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 SRP14

Basic gene info.	Gene symbol	SRP14
	Gene name	signal recognition particle 14kDa (homologous Alu RNA binding protein)
	Synonyms	ALURBP
	Cytomap	UCSC genome browser: 15q22
	Genomic location	chr15 :40327890-40331389
	Type of gene	protein-coding
	RefGenes	NM_003134.4, NR_104021.1,
	Ensembl id	ENSG00000140319
	Description	18 kDa Alu RNA-binding proteinsignal recognition particle 14 kDa protein
	Modification date	20141207
dbXrefs	MIM : 600708
	HGNC : HGNC
	Ensembl : ENSG00000140319
	HPRD : 02831
	Vega : OTTHUMG00000172391
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SRP14
	BioGPS: 6727
	Gene Expression Atlas: ENSG00000140319
	The Human Protein Atlas: ENSG00000140319
Pathway	NCI Pathway Interaction Database: SRP14
	KEGG: SRP14
	REACTOME: SRP14
	ConsensusPathDB
	Pathway Commons: SRP14
Metabolism	MetaCyc: SRP14
	HUMANCyc: SRP14
Regulation	Ensembl's Regulation: ENSG00000140319
	miRBase: chr15 :40,327,890-40,331,389
	TargetScan: NM_003134
	cisRED: ENSG00000140319
Context	iHOP: SRP14
	cancer metabolism search in PubMed: SRP14
	UCL Cancer Institute: SRP14
Assigned class in ccmGDB	C

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Phenotypic Information for SRP14(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SRP14
	Familial Cancer Database: SRP14

* 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: SRP14
	MedGen: SRP14 (Human Medical Genetics with Condition)
	ClinVar: SRP14
Phenotype	MGI: SRP14 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SRP14

Mutations for SRP14

* 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 SRP14 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
BQ015130	SRP14	18	551	15	40328242	40329550	C1orf198	545	690	1	230973433	230973578
CN337981	SRP14	2	135	15	40330565	40331323	EME2	136	615	16	1824946	1825879
AA984265	SRP14	1	141	15	40331085	40331369	ABCB11	142	458	2	169869119	169869435
BE836999	NUMB	35	229	14	73753961	73759574	SRP14	218	320	15	40331128	40331374

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=7)	Stat. for Synonymous SNVs (# total SNVs=2)

Stat. for Deletions (# total SNVs=2)	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
chr15:40328597-40328597	p.A116A	3
chr15:40330490-40330490	p.S68I	2
chr15:40328572-40328572	p.T125A	2
chr15:40330494-40330496	p.K66delK	2
chr15:40328545-40328545	p.A134T	1
chr15:40330484-40330484	p.V70A	1
chr15:40328566-40328566	p.A127T	1
chr15:40328590-40328590	p.A119T	1
chr15:40328614-40328614	p.A111P	1
chr15:40328617-40328617	p.A110T	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=1

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		2
# mutation																	1	1		2
nonsynonymous SNV																	1	1		2
synonymous SNV

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
chr15:40328545	p.A134S	1
chr15:40328590	p.A119T	1
chr15:40330484	p.V70A	1
chr15:40330529	p.K55T	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 SRP14 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 SRP14

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


ATP5G2,C12orf10,EMC7,C15orf57,HYPK,TMA7,COX17, COX6A1,COX7C,DNAJC17,EID1,IMP3,MGST2,MTHFS, NDUFA2,NDUFAF1,NDUFC1,PARK7,SERF2,SRP14,EMC4	C17orf49,C19orf43,BRK1,DAD1,DYNLRB1,EXOSC1,FAM127B, GABARAP,JTB,KRTCAP2,LSM3,OST4,POLE4,PSENEN, RBX1,RNF181,SEC61B,SNRPG,SRP14,TAF10,TOMM6

EMC7,C15orf57,HYPK,COPS2,DNAJC17,FAM103A1,FAM96A, FBXO22,IMP3,MTHFS,NDUFAF1,NOP10,PSMA4,RAB11A, RPUSD2,RSL24D1,SEC11A,SERF2,SNRPG,SRP14,EMC4	ACTR10,ATP5J,BUD31,C14orf119,CALM2,CAPZA2,MOB4, MYEOV2,NDUFA4,NDUFA6,NDUFB6,NDUFB8,NDUFV2,NEDD8, RBX1,SARNP,SRP14,TRAPPC3,TTC1,UBL5,UQCR11

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 SRP14

There's no related Drug.

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Cross referenced IDs for SRP14

* 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