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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SNRPD3 |
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Phenotypic Information for SNRPD3(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: SNRPD3 |
Familial Cancer Database: SNRPD3 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
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REACTOME_METABOLISM_OF_NON_CODING_RNA REACTOME_METABOLISM_OF_RNA |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: SNRPD3 |
MedGen: SNRPD3 (Human Medical Genetics with Condition) | |
ClinVar: SNRPD3 | |
Phenotype | MGI: SNRPD3 (International Mouse Phenotyping Consortium) |
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. |
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There's no structural variation information in COSMIC data for this gene. |
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* 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 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=11) | (# total SNVs=3) |
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(# total SNVs=0) | (# total SNVs=0) |
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* 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 |
chr22:24953658-24953658 | p.P6S | 2 |
chr22:24964112-24964112 | p.G96D | 2 |
chr22:24964128-24964128 | p.A101A | 2 |
chr22:24953654-24953654 | p.G4G | 2 |
chr22:24967917-24967917 | p.R118H | 1 |
chr22:24953726-24953726 | p.Y28Y | 1 |
chr22:24967919-24967919 | p.G119R | 1 |
chr22:24964007-24964007 | p.V61A | 1 |
chr22:24964015-24964015 | p.R64S | 1 |
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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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* 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 |
chr22:24964111 | p.G96C,SNRPD3 | 2 |
chr22:24953654 | p.G4G,SNRPD3 | 2 |
chr22:24953663 | p.V61A,SNRPD3 | 1 |
chr22:24953726 | p.G94V,SNRPD3 | 1 |
chr22:24964007 | p.G96V,SNRPD3 | 1 |
chr22:24964106 | p.A101V,SNRPD3 | 1 |
chr22:24964112 | p.R112G,SNRPD3 | 1 |
chr22:24964127 | p.G115V,SNRPD3 | 1 |
chr22:24967898 | p.R118H,SNRPD3 | 1 |
chr22:24953652 | p.G4R,SNRPD3 | 1 |
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* 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. |
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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 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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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 |
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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 |
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* 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 |
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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 |
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