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 RQCD1

Basic gene info.	Gene symbol	RQCD1
	Gene name	RCD1 required for cell differentiation1 homolog (S. pombe)
	Synonyms	CNOT9\|CT129\|RCD-1\|RCD1
	Cytomap	UCSC genome browser: 2q35
	Genomic location	chr2 :219433677-219458999
	Type of gene	protein-coding
	RefGenes	NM_001271634.1, NM_001271635.1,NM_005444.2,NR_073390.1,
	Ensembl id	ENSG00000144580
	Description	CCR4-NOT transcription complex subunit 9cancer/testis antigen 129cell differentiation protein RCD1 homologprotein involved in sexual development
	Modification date	20141207
dbXrefs	MIM : 612054
	HGNC : HGNC
	Ensembl : ENSG00000144580
	HPRD : 08828
	Vega : OTTHUMG00000154750
Protein	UniProt: Q92600 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RQCD1
	BioGPS: 9125
	Gene Expression Atlas: ENSG00000144580
	The Human Protein Atlas: ENSG00000144580
Pathway	NCI Pathway Interaction Database: RQCD1
	KEGG: RQCD1
	REACTOME: RQCD1
	ConsensusPathDB
	Pathway Commons: RQCD1
Metabolism	MetaCyc: RQCD1
	HUMANCyc: RQCD1
Regulation	Ensembl's Regulation: ENSG00000144580
	miRBase: chr2 :219,433,677-219,458,999
	TargetScan: NM_001271634
	cisRED: ENSG00000144580
Context	iHOP: RQCD1
	cancer metabolism search in PubMed: RQCD1
	UCL Cancer Institute: RQCD1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for RQCD1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RQCD1
	Familial Cancer Database: RQCD1

* 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 SKCM ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.sciencedirect.com/science/article/pii/S0092867415006340,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	612054; gene.
Orphanet
Disease	KEGG Disease: RQCD1
	MedGen: RQCD1 (Human Medical Genetics with Condition)
	ClinVar: RQCD1
Phenotype	MGI: RQCD1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RQCD1

Mutations for RQCD1

* 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 RQCD1 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
BF513238	LINS	15	77	15	101114437	101114499	RQCD1	72	584	2	219433669	219452382
AA324744	RQCD1	1	235	2	219445021	219445255	RQCD1	235	317	2	219433702	219433784

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=11

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=16)	Stat. for Synonymous SNVs (# total SNVs=11)

Stat. for Deletions (# total SNVs=3)	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
chr2:219449406-219449406	p.P131L	10
chr2:219447749-219447749	p.S87C	3
chr2:219447753-219447753	p.N88K	2
chr2:219449364-219449364	p.L119fs*29	2
chr2:219449430-219449430	p.S139N	2
chr2:219457386-219457386	p.L229L	2
chr2:219447751-219447751	p.N88Y	2
chr2:219452361-219452362	p.E162fs*14	1
chr2:219445338-219445338	p.N27D	1
chr2:219457418-219457418	p.S240L	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=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				5					2			2	2	1			5	2		4
# mutation				5					2			3	2	1			2	2		4
nonsynonymous SNV				3					2			2		1			2	1		2
synonymous SNV				2								1	2					1		2

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
chr2:219449406	p.P131L,RQCD1	4
chr2:219447753	p.N88N,RQCD1	2
chr2:219449361	p.R130R,RQCD1	1
chr2:219445338	p.T161T,RQCD1	1
chr2:219449404	p.R169Q,RQCD1	1
chr2:219445385	p.D193D,RQCD1	1
chr2:219445442	p.N27D,RQCD1	1
chr2:219452361	p.I212L,RQCD1	1
chr2:219445458	p.L42L,RQCD1	1
chr2:219452384	p.A226A,RQCD1	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 RQCD1 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 RQCD1

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


ANAPC1,BARD1,CASC5,CENPI,CKAP2L,CLSPN,GAS2L3, GTF3C3,NCKAP1,NUP155,NUP160,NUP205,R3HDM1,RIF1, RQCD1,SGOL2,SLC30A6,TOPBP1,TRIP12,USP37,XPO1	ASCC3,C9orf41,DDX52,GTF2H3,HSPA14,IARS,KDM1B, KRR1,MAP3K7,NAA15,NAA25,NEDD1,NUP153,NUP205, POLR2B,PRPF40A,RFX7,RQCD1,SLC30A9,NDC1,WDR12

BARD1,BUB1,DDIAS,PARPBP,CCDC138,CKAP2L,CTDSPL2, DEPDC1,DNA2,GSTCD,GTF2H3,HAT1,HNRNPLL,HSPA14, MCM6,MOB1A,PAFAH1B2,RACGAP1,RQCD1,SLC30A6,NDC1	BOLA3,CENPK,EBNA1BP2,ENOPH1,GNL3,HAUS1,MIS12, MRPL3,NUP37,POLE3,POLR1C,PRDX4,PREB,RAN, RQCD1,SLBP,SNRNP40,SNRPD1,SRPRB,TMEM165,UTP6

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 RQCD1

There's no related Drug.

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Cross referenced IDs for RQCD1

* 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