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 SNRPD1

Basic gene info.	Gene symbol	SNRPD1
	Gene name	small nuclear ribonucleoprotein D1 polypeptide 16kDa
	Synonyms	HsT2456\|SMD1\|SNRPD\|Sm-D1
	Cytomap	UCSC genome browser: 18q11.2
	Genomic location	chr18 :19192259-19210208
	Type of gene	protein-coding
	RefGenes	NM_001291916.1, NM_006938.3,
	Ensembl id	ENSG00000167088
	Description	Sm-D autoantigensmall nuclear ribonucleoprotein D1 polypeptide 16kDa pseudogenesmall nuclear ribonucleoprotein Sm D1snRNP core protein D1
	Modification date	20141207
dbXrefs	MIM : 601063
	HGNC : HGNC
	Ensembl : ENSG00000167088
	HPRD : 03040
	Vega : OTTHUMG00000178934
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SNRPD1
	BioGPS: 6632
	Gene Expression Atlas: ENSG00000167088
	The Human Protein Atlas: ENSG00000167088
Pathway	NCI Pathway Interaction Database: SNRPD1
	KEGG: SNRPD1
	REACTOME: SNRPD1
	ConsensusPathDB
	Pathway Commons: SNRPD1
Metabolism	MetaCyc: SNRPD1
	HUMANCyc: SNRPD1
Regulation	Ensembl's Regulation: ENSG00000167088
	miRBase: chr18 :19,192,259-19,210,208
	TargetScan: NM_001291916
	cisRED: ENSG00000167088
Context	iHOP: SNRPD1
	cancer metabolism search in PubMed: SNRPD1
	UCL Cancer Institute: SNRPD1
Assigned class in ccmGDB	C

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Phenotypic Information for SNRPD1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SNRPD1
	Familial Cancer Database: SNRPD1

* 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: SNRPD1
	MedGen: SNRPD1 (Human Medical Genetics with Condition)
	ClinVar: SNRPD1
Phenotype	MGI: SNRPD1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SNRPD1

Mutations for SNRPD1

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	SNRPD1	chr18	19206803	19206823	PAPSS1	chr4	108592424	108592444

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 SNRPD1 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
BU935289	SNRPD1	4	404	18	19192307	19209056	RPS13	403	576	11	17095944	17096746
BF808939	SNRPD1	12	234	18	19208415	19208637	JMJD1C	223	394	10	65139507	65139678
BI855676	NKX3-1	2	467	8	23536210	23536680	SNRPD1	465	586	18	19209074	19209196

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=5)	Stat. for Synonymous SNVs (# total SNVs=2)

Stat. for Deletions (# total SNVs=1)	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
chr18:19203788-19203788	p.T57T	2
chr18:19203843-19203843	p.L76V	1
chr18:19203854-19203854	p.L79L	1
chr18:19209027-19209038	p.R112_G115delRGRG	1
chr18:19192399-19192399	p.L3L	1
chr18:19209058-19209058	p.G107R	1
chr18:19202685-19202685	p.?	1
chr18:19209061-19209061	p.R108C	1
chr18:19203728-19203728	p.N37N	1
chr18:19209067-19209067	p.R110C	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			1	2									1					5		1
# mutation			1	3									1					4		1
nonsynonymous SNV				2									1					2		1
synonymous SNV			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
chr18:19209067	p.R69S,SNRPD1	2
chr18:19209061	p.L3L,SNRPD1	1
chr18:19192399	p.N37N	1
chr18:19203728	p.E56D	1
chr18:19203785	p.T57R	1
chr18:19203787	p.T57T	1
chr18:19203788	p.R61Q	1
chr18:19203799	p.L35V,SNRPD1	1
chr18:19203843	p.L38L,SNRPD1	1
chr18:19203854	p.R67C,SNRPD1	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 SNRPD1 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 SNRPD1

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


AURKB,C18orf21,CDCA3,CENPA,CKS2,H2AFZ,LSM2, MAGOH,MRPL51,NDC80,PDCD5,PTTG1,RANBP1,SKA1, SNRPA,SNRPC,SNRPD1,SNRPG,TXNL4A,UQCRH,UQCRHL	BYSL,DIABLO,DYRK4,EIF4A3,HDAC3,ILF2,LCMT1, LRRC42,METTL1,MRTO4,NPM3,OCIAD2,POLR1C,POLR2H, PTRH2,RAN,RPP38,SNRNP40,SNRPD1,SNRPF,TOMM34

AURKB,C18orf21,CENPM,COQ3,EIF4A1,EIF5A,EIF5AL1, H2AFZ,HMGA1,HNRNPC,NDC80,PSMA3,RAN,RCC1, RNF138,SRSF9,SKA1,SNRPD1,TIPIN,TUBA1B,TXNL4A	BOLA3,CENPK,EBNA1BP2,EEF1E1,EIF5AL1,H2AFZ,HSPE1, MAGOHB,MRPL3,NME1,NUP37,PPIH,PPIL1,PSMD14, RAN,RPL26L1,SNRNP40,SNRPD1,SNRPG,TOMM5,VRK1

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 SNRPD1

There's no related Drug.

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Cross referenced IDs for SNRPD1

* 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