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 RNPS1

Basic gene info.	Gene symbol	RNPS1
	Gene name	RNA binding protein S1, serine-rich domain
	Synonyms	E5.1
	Cytomap	UCSC genome browser: 16p13.3
	Genomic location	chr16 :2303099-2318413
	Type of gene	protein-coding
	RefGenes	NM_001286625.1, NM_001286626.1,NM_001286627.1,NM_006711.4,NM_080594.3, NR_104485.1,
	Ensembl id	ENSG00000205937
	Description	RNA-binding protein S1, serine-rich domainRNA-binding protein with serine-rich domain 1SR proteinSR-related protein LDC2
	Modification date	20141207
dbXrefs	MIM : 606447
	HGNC : HGNC
	Ensembl : ENSG00000205937
	HPRD : 07341
	Vega : OTTHUMG00000128828
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RNPS1
	BioGPS: 10921
	Gene Expression Atlas: ENSG00000205937
	The Human Protein Atlas: ENSG00000205937
Pathway	NCI Pathway Interaction Database: RNPS1
	KEGG: RNPS1
	REACTOME: RNPS1
	ConsensusPathDB
	Pathway Commons: RNPS1
Metabolism	MetaCyc: RNPS1
	HUMANCyc: RNPS1
Regulation	Ensembl's Regulation: ENSG00000205937
	miRBase: chr16 :2,303,099-2,318,413
	TargetScan: NM_001286625
	cisRED: ENSG00000205937
Context	iHOP: RNPS1
	cancer metabolism search in PubMed: RNPS1
	UCL Cancer Institute: RNPS1
Assigned class in ccmGDB	C

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Phenotypic Information for RNPS1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RNPS1
	Familial Cancer Database: RNPS1

* 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: RNPS1
	MedGen: RNPS1 (Human Medical Genetics with Condition)
	ClinVar: RNPS1
Phenotype	MGI: RNPS1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RNPS1

Mutations for RNPS1

* 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	RNPS1	chr16	2316974	2316994	UBA2	chr19	34923086	34923106
pancreas	RNPS1	chr16	2318264	2318284	GFER	chr16	2036880	2036900

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 RNPS1 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
BM750508	ZNF223	1	277	19	44556189	44564641	RNPS1	268	562	16	2312373	2313235
BG272918	GFRA1	7	331	10	117823236	117823560	RNPS1	328	424	16	2312286	2312382
DA134109	RNU12	1	71	22	43011251	43011321	RNPS1	72	568	16	2313127	2314752
DA783540	RNPS1	1	447	16	2313246	2318115	ZEB2	444	601	2	145154061	145155926

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

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
chr16:2313134-2313134	p.R128R	2
chr16:2314208-2314208	p.R66C	2
chr16:2305707-2305707	p.I233V	1
chr16:2305708-2305708	p.E232D	1
chr16:2313224-2313224	p.S98R	1
chr16:2312306-2312306	p.E217K	1
chr16:2313274-2313274	p.S81L	1
chr16:2312324-2312324	p.E211Q	1
chr16:2312359-2312359	p.P199L	1
chr16:2314218-2314218	p.T62T	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	2	1		2			1		1	1		2	1	3			2	1		3
# mutation	2	1		2			1		1	1		2	1	3			2	1		3
nonsynonymous SNV	1			2			1			1			1	2			1	1		3
synonymous SNV	1	1							1			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
chr16:2314218	p.T39T,RNPS1	2
chr16:2312306	p.S114S,RNPS1	1
chr16:2314307	p.R112R,RNPS1	1
chr16:2312359	p.S75R,RNPS1	1
chr16:2314313	p.S58L,RNPS1	1
chr16:2312402	p.R43C,RNPS1	1
chr16:2314602	p.D10Y,RNPS1	1
chr16:2312759	p.P230S,RNPS1	1
chr16:2312776	p.R8C,RNPS1	1
chr16:2313105	p.P218P,RNPS1	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 RNPS1 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 RNPS1

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


AXIN1,C16orf59,C16orf91,CHTF18,KCTD5,KIF22,MLST8, MRPS34,NPRL3,NUBP2,PPP4C,PRR14,RNPS1,RPUSD1, TBL3,THOC6,PAM16,TRAF7,TRAP1,UBE2I,ZNF598	ABT1,BCL2L12,C16orf91,ETHE1,FBRSL1,HSPBP1,KAT8, NSUN5,OTUB1,PRCC,RCE1,RNPS1,RPS21,SF3A2, SLC35C2,SNRPB,TARBP2,THAP7,THOC6,TRIM28,ZNF414

AXIN1,C16orf13,TSR3,E4F1,EEF2KMT,GFER,MRPL28, MRPS34,NARFL,NPRL3,NUBP2,NUTF2,RAB40C,RNPS1, RPUSD1,TELO2,TFAP4,THOC6,UBE2I,ZNF205,ZNF263	BYSL,C19orf47,C7orf26,CCDC86,CD3EAP,CDC42EP1,FARSA, GRWD1,MRPL4,NAP1L4,PES1,PPAN,RNPS1,RRP1, RRP9,RUVBL2,SGTA,TOMM40,TRMT1,UBIAD1,ZMYND19

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 RNPS1

There's no related Drug.

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Cross referenced IDs for RNPS1

* 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