs MIM : 602122
HGNC : HGNC
HPRD : 03671
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SRP72
BioGPS: 6731
Gene Expression Atlas: ENSG00000174780
The Human Protein Atlas: ENSG00000174780
PathwayNCI Pathway Interaction Database: SRP72
KEGG: SRP72
REACTOME: SRP72
ConsensusPathDB
Pathway Commons: SRP72
MetabolismMetaCyc: SRP72
HUMANCyc: SRP72
RegulationEnsembl's Regulation: ENSG00000174780
miRBase: chr4 :57,333,761-57,369,847
TargetScan: NM_001267722
cisRED: ENSG00000174780
ContextiHOP: SRP72
cancer metabolism search in PubMed: SRP72
UCL Cancer Institute: SRP72
Assigned class in ccmGDBC

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Phenotypic Information for SRP72(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SRP72
Familial Cancer Database: SRP72
* 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_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SRP72
MedGen: SRP72 (Human Medical Genetics with Condition)
ClinVar: SRP72
PhenotypeMGI: SRP72 (International Mouse Phenotyping Consortium)
PhenomicDB: SRP72

Mutations for SRP72
* 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
ovarySRP72chr45735776057357780SRP72chr45735781257357832
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 SRP72 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
U81554CAMK2G1165107559722675602293SRP7216691045734937557357734
CV357489OXSR1638833828904638289311SRP728018445733896857339072

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=53)
Stat. for Synonymous SNVs
(# total SNVs=18)
Stat. for Deletions
(# total SNVs=2)
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
chr4:57333822-57333822p.G7G3
chr4:57350915-57350915p.R324L3
chr4:57356562-57356562p.R462W3
chr4:57361553-57361553p.K557K2
chr4:57349351-57349351p.A291V2
chr4:57337912-57337912p.Y86C2
chr4:57349352-57349352p.A291A2
chr4:57357604-57357604p.K504fs*112
chr4:57333838-57333838p.A13P2
chr4:57354125-57354125p.S390S2

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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
# sample22 7    3  4431 15112
# mutation22 8    3  5431 15113
nonsynonymous SNV11 7    2  4221  5111
synonymous SNV11 1    1  121  1  2
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
chr4:57354131p.A331A,SRP722
chr4:57342839p.L205I,SRP722
chr4:57340227p.S139Y,SRP721
chr4:57357634p.R263L,SRP721
chr4:57344578p.K493K,SRP721
chr4:57354130p.V154L,SRP721
chr4:57340275p.P274P,SRP721
chr4:57357655p.P507Q,SRP721
chr4:57344662p.E167D,SRP721
chr4:57340281p.F303L,SRP721

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 SRP72 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 SRP72

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

AASDH,ABCE1,NOA1,CEP135,CLOCK,DCUN1D4,EXOC1,
FIP1L1,IARS,LARP1B,NAA15,NAA25,PAICS,POLR2B,
PPAT,SCFD2,SLC30A6,SMARCA5,SMEK2,SRP72,USP46
ABCE1,API5,BCLAF1,DDX18,DDX52,DHX40,CFAP97,
MATR3,PPAT,PRPF40A,PRRC1,PTBP3,SENP1,SMARCAD1,
SRP72,SYNCRIP,TFAM,WAPAL,WDR35,ZNF146,ZNF562

ABCE1,NOA1,C4orf46,CISD2,COPS4,DCK,DHX15,
DR1,GRSF1,HMGXB4,NUP54,PAICS,PAQR3,PGM2,
POLR2B,PPAT,RCHY1,SRP72,TMEM165,UBE2D3,USP46
ACTL6A,BRIX1,C4orf46,CCT2,CDK4,DCUN1D5,DDX47,
EEF1E1,ENOPH1,EXOSC2,MRPL3,NPM1,NUDCD1,NUP35,
POLE3,POT1,PRMT1,PRMT5,PRPF4,SRP72,UBA2
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 SRP72


There's no related Drug.
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Cross referenced IDs for SRP72
* 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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