Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	KHSRP
	Gene name	KH-type splicing regulatory protein
	Synonyms	FBP2\|FUBP2\|KSRP
	Cytomap	UCSC genome browser: 19p13.3
	Genomic location	chr19 :6413118-6424822
	Type of gene	protein-coding
	RefGenes	NM_003685.2,
	Ensembl id	ENSG00000088247
	Description	FUSE binding protein 2FUSE-binding protein 2KH type-splicing regulatory proteinfar upstream element-binding protein 2p75
	Modification date	20141207
dbXrefs	MIM : 603445
	HGNC : HGNC
	Ensembl : ENSG00000088247
	HPRD : 10350
	Vega : OTTHUMG00000180850
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_KHSRP
	BioGPS: 8570
	Gene Expression Atlas: ENSG00000088247
	The Human Protein Atlas: ENSG00000088247
Pathway	NCI Pathway Interaction Database: KHSRP
	KEGG: KHSRP
	REACTOME: KHSRP
	ConsensusPathDB
	Pathway Commons: KHSRP
Metabolism	MetaCyc: KHSRP
	HUMANCyc: KHSRP
Regulation	Ensembl's Regulation: ENSG00000088247
	miRBase: chr19 :6,413,118-6,424,822
	TargetScan: NM_003685
	cisRED: ENSG00000088247
Context	iHOP: KHSRP
	cancer metabolism search in PubMed: KHSRP
	UCL Cancer Institute: KHSRP
Assigned class in ccmGDB	C

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Phenotypic Information for KHSRP(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: KHSRP
	MedGen: KHSRP (Human Medical Genetics with Condition)
	ClinVar: KHSRP
Phenotype	MGI: KHSRP (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows KHSRP related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BU902214	KHSRP	10	76	19	6424675	6424741	CRTAP	74	896	3	33155645	33171525
BU619509	KHSRP	14	188	19	6413362	6414007	KHSRP	186	531	19	6413834	6414179
AA628946	KHSRP	1	501	19	6413849	6414351	IGFBP5	495	603	2	217541404	217541512
M64437	KHSRP	353	378	19	6424751	6424776	BHLHE41	362	658	12	26275216	26275577

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr19:6416504-6416504	p.I495I	3
chr19:6422425-6422425	p.D91G	3
chr19:6418513-6418513	p.G287E	3
chr19:6420483-6420483	p.?	2
chr19:6421313-6421313	p.L134R	2
chr19:6417826-6417826	p.G335G	2
chr19:6416853-6416853	p.P408R	2
chr19:6421699-6421699	p.D116G	2
chr19:6422415-6422415	p.T94T	2
chr19:6418059-6418059	p.R304Q	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		12	1		2					6	2				4	4		9
# mutation	1	1		9	1		2					6	2				4	4		13
nonsynonymous SNV	1	1		7	1		2					4	1				3	3		5
synonymous SNV				2								2	1				1	1		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr19:6416504	p.I495I	4
chr19:6417826	p.P408L	2
chr19:6416853	p.G335G	2
chr19:6422415	p.T94T	2
chr19:6417776	p.R284H	1
chr19:6418557	p.G424G	1
chr19:6422425	p.R284C	1
chr19:6416628	p.G416V	1
chr19:6418740	p.D272D	1
chr19:6422426	p.K251K	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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