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 RPL7A

Basic gene info.	Gene symbol	RPL7A
	Gene name	ribosomal protein L7a
	Synonyms	L7A\|SURF3\|TRUP
	Cytomap	UCSC genome browser: 9q34
	Genomic location	chr9 :136215068-136218280
	Type of gene	protein-coding
	RefGenes	NM_000972.2,
	Ensembl id	ENSG00000260501
	Description	60S ribosomal protein L7aPLA-X polypeptidesurfeit 3surfeit locus protein 3thyroid hormone receptor uncoupling protein
	Modification date	20141207
dbXrefs	MIM : 185640
	HGNC : HGNC
	Ensembl : ENSG00000148303
	HPRD : 01712
	Vega : OTTHUMG00000020864
Protein	UniProt: P62424 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL7A
	BioGPS: 6130
	Gene Expression Atlas: ENSG00000260501
	The Human Protein Atlas: ENSG00000260501
Pathway	NCI Pathway Interaction Database: RPL7A
	KEGG: RPL7A
	REACTOME: RPL7A
	ConsensusPathDB
	Pathway Commons: RPL7A
Metabolism	MetaCyc: RPL7A
	HUMANCyc: RPL7A
Regulation	Ensembl's Regulation: ENSG00000260501
	miRBase: chr9 :136,215,068-136,218,280
	TargetScan: NM_000972
	cisRED: ENSG00000260501
Context	iHOP: RPL7A
	cancer metabolism search in PubMed: RPL7A
	UCL Cancer Institute: RPL7A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for RPL7A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL7A
	Familial Cancer Database: RPL7A

* 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	185640; gene.
Orphanet
Disease	KEGG Disease: RPL7A
	MedGen: RPL7A (Human Medical Genetics with Condition)
	ClinVar: RPL7A
Phenotype	MGI: RPL7A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL7A

Mutations for RPL7A

* 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 RPL7A 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
DA868683	RPL7A	1	68	9	136217701	136217768	ST7-AS1	68	549	7	116593398	116759710
BU681467	RPL7A	17	563	9	136216808	136218282	CDH1	562	685	16	68846067	68847239
BC012174	RPL7A	14	872	9	136215776	136218281	RDX	873	1705	11	110128554	110167324
X06704	RPL7A	1	154	9	136215069	136215897	NTRK1	154	1558	1	156844362	156851642

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=12)	Stat. for Synonymous SNVs (# total SNVs=4)

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
chr9:136217156-136217156	p.H159H	2
chr9:136215778-136215778	p.P2R	2
chr9:136215864-136215864	p.L31V	2
chr9:136216773-136216773	p.Q94R	1
chr9:136216887-136216887	p.R132T	1
chr9:136217103-136217103	p.T142A	1
chr9:136217157-136217157	p.D160N	1
chr9:136215820-136215820	p.P16L	1
chr9:136217463-136217463	p.F169L	1
chr9:136217493-136217493	p.V179V	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			1	1	1				1			1	1				1	4		2
# mutation			1	1	1				1			1	1				1	4		2
nonsynonymous SNV			1	1					1			1	1				1	2		2
synonymous SNV					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
chr9:136216438	p.R53S	3
chr9:136217156	p.H159H	2
chr9:136217463	p.A214T	1
chr9:136217511	p.L253L	1
chr9:136217870	p.E260E	1
chr9:136218179	p.A68G	1
chr9:136218200	p.Q94R	1
chr9:136216484	p.R132T	1
chr9:136216773	p.T142A	1
chr9:136216887	p.D160N	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 RPL7A 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 RPL7A

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


GNB2L1,NACA,RPL10A,RPL11,RPL12,RPL13A,RPL24, RPL29,RPL31,RPL32,RPL35,RPL3,RPL37A,RPL6, RPL7A,RPS11,RPS14,RPS18,RPS2,RPS4X,RPS8	EEF1G,FBL,GNB2L1,NOB1,RPL10,RPL12,RPL13, RPL13A,RPL14,RPL18,RPL19,RPL29,RPL3,RPL36, RPL7A,RPL8,RPS14,RPS18,RPS2,RPS3,RPS8

RPL10A,RPL12,RPL24,RPL29,RPL31,RPL32,RPL35, RPL35A,RPL36,RPL37A,RPL7A,RPS10,RPS12,RPS14, RPS18,RPS23,RPS25,RPS27A,RPS6,RPS8,RPS9	EEF1A1,EEF1A1P9,RPL10,RPL10A,RPL12,RPL14,RPL15, RPL19,RPL29,RPL32,RPL3,RPL7A,RPL8,RPLP0, RPLP1,RPS11,RPS12,RPS13,RPS3,RPS5,RPS8

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 RPL7A

There's no related Drug.

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Cross referenced IDs for RPL7A

* 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