Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 SNRPD2
Basic gene info.Gene symbolSNRPD2
Gene namesmall nuclear ribonucleoprotein D2 polypeptide 16.5kDa
SynonymsSMD2|SNRPD1|Sm-D2
CytomapUCSC genome browser: 19q13.2
Genomic locationchr19 :46190711-46195443
Type of geneprotein-coding
RefGenesNM_004597.5,
NM_177542.2,
Ensembl idENSG00000125743
Descriptionsmall nuclear ribonucleoprotein Sm D2snRNP core protein D2
Modification date20141207
dbXrefs MIM : 601061
HGNC : HGNC
Ensembl : ENSG00000125743
HPRD : 03038
Vega : OTTHUMG00000182130
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SNRPD2
BioGPS: 6633
Gene Expression Atlas: ENSG00000125743
The Human Protein Atlas: ENSG00000125743
PathwayNCI Pathway Interaction Database: SNRPD2
KEGG: SNRPD2
REACTOME: SNRPD2
ConsensusPathDB
Pathway Commons: SNRPD2
MetabolismMetaCyc: SNRPD2
HUMANCyc: SNRPD2
RegulationEnsembl's Regulation: ENSG00000125743
miRBase: chr19 :46,190,711-46,195,443
TargetScan: NM_004597
cisRED: ENSG00000125743
ContextiHOP: SNRPD2
cancer metabolism search in PubMed: SNRPD2
UCL Cancer Institute: SNRPD2
Assigned class in ccmGDBC

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Phenotypic Information for SNRPD2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SNRPD2
Familial Cancer Database: SNRPD2
* 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_NON_CODING_RNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SNRPD2
MedGen: SNRPD2 (Human Medical Genetics with Condition)
ClinVar: SNRPD2
PhenotypeMGI: SNRPD2 (International Mouse Phenotyping Consortium)
PhenomicDB: SNRPD2

Mutations for SNRPD2
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SNRPD2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI868400SNRPD21412194619079346195172COL24A140642518652057186520590
BE336906SNRPD247540194619072346195195VCP54067793506108235061616
AI338353TAGLN3172063111732547111732732SNRPD2190455194619095546195198
BF885323SNRPD22255194619075346190786SNRPD249259194619164446195174

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1        
GAIN (# sample)        1        
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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check002.gifSNV 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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=8)
Stat. for Synonymous SNVs
(# total SNVs=4)
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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr19:46190942-46190942p.E76K2
chr19:46191819-46191819p.L3P1
chr19:46190926-46190926p.G81D1
chr19:46191820-46191820p.L3I1
chr19:46190938-46190938p.V77A1
chr19:46190964-46190964p.E68E1
chr19:46191650-46191650p.F59F1
chr19:46190822-46190822p.A116T1
chr19:46191653-46191653p.A58A1
chr19:46190825-46190825p.I115V1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample  12  3     2    3 1
# mutation  12  3     2    3 1
nonsynonymous SNV  1   2     2    3 1
synonymous SNV   2  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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr19:46191650p.E20G,SNRPD21
chr19:46191662p.Q17H,SNRPD21
chr19:46191768p.E14A,SNRPD21
chr19:46191776p.L3I1
chr19:46191786p.A116T,SNRPD21
chr19:46190822p.R111R,SNRPD21
chr19:46191820p.V106F,SNRPD21
chr19:46190835p.G81D,SNRPD21
chr19:46190852p.K79N,SNRPD21
chr19:46190926p.E76K,SNRPD21

check002.gifOther 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

check002.gifCopy Number for SNRPD2 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 SNRPD2

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

AP2S1,COX6B1,ERCC1,EXOSC5,GEMIN7,LSM7,MYPOP,
NDUFA11,NDUFB7,POLR2I,RPL18,RPL28,RPL35,RPL36,
RPLP2,RPS11,RPS19,RUVBL2,SNRPA,SNRPD2,TOMM40
CNPY2,CUTA,EIF3G,FAU,NME2,NSMCE1,PFDN5,
RPL13,RPL13A,RPL18,RPL24,RPL27A,RPL35,RPL36,
RPL8,RPLP1,RPS11,RPS3,RPS8,SNRPD2,SNRPF

C19orf53,EXOSC5,GEMIN7,LSM7,MRPS12,MYEOV2,POLR2I,
PRMT1,PSMD8,RPL18,RPL27,RPLP0,RPS11,RPS16,
RPS19,RPS5,RPS9,SNRPD2,SNRPG,TIMM50,UBL5
ADSL,ANAPC11,TMEM261,FAU,HAX1,LSM2,POLR2G,
RPL24,RPL27A,RPL35,RPL41,RPS10,RPS11,RPS13,
RPS18,RPS3A,RPS6,RPS7,RPSAP58,SNRPC,SNRPD2
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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 SNRPD2


There's no related Drug.
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Cross referenced IDs for SNRPD2
* 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



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