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 SRP14
Basic gene info.Gene symbolSRP14
Gene namesignal recognition particle 14kDa (homologous Alu RNA binding protein)
SynonymsALURBP
CytomapUCSC genome browser: 15q22
Genomic locationchr15 :40327890-40331389
Type of geneprotein-coding
RefGenesNM_003134.4,
NR_104021.1,
Ensembl idENSG00000140319
Description18 kDa Alu RNA-binding proteinsignal recognition particle 14 kDa protein
Modification date20141207
dbXrefs MIM : 600708
HGNC : HGNC
Ensembl : ENSG00000140319
HPRD : 02831
Vega : OTTHUMG00000172391
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SRP14
BioGPS: 6727
Gene Expression Atlas: ENSG00000140319
The Human Protein Atlas: ENSG00000140319
PathwayNCI Pathway Interaction Database: SRP14
KEGG: SRP14
REACTOME: SRP14
ConsensusPathDB
Pathway Commons: SRP14
MetabolismMetaCyc: SRP14
HUMANCyc: SRP14
RegulationEnsembl's Regulation: ENSG00000140319
miRBase: chr15 :40,327,890-40,331,389
TargetScan: NM_003134
cisRED: ENSG00000140319
ContextiHOP: SRP14
cancer metabolism search in PubMed: SRP14
UCL Cancer Institute: SRP14
Assigned class in ccmGDBC

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Phenotypic Information for SRP14(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SRP14
Familial Cancer Database: SRP14
* 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: SRP14
MedGen: SRP14 (Human Medical Genetics with Condition)
ClinVar: SRP14
PhenotypeMGI: SRP14 (International Mouse Phenotyping Consortium)
PhenomicDB: SRP14

Mutations for SRP14
* 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 SRP14 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ015130SRP1418551154032824240329550C1orf1985456901230973433230973578
CN337981SRP142135154033056540331323EME21366151618249461825879
AA984265SRP141141154033108540331369ABCB111424582169869119169869435
BE836999NUMB35229147375396173759574SRP14218320154033112840331374

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=7)
Stat. for Synonymous SNVs
(# total SNVs=2)
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
chr15:40328597-40328597p.A116A3
chr15:40330490-40330490p.S68I2
chr15:40328572-40328572p.T125A2
chr15:40330494-40330496p.K66delK2
chr15:40328545-40328545p.A134T1
chr15:40330484-40330484p.V70A1
chr15:40328566-40328566p.A127T1
chr15:40328590-40328590p.A119T1
chr15:40328614-40328614p.A111P1
chr15:40328617-40328617p.A110T1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample                11 2
# mutation                11 2
nonsynonymous SNV                11 2
synonymous SNV                    
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
chr15:40328545p.A134S1
chr15:40328590p.A119T1
chr15:40330484p.V70A1
chr15:40330529p.K55T1

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 SRP14 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 SRP14

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

ATP5G2,C12orf10,EMC7,C15orf57,HYPK,TMA7,COX17,
COX6A1,COX7C,DNAJC17,EID1,IMP3,MGST2,MTHFS,
NDUFA2,NDUFAF1,NDUFC1,PARK7,SERF2,SRP14,EMC4
C17orf49,C19orf43,BRK1,DAD1,DYNLRB1,EXOSC1,FAM127B,
GABARAP,JTB,KRTCAP2,LSM3,OST4,POLE4,PSENEN,
RBX1,RNF181,SEC61B,SNRPG,SRP14,TAF10,TOMM6

EMC7,C15orf57,HYPK,COPS2,DNAJC17,FAM103A1,FAM96A,
FBXO22,IMP3,MTHFS,NDUFAF1,NOP10,PSMA4,RAB11A,
RPUSD2,RSL24D1,SEC11A,SERF2,SNRPG,SRP14,EMC4
ACTR10,ATP5J,BUD31,C14orf119,CALM2,CAPZA2,MOB4,
MYEOV2,NDUFA4,NDUFA6,NDUFB6,NDUFB8,NDUFV2,NEDD8,
RBX1,SARNP,SRP14,TRAPPC3,TTC1,UBL5,UQCR11
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 SRP14


There's no related Drug.
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Cross referenced IDs for SRP14
* 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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