Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 RPS12

Basic gene info.	Gene symbol	RPS12
	Gene name	ribosomal protein S12
	Synonyms	S12
	Cytomap	UCSC genome browser: 6q23.2
	Genomic location	chr6 :133135707-133138703
	Type of gene	protein-coding
	RefGenes	NM_001016.3,
	Ensembl id	ENSG00000112306
	Description	40S ribosomal protein S12
	Modification date	20141207
dbXrefs	MIM : 603660
	HGNC : HGNC
	HPRD : 04714
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPS12
	BioGPS: 6206
	Gene Expression Atlas: ENSG00000112306
	The Human Protein Atlas: ENSG00000112306
Pathway	NCI Pathway Interaction Database: RPS12
	KEGG: RPS12
	REACTOME: RPS12
	ConsensusPathDB
	Pathway Commons: RPS12
Metabolism	MetaCyc: RPS12
	HUMANCyc: RPS12
Regulation	Ensembl's Regulation: ENSG00000112306
	miRBase: chr6 :133,135,707-133,138,703
	TargetScan: NM_001016
	cisRED: ENSG00000112306
Context	iHOP: RPS12
	cancer metabolism search in PubMed: RPS12
	UCL Cancer Institute: RPS12
Assigned class in ccmGDB	C

Top

Phenotypic Information for RPS12(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPS12
	Familial Cancer Database: RPS12

* 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 REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: RPS12
	MedGen: RPS12 (Human Medical Genetics with Condition)
	ClinVar: RPS12
Phenotype	MGI: RPS12 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPS12

Mutations for RPS12

* 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 RPS12 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
DA436799	RPS12	1	65	6	133137948	133138012	SERINC1	64	591	6	122775296	122792957
AI394068	RPS12	4	65	6	133138642	133138703	NIPAL3	60	235	1	24745780	24745955
CD050400	RPS12	19	516	6	133135708	133138698	PAK4	515	565	19	39669994	39670044
BP319882	RPS12	1	505	6	133135708	133138703	SMYD3	505	582	1	246433107	246433184

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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=13

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=5)	Stat. for Synonymous SNVs (# total SNVs=16)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

Top

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
chr6:133138146-133138146	p.I94I	13
chr6:133137703-133137703	p.?	2
chr6:133138134-133138134	p.G90G	2
chr6:133136170-133136171	p.L26fs*32	1
chr6:133136205-133136205	p.E37K	1
chr6:133136222-133136222	p.L42F	1
chr6:133136223-133136223	p.D43N	1
chr6:133137658-133137658	p.L64L	1
chr6:133137686-133137686	p.Q73R	1
chr6:133138123-133138123	p.E87K	1

Top

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	1					1		3
# mutation			1									1	1					1		3
nonsynonymous SNV												1	1							3
synonymous SNV			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])

Top

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
chr6:133138134	p.G90G	2
chr6:133136205	p.E37K	1
chr6:133136222	p.L42F	1
chr6:133136223	p.D43N	1
chr6:133137686	p.Q73R	1
chr6:133138165	p.R101S	1
chr6:133138166	p.R101H	1
chr6:133138636	p.S118S	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 RPS12 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]

Top

Gene Expression for RPS12

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


EEF1A1P9,EEF1G,RPL10A,RPL11,RPL13,RPL17,RPL18A, RPL27A,RPL31,RPL32,RPL36,RPL37A,RPL6,RPLP0, RPS10,RPS12,RPS18,RPS27A,RPS8,RPSAP58,UBA52	EEF1A1P9,RPL10,RPL14,RPL29,RPL31,RPL32,RPL35A, RPL37,RPL4,RPL5,RPL6,RPLP0,RPS12,RPS14, RPS23,RPS27A,RPS6,RPS7,RPS8,RPSA,RPSAP58

GAS5,LRRC75A-AS1,RPL10A,RPL12,RPL13A,RPL26,RPL31, RPL35A,RPL36,RPL37A,RPL7A,RPLP0,RPS10,RPS11, RPS12,RPS16,RPS17,RPS18,RPS23,RPS25,RPS27A	EEF1A1,RPL10,RPL10A,RPL14,RPL15,RPL19,RPL30, RPL32,RPL3,RPL38,RPL6,RPL7A,RPLP0,RPS11, RPS12,RPS13,RPS23,RPS25,RPS3,RPS5,RPS8

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for RPS12

There's no related Drug.

Top

Cross referenced IDs for RPS12

* 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