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 SRP68
Basic gene info.Gene symbolSRP68
Gene namesignal recognition particle 68kDa
Synonyms-
CytomapUCSC genome browser: 17q25.1
Genomic locationchr17 :74035190-74068607
Type of geneprotein-coding
RefGenesNM_001260502.1,
NM_001260503.1,NM_014230.3,NR_048541.1,
Ensembl idENSG00000167881
Descriptionsignal recognition particle 68 kDa proteinsignal recognition particle 68kDsignal recognition particle subunit SRP68
Modification date20141207
dbXrefs MIM : 604858
HGNC : HGNC
Ensembl : ENSG00000167881
HPRD : 05331
Vega : OTTHUMG00000180054
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SRP68
BioGPS: 6730
Gene Expression Atlas: ENSG00000167881
The Human Protein Atlas: ENSG00000167881
PathwayNCI Pathway Interaction Database: SRP68
KEGG: SRP68
REACTOME: SRP68
ConsensusPathDB
Pathway Commons: SRP68
MetabolismMetaCyc: SRP68
HUMANCyc: SRP68
RegulationEnsembl's Regulation: ENSG00000167881
miRBase: chr17 :74,035,190-74,068,607
TargetScan: NM_001260502
cisRED: ENSG00000167881
ContextiHOP: SRP68
cancer metabolism search in PubMed: SRP68
UCL Cancer Institute: SRP68
Assigned class in ccmGDBC

Top
Phenotypic Information for SRP68(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SRP68
Familial Cancer Database: SRP68
* 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: SRP68
MedGen: SRP68 (Human Medical Genetics with Condition)
ClinVar: SRP68
PhenotypeMGI: SRP68 (International Mouse Phenotyping Consortium)
PhenomicDB: SRP68

Mutations for SRP68
* 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
ovarySRP68chr177403521574035235EVPLchr177401761174017631
ovarySRP68chr177404500174045021FOXJ1chr177413558474135604
ovarySRP68chr177406183574061855RAI1chr171763478317634803
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 SRP68 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CD365788DNAJA226315164698927446989563SRP68308653177404402974056471
AA911044SRP68199177403518774035285PARP1953251226578231226595529
BG119358SRP68582177403557174035648SRP6880490177403518674035596
BG005598SRP68114332177406334474068473NEAT1328435116519054165190648
DA276739FAM178B132329763476997635091SRP68324575177406018274066525

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     1 1      
GAIN (# sample)  1     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)

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=46)
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.

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
chr17:74037022-74037022p.R521Q3
chr17:74057619-74057619p.E200*2
chr17:74046604-74046604p.E328K2
chr17:74060213-74060213p.W135C2
chr17:74037019-74037019p.S522L1
chr17:74053486-74053486p.Q326K1
chr17:74068503-74068503p.G24C1
chr17:74041399-74041399p.L456L1
chr17:74057616-74057616p.H201N1
chr17:74035844-74035844p.Q609H1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample63112  1 5  313  54 9
# mutation73112  1 5  313  54 10
nonsynonymous SNV62 10  1 4  113  52 7
synonymous SNV1112    1  2     2 3
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
chr17:74039952p.T272T,SRP681
chr17:74060232p.R65R,SRP681
chr17:74046574p.E162Q,SRP681
chr17:74068513p.G47R,SRP681
chr17:74035838p.Q270H,SRP681
chr17:74057619p.S50P,SRP681
chr17:74041393p.T144A,SRP681
chr17:74063360p.S45L,SRP681
chr17:74046600p.F251L,SRP681
chr17:74068540p.Q38K,SRP681

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 SRP68 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 SRP68

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

ACOX1,METTL23,COG1,EXOC7,GGA3,H3F3B,H3F3C,
ICT1,JMJD6,MIF4GD,MRPL38,MRPS7,NUP85,PRPSAP1,
SAP30BP,SEPT9,SRP68,TMEM104,UBE2O,UNK,WBP2
ATP5H,APOPT1,C1orf43,C21orf33,DRG1,HADHA,HAX1,
IDH3B,KARS,LOC442454,MRPL37,MRPL40,MRPL46,MRPS33,
MRPS7,OXA1L,SAMM50,SLC25A3,SRP68,UQCRC2,VDAC2

OGFOD3,EFTUD2,EIF4A3,FAM104A,GOSR1,GRB2,H3F3B,
JMJD6,LRRC59,MRPS7,NMT1,P4HB,PRPSAP1,SAP30BP,
SLC35B1,SRP68,TBCD,ALYREF,UBE2O,UBE2Z,WDR45B
AARS,KIAA1549L,DDX24,EIF5B,IARS,IPO9,LDHB,
LDLRAD3,MID1IP1,NUCKS1,NUDC,OGFOD1,PHF19,PLEKHO2,
RECQL,SLC43A3,SRP68,TSR1,TUBB,TUBG1,USP14
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 SRP68


There's no related Drug.
Top
Cross referenced IDs for SRP68
* 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