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 SRPR

Basic gene info.	Gene symbol	SRPR
	Gene name	signal recognition particle receptor (docking protein)
	Synonyms	DP\|Sralpha
	Cytomap	UCSC genome browser: 11q24.2
	Genomic location	chr11 :126132813-126138877
	Type of gene	protein-coding
	RefGenes	NM_001177842.1, NM_003139.3,
	Ensembl id	ENSG00000182934
	Description	DP-alphaSR-alphaSRP-alphadocking protein alphasignal recognition particle receptor subunit alpha
	Modification date	20141207
dbXrefs	MIM : 182180
	HGNC : HGNC
	Ensembl : ENSG00000182934
	HPRD : 01645
	Vega : OTTHUMG00000165826
Protein	UniProt: P08240 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SRPR
	BioGPS: 6734
	Gene Expression Atlas: ENSG00000182934
	The Human Protein Atlas: ENSG00000182934
Pathway	NCI Pathway Interaction Database: SRPR
	KEGG: SRPR
	REACTOME: SRPR
	ConsensusPathDB
	Pathway Commons: SRPR
Metabolism	MetaCyc: SRPR
	HUMANCyc: SRPR
Regulation	Ensembl's Regulation: ENSG00000182934
	miRBase: chr11 :126,132,813-126,138,877
	TargetScan: NM_001177842
	cisRED: ENSG00000182934
Context	iHOP: SRPR
	cancer metabolism search in PubMed: SRPR
	UCL Cancer Institute: SRPR
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: SRPR
	Familial Cancer Database: SRPR

* 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 BRCA 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.nature.com/nature/journal/v490/n7418/full/nature11412.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	182180; gene.
Orphanet
Disease	KEGG Disease: SRPR
	MedGen: SRPR (Human Medical Genetics with Condition)
	ClinVar: SRPR
Phenotype	MGI: SRPR (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SRPR

Mutations for SRPR

* 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 SRPR 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
DA280072	SNHG1	1	57	11	62621379	62621435	SRPR	58	588	11	126136495	126137913
BE166221	SRPR	1	94	11	126134084	126134178	SRPR	88	227	11	126134269	126134408
BE166227	SRPR	1	94	11	126134084	126134178	SRPR	88	233	11	126134269	126134412
BE764327	USH1C	1	247	11	17515806	17519781	SRPR	241	314	11	126135594	126135667

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=49)	Stat. for Synonymous SNVs (# total SNVs=14)

Stat. for Deletions (# total SNVs=13)	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
chr11:126137087-126137087	p.K170fs*33	13
chr11:126135645-126135645	p.M375I	3
chr11:126135167-126135167	p.A436V	3
chr11:126134309-126134309	p.G551*	2
chr11:126134415-126134415	p.D515E	2
chr11:126136799-126136799	p.A182D	2
chr11:126135202-126135202	p.C424C	2
chr11:126137525-126137525	p.R95H	2
chr11:126137085-126137085	p.G171R	2
chr11:126135974-126135974	p.A312V	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	7		3	1		2	1				5	2			1	2	10	1	15
# mutation	2	8		3	1		2	1				8	2			1	3	10	1	15
nonsynonymous SNV	2	8		2	1		2	1				6	2			1	2	9	1	11
synonymous SNV				1								2					1	1		4

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
chr11:126135202	p.C396C,SRPR	2
chr11:126136799	p.T235A,SRPR	1
chr11:126134929	p.K109N,SRPR	1
chr11:126137506	p.R218R,SRPR	1
chr11:126135645	p.A104S,SRPR	1
chr11:126136475	p.R389L,SRPR	1
chr11:126136800	p.P209S,SRPR	1
chr11:126134958	p.R103C,SRPR	1
chr11:126137525	p.L595V,SRPR	1
chr11:126135714	p.R387H,SRPR	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 SRPR 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 SRPR

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


ALG3,BOLA3,CMC2,C20orf24,CCDC58,COPG1,DNAJB11, DRG1,ECE2,HM13,MRPL3,MRPS22,NDUFA6,OSTC, P4HB,PRDX4,RPN1,SEC61A1,SRPRB,TOMM22,UFD1L	CIAPIN1,DDOST,DPAGT1,EIF4A1,GMDS,HSPA5,ILF2, MANF,OSTC,PDIA3,PDIA6,PPIA,RAN,RPN1, RPN2,SEC61A1,SRSF9,SRPRB,SSR2,TM9SF1,TMED3

CCDC58,CHAC2,ECE2,GTPBP8,LSM2,MRPL3,MRPL54, MRPS22,NDUFB6,OSTC,POLE3,PPIL1,RPN1,SEC61B, SELT,SERP1,SRPRB,SSR3,STOML2,TIMM8B,TRIAP1	C1QBP,CCT2,CDC123,CHAC2,DCAF13,GLRX3,GNL3, HSPE1,METTL1,MRPL3,MRTO4,PAK1IP1,PGAM5,PNO1, POLR1C,PRDX4,PREB,RAN,SNRNP40,SRPRB,TOMM5

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 SRPR

There's no related Drug.

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Cross referenced IDs for SRPR

* 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