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 SNRPD3

Basic gene info.	Gene symbol	SNRPD3
	Gene name	small nuclear ribonucleoprotein D3 polypeptide 18kDa
	Synonyms	SMD3\|Sm-D3
	Cytomap	UCSC genome browser: 22q11.23
	Genomic location	chr22 :24951617-24968509
	Type of gene	protein-coding
	RefGenes	NM_001278656.1, NM_004175.4,NR_103819.1,
	Ensembl id	ENSG00000100028
	Description	small nuclear ribonucleoprotein Sm D3snRNP core protein D3
	Modification date	20141217
dbXrefs	MIM : 601062
	HGNC : HGNC
	HPRD : 03039
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SNRPD3
	BioGPS: 6634
	Gene Expression Atlas: ENSG00000100028
	The Human Protein Atlas: ENSG00000100028
Pathway	NCI Pathway Interaction Database: SNRPD3
	KEGG: SNRPD3
	REACTOME: SNRPD3
	ConsensusPathDB
	Pathway Commons: SNRPD3
Metabolism	MetaCyc: SNRPD3
	HUMANCyc: SNRPD3
Regulation	Ensembl's Regulation: ENSG00000100028
	miRBase: chr22 :24,951,617-24,968,509
	TargetScan: NM_001278656
	cisRED: ENSG00000100028
Context	iHOP: SNRPD3
	cancer metabolism search in PubMed: SNRPD3
	UCL Cancer Institute: SNRPD3
Assigned class in ccmGDB	C

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Phenotypic Information for SNRPD3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SNRPD3
	Familial Cancer Database: SNRPD3

* 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_NON_CODING_RNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: SNRPD3
	MedGen: SNRPD3 (Human Medical Genetics with Condition)
	ClinVar: SNRPD3
Phenotype	MGI: SNRPD3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SNRPD3

Mutations for SNRPD3

* 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 SNRPD3 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
CB053297	SNRPD3	10	283	22	24970020	24970293	SNRPD3	276	440	22	24969661	24969825
AW603119	SYT7	7	74	11	61285041	61285108	SNRPD3	71	245	22	24967917	24968091

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=11)	Stat. for Synonymous SNVs (# total SNVs=3)

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
chr22:24964111-24964111	p.G96S	3
chr22:24964128-24964128	p.A101A	2
chr22:24953654-24953654	p.G4G	2
chr22:24953658-24953658	p.P6S	2
chr22:24964112-24964112	p.G96D	2
chr22:24953652-24953652	p.G4R	1
chr22:24967898-24967898	p.R112G	1
chr22:24953655-24953655	p.V5M	1
chr22:24967908-24967908	p.G115V	1
chr22:24967917-24967917	p.R118H	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			1					2	1	1				3		4
# mutation				2			1					2	1	1				3		4
nonsynonymous SNV				2								2	1					2		3
synonymous SNV							1							1				1		1

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
chr22:24953654	p.G4G,SNRPD3	2
chr22:24964111	p.G96C,SNRPD3	2
chr22:24953652	p.G4R,SNRPD3	1
chr22:24967908	p.P6S,SNRPD3	1
chr22:24967917	p.I7I,SNRPD3	1
chr22:24953658	p.Y28Y,SNRPD3	1
chr22:24953663	p.V61A,SNRPD3	1
chr22:24953726	p.G94V,SNRPD3	1
chr22:24964007	p.G96V,SNRPD3	1
chr22:24964106	p.A101V,SNRPD3	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 SNRPD3 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 SNRPD3

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


ANKRD54,CHEK2,DDT,DRG1,MCAT,MIF,MRPL40, NDUFA6,NHP2L1,PES1,PHF5A,POLR2F,RANBP1,RBX1, SMARCB1,SNRPD3,TOMM22,UBE2L3,UFD1L,UQCR10,YDJC	ARFIP2,C21orf59,DCAF11,EBNA1BP2,EIF2B5,FXYD3,GCAT, LCMT1,MRFAP1L1,MRPL49,PRKCZ,PRPF19,RFC2,SNRPD3, SNRPF,SNRPN,SPINT2,STARD10,STK16,NELFCD,WRNIP1

CDC45,CENPM,CHEK2,DRG1,EWSR1,MCAT,MRPL40, MTFP1,NHP2L1,PES1,POLR2F,RANBP1,SMARCB1,SNRPD3, TRMT2A,TRMU,TXN2,UBE2L3,UFD1L,UQCR10,XRCC6	COPZ1,EXOSC3,EXOSC8,H2AFZ,KIAA0101,MAGOH,NUDT5, NUF2,NUP37,NABP2,PCNA,PFDN6,POP5,PPIH, RAD51AP1,RANBP1,RPL26L1,SNRPA1,SNRPD3,TXNL4A,UBE2T

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 SNRPD3

There's no related Drug.

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Cross referenced IDs for SNRPD3

* 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