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 XRN2

Basic gene info.	Gene symbol	XRN2
	Gene name	5'-3' exoribonuclease 2
	Synonyms	-
	Cytomap	UCSC genome browser: 20p11.2-p11.1
	Genomic location	chr20 :21283941-21370463
	Type of gene	protein-coding
	RefGenes	NM_012255.3,
	Ensembl id	ENSG00000088930
	Description	DHP proteinDhm1-like protein (mouse homolog)
	Modification date	20141207
dbXrefs	MIM : 608851
	HGNC : HGNC
	Ensembl : ENSG00000088930
	HPRD : 10309
	Vega : OTTHUMG00000032025
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_XRN2
	BioGPS: 22803
	Gene Expression Atlas: ENSG00000088930
	The Human Protein Atlas: ENSG00000088930
Pathway	NCI Pathway Interaction Database: XRN2
	KEGG: XRN2
	REACTOME: XRN2
	ConsensusPathDB
	Pathway Commons: XRN2
Metabolism	MetaCyc: XRN2
	HUMANCyc: XRN2
Regulation	Ensembl's Regulation: ENSG00000088930
	miRBase: chr20 :21,283,941-21,370,463
	TargetScan: NM_012255
	cisRED: ENSG00000088930
Context	iHOP: XRN2
	cancer metabolism search in PubMed: XRN2
	UCL Cancer Institute: XRN2
Assigned class in ccmGDB	C

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Phenotypic Information for XRN2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: XRN2
	Familial Cancer Database: XRN2

* 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_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: XRN2
	MedGen: XRN2 (Human Medical Genetics with Condition)
	ClinVar: XRN2
Phenotype	MGI: XRN2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: XRN2

Mutations for XRN2

* 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

* 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	XRN2	chr20	21296317	21296337	XRN2	chr20	21299139	21299159
pancreas	XRN2	chr20	21301630	21301650	XRN2	chr20	21292803	21292823
pancreas	XRN2	chr20	21308520	21308540	XRN2	chr20	21309134	21309154

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 XRN2 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
BG004570	XRN2	8	163	20	21311260	21312271	EEF1D	159	283	8	144674315	144674439
BP273629	FAM172A	1	408	5	93018889	93019294	XRN2	409	573	20	21309207	21311181
BQ683058	WASF3	12	227	13	27261627	27261841	XRN2	227	963	20	21346298	21370268
BF356570	TARDBP	16	95	1	11082473	11082553	XRN2	91	387	20	21314397	21315172
AI917076	GPRC5A	2	305	12	13066290	13066593	XRN2	301	474	20	21322504	21322677
BF947784	XRN2	39	443	20	21308509	21308913	TCERG1	440	633	5	145843511	145843704

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=70)	Stat. for Synonymous SNVs (# total SNVs=30)

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
chr20:21312958-21312958	p.P246P	5
chr20:21306923-21306923	p.E28K	3
chr20:21329006-21329006	p.V601I	2
chr20:21327166-21327166	p.W548L	2
chr20:21327175-21327175	p.R551I	2
chr20:21314251-21314251	p.R310C	2
chr20:21312980-21312980	p.E254*	2
chr20:21312985-21312985	p.F255F	2
chr20:21309203-21309203	p.R108C	2
chr20:21328891-21328891	p.P591P	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=3

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	4	3	2	8	2		5		7			6	3	1			6	11	1	18
# mutation	4	3	2	8	2		5		7			6	3	1			7	14	1	29
nonsynonymous SNV	3	3	2	6	1		4		6			6	2	1			4	12	1	18
synonymous SNV	1			2	1		1		1				1				3	2		11

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
chr20:21327175	p.P246P	3
chr20:21312958	p.R551K	3
chr20:21309203	p.F255L	2
chr20:21328891	p.R108C	2
chr20:21312985	p.P591P	2
chr20:21307158	p.R946K	1
chr20:21321376	p.G104R	1
chr20:21337273	p.A460A	1
chr20:21311306	p.G600R	1
chr20:21367535	p.A779T	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 XRN2 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 XRN2

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


APC,ATRN,SLX4IP,CRNKL1,CSNK2A1,CSNK2A3,DHX9, DPP8,ESF1,GTF2H3,ITCH,PPP4R2,RBBP9,RBM12, SEC23B,SRFBP1,TGFBRAP1,TSTD2,TTC37,XRN2,ZNF81	ACTL6A,ADNP,CASK,DCLRE1A,DHX15,DHX9,LRBA, OCLN,PRPF40A,PTPRK,RBBP4,SAMD12,SMARCA5,SNX30, TEX9,NDC1,TOP2B,XRCC5,XRN2,ZNF268,ZNF28

ANKEF1,DZANK1,APMAP,MGME1,CRNKL1,CSNK2A1,CSNK2A3, CSRP2BP,ESF1,GINS1,NAA20,NANP,POLR3F,RALGAPA2, RBBP9,SEC23B,SNRPB2,SNX5,TASP1,TRMT6,XRN2	DPH6,C12orf45,CACYBP,CCT4,COPS4,DAP3,DDX47, DNAJB9,EIF3M,HSPA13,MRPL1,MRPL39,MRPS28,RB1, RGS18,SSR3,STAM,STRAP,TSN,WDR12,XRN2

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 XRN2

There's no related Drug.

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Cross referenced IDs for XRN2

* 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