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 SNRPD1
Basic gene info.Gene symbolSNRPD1
Gene namesmall nuclear ribonucleoprotein D1 polypeptide 16kDa
SynonymsHsT2456|SMD1|SNRPD|Sm-D1
CytomapUCSC genome browser: 18q11.2
Genomic locationchr18 :19192259-19210208
Type of geneprotein-coding
RefGenesNM_001291916.1,
NM_006938.3,
Ensembl idENSG00000167088
DescriptionSm-D autoantigensmall nuclear ribonucleoprotein D1 polypeptide 16kDa pseudogenesmall nuclear ribonucleoprotein Sm D1snRNP core protein D1
Modification date20141207
dbXrefs MIM : 601063
HGNC : HGNC
Ensembl : ENSG00000167088
HPRD : 03040
Vega : OTTHUMG00000178934
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SNRPD1
BioGPS: 6632
Gene Expression Atlas: ENSG00000167088
The Human Protein Atlas: ENSG00000167088
PathwayNCI Pathway Interaction Database: SNRPD1
KEGG: SNRPD1
REACTOME: SNRPD1
ConsensusPathDB
Pathway Commons: SNRPD1
MetabolismMetaCyc: SNRPD1
HUMANCyc: SNRPD1
RegulationEnsembl's Regulation: ENSG00000167088
miRBase: chr18 :19,192,259-19,210,208
TargetScan: NM_001291916
cisRED: ENSG00000167088
ContextiHOP: SNRPD1
cancer metabolism search in PubMed: SNRPD1
UCL Cancer Institute: SNRPD1
Assigned class in ccmGDBC

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Phenotypic Information for SNRPD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_NON_CODING_RNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SNRPD1
MedGen: SNRPD1 (Human Medical Genetics with Condition)
ClinVar: SNRPD1
PhenotypeMGI: SNRPD1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasSNRPD1chr181920680319206823PAPSS1chr4108592424108592444
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SNRPD1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU935289SNRPD14404181919230719209056RPS13403576111709594417096746
BF808939SNRPD112234181920841519208637JMJD1C223394106513950765139678
BI855676NKX3-1246782353621023536680SNRPD1465586181920907419209196

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
There's no copy number variation information in COSMIC data for this gene.

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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=3

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check002.gifSomatic 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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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
chr18:19203788-19203788p.T57T2
chr18:19192399-19192399p.L3L1
chr18:19209058-19209058p.G107R1
chr18:19202685-19202685p.?1
chr18:19209061-19209061p.R108C1
chr18:19203728-19203728p.N37N1
chr18:19209067-19209067p.R110C1
chr18:19203785-19203785p.E56D1
chr18:19203787-19203787p.T57R1
chr18:19203799-19203799p.R61Q1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample  12        1    5 1
# mutation  13        1    4 1
nonsynonymous SNV   2        1    2 1
synonymous SNV  11             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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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
chr18:19209067p.R69S,SNRPD12
chr18:19192399p.L3L,SNRPD11
chr18:19203728p.N37N1
chr18:19203785p.E56D1
chr18:19203787p.T57R1
chr18:19203788p.T57T1
chr18:19203799p.R61Q1
chr18:19203843p.L35V,SNRPD11
chr18:19203854p.L38L,SNRPD11
chr18:19209061p.R67C,SNRPD11

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 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

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

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
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 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



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