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 NCBP2

Basic gene info.	Gene symbol	NCBP2
	Gene name	nuclear cap binding protein subunit 2, 20kDa
	Synonyms	CBC2\|CBP20\|NIP1
	Cytomap	UCSC genome browser: 3q29
	Genomic location	chr3 :196662272-196669464
	Type of gene	protein-coding
	RefGenes	NM_001042540.1, NM_007362.3,
	Ensembl id	ENSG00000114503
	Description	20 kDa nuclear cap-binding proteinNCBP 20 kDa subunitNCBP interacting protein 1NCBP-interacting protein 1cell proliferation-inducing gene 55 proteinnuclear cap binding protein subunit 2, 20kDnuclear cap-binding protein subunit 2
	Modification date	20141207
dbXrefs	MIM : 605133
	HGNC : HGNC
	Ensembl : ENSG00000114503
	HPRD : 05503
	Vega : OTTHUMG00000155520
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NCBP2
	BioGPS: 22916
	Gene Expression Atlas: ENSG00000114503
	The Human Protein Atlas: ENSG00000114503
Pathway	NCI Pathway Interaction Database: NCBP2
	KEGG: NCBP2
	REACTOME: NCBP2
	ConsensusPathDB
	Pathway Commons: NCBP2
Metabolism	MetaCyc: NCBP2
	HUMANCyc: NCBP2
Regulation	Ensembl's Regulation: ENSG00000114503
	miRBase: chr3 :196,662,272-196,669,464
	TargetScan: NM_001042540
	cisRED: ENSG00000114503
Context	iHOP: NCBP2
	cancer metabolism search in PubMed: NCBP2
	UCL Cancer Institute: NCBP2
Assigned class in ccmGDB	C

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Phenotypic Information for NCBP2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: NCBP2
	Familial Cancer Database: NCBP2

* 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_NON_CODING_RNA REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: NCBP2
	MedGen: NCBP2 (Human Medical Genetics with Condition)
	ClinVar: NCBP2
Phenotype	MGI: NCBP2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: NCBP2

Mutations for NCBP2

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	NCBP2	chr3	196662594	196662614	MAST4	chr5	66414017	66414037

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NCBP2 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
DA659977	NCBP2	1	81	3	196669297	196669377	FBXL2	82	569	3	33400769	33415357
AA625748	NCBP2	54	392	3	196662329	196662667	PEX5	393	548	12	7362279	7362434
BU536214	YBX1	4	266	1	43148098	43148360	NCBP2	267	497	3	196663726	196663955
F01144	NCBP2	1	177	3	196662339	196662515	GDF9	175	337	5	132202339	132202681

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=14)	Stat. for Synonymous SNVs (# total SNVs=3)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr3:196664391-196664391	p.S130Y	2
chr3:196663898-196663898	p.L152P	1
chr3:196664484-196664484	p.R99Q	1
chr3:196663913-196663913	p.G147A	1
chr3:196664485-196664485	p.R99W	1
chr3:196663942-196663942	p.E137D	1
chr3:196664498-196664498	p.A94A	1
chr3:196663950-196663950	p.R135W	1
chr3:196664509-196664509	p.R91C	1
chr3:196666226-196666226	p.T52T	1

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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=2

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				5	1		2					1						1		4
# mutation				4	1		2					1						1		4
nonsynonymous SNV				2	1		2					1								3
synonymous SNV				2														1		1

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
chr3:196664498	p.A41A,NCBP2	2
chr3:196663898	p.D63D,NCBP2	1
chr3:196666226	p.I57M,NCBP2	1
chr3:196663927	p.R56Q,NCBP2	1
chr3:196669358	p.R46Q,NCBP2	1
chr3:196663950	p.R46W,NCBP2	1
chr3:196669371	p.T52T	1
chr3:196664404	p.L6Q,NCBP2	1
chr3:196664405	p.S2T,NCBP2	1
chr3:196664432	p.L99P,NCBP2	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 NCBP2 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 NCBP2

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


ACTL6A,DLG1,DNAJB11,DVL3,FBXO45,FXR1,FYTTD1, LOC220729,LSG1,MRPL47,NCBP2,OPA1,PAK2,PARL, PIGX,RFC4,SENP5,TBCCD1,TMEM41A,TRA2B,WDR53	SMIM15,CAND1,CCT2,CNOT2,COPB1,DCAF13,HNRNPK, ITFG1,NCBP2,NUP107,PIGX,RAB22A,RARS,SLMO2, SMARCE1,SUB1,THUMPD3,TWF1,UBE2K,VPS35,YEATS4

ACVR2B,ALG3,ANAPC13,ATP13A3,CMTM8,DDX27,DNAJC19, E2F3,FBXO45,IGF2BP2,LOC152217,MPHOSPH10,NCBP2,RAB7A, RNF114,SENP5,U2SURP,TMEM41A,TSEN2,UBE2V1,WDR53	URI1,DNAI2,TVP23B,GAB1,GABPA,HDHD2,NCBP2, P4HA1,PPP3CA,DESI2,PSG9,SMAD1,SPHAR,SPOPL, SYTL4,TLK1,TMC1,TMEM30A,WEE2,ZNF24,ZNF442

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 NCBP2

There's no related Drug.

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Cross referenced IDs for NCBP2

* 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