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 UROD

Basic gene info.	Gene symbol	UROD
	Gene name	uroporphyrinogen decarboxylase
	Synonyms	PCT\|UPD
	Cytomap	UCSC genome browser: 1p34
	Genomic location	chr1 :45477804-45481341
	Type of gene	protein-coding
	RefGenes	NM_000374.4, NR_036510.1,
	Ensembl id	ENSG00000126088
	Description	uroporphyrinogen III decarboxylase
	Modification date	20141219
dbXrefs	MIM : 613521
	HGNC : HGNC
	Ensembl : ENSG00000126088
	HPRD : 01441
	Vega : OTTHUMG00000008949
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_UROD
	BioGPS: 7389
	Gene Expression Atlas: ENSG00000126088
	The Human Protein Atlas: ENSG00000126088
Pathway	NCI Pathway Interaction Database: UROD
	KEGG: UROD
	REACTOME: UROD
	ConsensusPathDB
	Pathway Commons: UROD
Metabolism	MetaCyc: UROD
	HUMANCyc: UROD
Regulation	Ensembl's Regulation: ENSG00000126088
	miRBase: chr1 :45,477,804-45,481,341
	TargetScan: NM_000374
	cisRED: ENSG00000126088
Context	iHOP: UROD
	cancer metabolism search in PubMed: UROD
	UCL Cancer Institute: UROD
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: UROD
	Familial Cancer Database: UROD

* 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
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM REACTOME_METABOLISM_OF_PORPHYRINS

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

Mutations for UROD

* 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 UROD 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
BU157543	NSRP1	184	209	17	28503625	28503653	UROD	210	646	1	45478873	45479740
AA368910	UROD	1	204	1	45481049	45481492	UROD	194	335	1	45479387	45479642
AW385230	UROD	1	65	1	45480445	45480509	MCM3AP-AS1	61	483	21	47654247	47654670
BE772547	HIPK1	1	319	1	114515938	114516256	UROD	316	530	1	45480619	45481163
BE772548	HIPK1	4	338	1	114515938	114516275	UROD	335	557	1	45480619	45481171
BM718816	LMO4	17	156	1	87810949	87811091	UROD	149	220	1	45481176	45481247

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

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

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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=13)	Stat. for Synonymous SNVs (# total SNVs=7)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr1:45477941-45477941	p.E2K	2
chr1:45479709-45479709	p.P201P	2
chr1:45479683-45479683	p.R193C	1
chr1:45480657-45480658	p.C308fs*7	1
chr1:45479706-45479706	p.V200V	1
chr1:45481012-45481012	p.E316K	1
chr1:45477952-45477952	p.G5G	1
chr1:45481027-45481027	p.V321M	1
chr1:45478626-45478626	p.A23V	1
chr1:45480122-45480122	p.L216L	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=1

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			4			3		2	1			1	2			1	1		1
# mutation	1			4			3		2	1			1	2			1	1		1
nonsynonymous SNV				2			1		1	1			1	1				1		1
synonymous SNV	1			2			2		1					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
chr1:45480182	p.Q302H	1
chr1:45477952	p.V321M	1
chr1:45480410	p.M345V	1
chr1:45478626	p.R365Q	1
chr1:45480612	p.G5G	1
chr1:45478653	p.A23V	1
chr1:45480642	p.P32L	1
chr1:45478860	p.P62P	1
chr1:45481027	p.I82I	1
chr1:45478996	p.R122Q	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 UROD 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 UROD

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


ARL6IP4,AURKAIP1,B4GALT7,C19orf70,C1orf122,C1orf123,C1orf86, PRADC1,LAMTOR4,DMAP1,DPM3,ERI3,GADD45GIP1,LSM10, NDUFA13,NDUFB7,NDUFS7,THAP3,UROD,ZNF593,ZNHIT1	ABHD14A,ANXA11,ARL2,BLOC1S1,BLVRB,LAMTOR1,CCDC23, CCM2,CD63,GPX1,GPX4,HINT2,LRP3,MYL6, NEDD8,NUCB1,POLR2L,PSMD8,RNPEPL1,SNX17,UROD

ADPRHL2,AKR1A1,ATP6V0B,BLOC1S1,C1orf123,SMIM12,ECI1, DGCR6L,LSM10,NAA38,PEF1,POLR2L,PSMB10,PSMB6, PSME1,SCO2,SRA1,STX8,TRAPPC3,TRNAU1AP,UROD	ANAPC16,ARL2,BOLA1,BRK1,CCDC23,DCTN3,FBXL5, FIS1,FUNDC2,MANBAL,MRPL40,PFDN1,RWDD2B,SNAPIN, SNX3,THTPA,TPD52L2,UROD,YPEL5,ZMAT5,ZNF32

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 UROD

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00145	uroporphyrinogen decarboxylase	approved; nutraceutical	Glycine

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Cross referenced IDs for UROD

* 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