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 SRP72

Basic gene info.	Gene symbol	SRP72
	Gene name	signal recognition particle 72kDa
	Synonyms	BMFF\|BMFS1\|HEL103
	Cytomap	UCSC genome browser: 4q11
	Genomic location	chr4 :57333761-57369847
	Type of gene	protein-coding
	RefGenes	NM_001267722.1, NM_006947.3,
	Ensembl id	ENSG00000174780
	Description	epididymis luminal protein 103signal recognition particle 72 kDa proteinsignal recognition particle 72kDsignal recognition particle subunit SRP72
	Modification date	20141207
dbXrefs	MIM : 602122
	HGNC : HGNC
	HPRD : 03671
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SRP72
	BioGPS: 6731
	Gene Expression Atlas: ENSG00000174780
	The Human Protein Atlas: ENSG00000174780
Pathway	NCI Pathway Interaction Database: SRP72
	KEGG: SRP72
	REACTOME: SRP72
	ConsensusPathDB
	Pathway Commons: SRP72
Metabolism	MetaCyc: SRP72
	HUMANCyc: SRP72
Regulation	Ensembl's Regulation: ENSG00000174780
	miRBase: chr4 :57,333,761-57,369,847
	TargetScan: NM_001267722
	cisRED: ENSG00000174780
Context	iHOP: SRP72
	cancer metabolism search in PubMed: SRP72
	UCL Cancer Institute: SRP72
Assigned class in ccmGDB	C

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Phenotypic Information for SRP72(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SRP72
	Familial Cancer Database: SRP72

* 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

Others
OMIM
Orphanet
Disease	KEGG Disease: SRP72
	MedGen: SRP72 (Human Medical Genetics with Condition)
	ClinVar: SRP72
Phenotype	MGI: SRP72 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SRP72

Mutations for SRP72

* 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

There's no inter-chromosomal structural variation.

- 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	SRP72	chr4	57357760	57357780	SRP72	chr4	57357812	57357832

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 SRP72 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
U81554	CAMK2G	1	165	10	75597226	75602293	SRP72	166	910	4	57349375	57357734
CV357489	OXSR1	63	88	3	38289046	38289311	SRP72	80	184	4	57338968	57339072

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=53)	Stat. for Synonymous SNVs (# total SNVs=18)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=1)

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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
chr4:57350915-57350915	p.R324L	3
chr4:57356562-57356562	p.R462W	3
chr4:57333822-57333822	p.G7G	3
chr4:57354131-57354131	p.A392A	2
chr4:57367935-57367935	p.I642V	2
chr4:57361553-57361553	p.K557K	2
chr4:57349351-57349351	p.A291V	2
chr4:57337912-57337912	p.Y86C	2
chr4:57349352-57349352	p.A291A	2
chr4:57357604-57357604	p.K504fs*11	2

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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	2		7					3			4	4	3	1		1	5	1	12
# mutation	2	2		8					3			5	4	3	1		1	5	1	13
nonsynonymous SNV	1	1		7					2			4	2	2	1			5	1	11
synonymous SNV	1	1		1					1			1	2	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
chr4:57342839	p.A331A,SRP72	2
chr4:57354131	p.L205I,SRP72	2
chr4:57367903	p.V154L,SRP72	1
chr4:57352496	p.P274P,SRP72	1
chr4:57335866	p.P507Q,SRP72	1
chr4:57357606	p.E167D,SRP72	1
chr4:57342840	p.F303L,SRP72	1
chr4:57352556	p.R520Q,SRP72	1
chr4:57340227	p.H176Y,SRP72	1
chr4:57357634	p.I323M,SRP72	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 SRP72 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 SRP72

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


AASDH,ABCE1,NOA1,CEP135,CLOCK,DCUN1D4,EXOC1, FIP1L1,IARS,LARP1B,NAA15,NAA25,PAICS,POLR2B, PPAT,SCFD2,SLC30A6,SMARCA5,SMEK2,SRP72,USP46	ABCE1,API5,BCLAF1,DDX18,DDX52,DHX40,CFAP97, MATR3,PPAT,PRPF40A,PRRC1,PTBP3,SENP1,SMARCAD1, SRP72,SYNCRIP,TFAM,WAPAL,WDR35,ZNF146,ZNF562

ABCE1,NOA1,C4orf46,CISD2,COPS4,DCK,DHX15, DR1,GRSF1,HMGXB4,NUP54,PAICS,PAQR3,PGM2, POLR2B,PPAT,RCHY1,SRP72,TMEM165,UBE2D3,USP46	ACTL6A,BRIX1,C4orf46,CCT2,CDK4,DCUN1D5,DDX47, EEF1E1,ENOPH1,EXOSC2,MRPL3,NPM1,NUDCD1,NUP35, POLE3,POT1,PRMT1,PRMT5,PRPF4,SRP72,UBA2

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 SRP72

There's no related Drug.

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Cross referenced IDs for SRP72

* 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