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 RPL37A

Basic gene info.	Gene symbol	RPL37A
	Gene name	ribosomal protein L37a
	Synonyms	L37A
	Cytomap	UCSC genome browser: 2q35
	Genomic location	chr2 :217363519-217366188
	Type of gene	protein-coding
	RefGenes	NM_000998.4,
	Ensembl id	ENSG00000197756
	Description	60S ribosomal protein L37a
	Modification date	20141207
dbXrefs	MIM : 613314
	HGNC : HGNC
	HPRD : 17997
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL37A
	BioGPS: 6168
	Gene Expression Atlas: ENSG00000197756
	The Human Protein Atlas: ENSG00000197756
Pathway	NCI Pathway Interaction Database: RPL37A
	KEGG: RPL37A
	REACTOME: RPL37A
	ConsensusPathDB
	Pathway Commons: RPL37A
Metabolism	MetaCyc: RPL37A
	HUMANCyc: RPL37A
Regulation	Ensembl's Regulation: ENSG00000197756
	miRBase: chr2 :217,363,519-217,366,188
	TargetScan: NM_000998
	cisRED: ENSG00000197756
Context	iHOP: RPL37A
	cancer metabolism search in PubMed: RPL37A
	UCL Cancer Institute: RPL37A
Assigned class in ccmGDB	C

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Phenotypic Information for RPL37A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL37A
	Familial Cancer Database: RPL37A

* 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: RPL37A
	MedGen: RPL37A (Human Medical Genetics with Condition)
	ClinVar: RPL37A
Phenotype	MGI: RPL37A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL37A

Mutations for RPL37A

* 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 RPL37A 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
CD365929	RPL37A	12	133	2	217366069	217366190	HCK	130	658	20	30659522	30671812
AW246883	RPL37A	7	347	2	217363991	217366190	CBX6	345	477	22	39262273	39262405
BG478185	PRPF8	2	209	17	1581811	1582127	RPL37A	203	547	2	217363988	217366190
BU954401	RPL37A	7	375	2	217363568	217366187	MYL6	376	472	12	56553913	56554103
BQ227726	RPL37A	1	348	2	217363589	217366187	PPIA	349	432	7	44839426	44840921
AK001254	CCDC88A	1	2204	2	55522937	55555532	RPL37A	2203	2291	2	217366095	217366183
DR759675	RPL37A	1	72	2	217363588	217364051	DHX57	72	868	2	39025430	39046202
AA631668	RPL37A	20	215	2	217364685	217366190	KLHL12	211	327	1	202887306	202887422
CD049225	RPL37A	10	88	2	217366106	217366184	EIF4A1	89	889	17	7477605	7480964
BC000136	DNM1L	22	3143	12	32854346	32897354	RPL37A	3126	3213	2	217366103	217366190

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=8)	Stat. for Synonymous SNVs (# total SNVs=2)

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
chr2:217364706-217364706	p.H56R	2
chr2:217364707-217364707	p.H56H	1
chr2:217364716-217364716	p.S59S	1
chr2:217364733-217364733	p.A65D	1
chr2:217366081-217366081	p.T78M	1
chr2:217366090-217366090	p.S81F	1
chr2:217364056-217364056	p.R23W	1
chr2:217366124-217366124	p.Q92Q	1
chr2:217364070-217364070	p.K27N	1
chr2:217364099-217364099	p.Y37S	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=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				2			1			1				1				2		1
# mutation				1			1			1				1				2		1
nonsynonymous SNV				1			1													1
synonymous SNV										1				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
chr2:217364706	p.H56R	2
chr2:217364725	p.R23W	1
chr2:217366124	p.Y37S	1
chr2:217364056	p.A51A	1
chr2:217364099	p.H56H	1
chr2:217364692	p.S59S	1
chr2:217364707	p.K62N	1
chr2:217364716	p.Q92Q	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 RPL37A 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 RPL37A

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


RPL11,RPL13,RPL18,RPL24,RPL27A,RPL28,RPL29, RPL31,RPL32,RPL35,RPL36,RPL37,RPL37A,RPLP2, RPS10,RPS11,RPS14,RPS15,RPS19,RPS8,RPS9	PHB2,RPL10,RPL13,RPL14,RPL18,RPL18A,RPL19, RPL29,RPL32,RPL35,RPL37,RPL37A,RPL4,RPS11, RPS12,RPS14,RPS16,RPS21,RPS23,RPS6,RPS8

EEF1B2,RPL10A,RPL12,RPL14,RPL29,RPL31,RPL32, RPL35A,RPL36,RPL37,RPL37A,RPL38,RPL7A,RPS13, RPS17,RPS18,RPS23,RPS25,RPS27A,RPS6,RPS7	RPL18,RPL18A,RPL19,RPL32,RPL36,RPL37,RPL37A, RPL38,RPL7A,RPL8,RPLP0,RPLP1,RPS10,RPS12, RPS16,RPS19,RPS21,RPS23,RPS29,RPS3,RPS9

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 RPL37A

There's no related Drug.

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Cross referenced IDs for RPL37A

* 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