Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 KHSRP
Basic gene info.Gene symbolKHSRP
Gene nameKH-type splicing regulatory protein
SynonymsFBP2|FUBP2|KSRP
CytomapUCSC genome browser: 19p13.3
Genomic locationchr19 :6413118-6424822
Type of geneprotein-coding
RefGenesNM_003685.2,
Ensembl idENSG00000088247
DescriptionFUSE binding protein 2FUSE-binding protein 2KH type-splicing regulatory proteinfar upstream element-binding protein 2p75
Modification date20141207
dbXrefs MIM : 603445
HGNC : HGNC
Ensembl : ENSG00000088247
HPRD : 10350
Vega : OTTHUMG00000180850
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KHSRP
BioGPS: 8570
Gene Expression Atlas: ENSG00000088247
The Human Protein Atlas: ENSG00000088247
PathwayNCI Pathway Interaction Database: KHSRP
KEGG: KHSRP
REACTOME: KHSRP
ConsensusPathDB
Pathway Commons: KHSRP
MetabolismMetaCyc: KHSRP
HUMANCyc: KHSRP
RegulationEnsembl's Regulation: ENSG00000088247
miRBase: chr19 :6,413,118-6,424,822
TargetScan: NM_003685
cisRED: ENSG00000088247
ContextiHOP: KHSRP
cancer metabolism search in PubMed: KHSRP
UCL Cancer Institute: KHSRP
Assigned class in ccmGDBC

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

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

Mutations for KHSRP
* 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 KHSRP related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU902214KHSRP10761964246756424741CRTAP7489633315564533171525
BU619509KHSRP141881964133626414007KHSRP1865311964138346414179
AA628946KHSRP15011964138496414351IGFBP54956032217541404217541512
M64437KHSRP3533781964247516424776BHLHE41362658122627521626275577

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 # sample1                
GAIN (# sample)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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=40)
Stat. for Synonymous SNVs
(# total SNVs=17)
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
chr19:6416504-6416504p.I495I3
chr19:6422425-6422425p.D91G3
chr19:6418513-6418513p.G287E3
chr19:6421699-6421699p.D116G2
chr19:6422415-6422415p.T94T2
chr19:6418059-6418059p.R304Q2
chr19:6420483-6420483p.?2
chr19:6421313-6421313p.L134R2
chr19:6417826-6417826p.G335G2
chr19:6416853-6416853p.P408R2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 121 2    62   44 9
# mutation11 91 2    62   44 13
nonsynonymous SNV11 71 2    41   33 5
synonymous SNV   2       21   11 8
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
chr19:6416504p.I495I4
chr19:6422415p.P408L2
chr19:6417826p.G335G2
chr19:6416853p.T94T2
chr19:6418523p.D288H1
chr19:6416554p.D91N1
chr19:6417776p.K448I1
chr19:6418557p.G287E1
chr19:6422425p.M427I1
chr19:6416628p.R284H1

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 KHSRP 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 KHSRP

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

AURKB,CAD,CDCA7,CHAF1A,DNMT1,DUS3L,ELAVL1,
FAM64A,GATAD2A,ILF3,INCENP,KHSRP,KIF18B,LMNB2,
MCM7,MLLT1,ORC1,RAD54L,SMARCA4,SPC24,UHRF1
AARS2,PRRC2A,DHX37,EHMT1,ILF3,KDM5C,KHSRP,
PPP1R26,MYBBP1A,NCOR2,PACSIN2,PHRF1,PRR12,SAFB2,
SETD1A,SMARCA4,SURF6,TNRC18,UBE2O,ZC3H18,ZNF512B

CHAF1A,CHERP,DNMT1,DUS3L,ELAVL1,FARSA,FEM1A,
GATAD2A,GTF2F1,HNRNPM,ILF3,KHSRP,CAMSAP3,LMNB2,
MLLT1,PTBP1,RANBP3,RAVER1,SMARCA4,TCF3,TNPO2
BMS1,NOP9,DIS3L2,EIF3B,EIF4G1,ELAVL1,GCN1L1,
HNRNPM,ILF3,KHSRP,NUP188,PFAS,PRKDC,PRPF8,
SAFB,SF3B3,SMPD4,THADA,TMEM201,VARS,ZC3H18
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 KHSRP


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