|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SMARCD3 |
Basic gene info. | Gene symbol | SMARCD3 |
Gene name | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 | |
Synonyms | BAF60C|CRACD3|Rsc6p | |
Cytomap | UCSC genome browser: 7q35-q36 | |
Genomic location | chr7 :150936058-150945749 | |
Type of gene | protein-coding | |
RefGenes | NM_001003801.1, NM_001003802.1,NM_003078.3, | |
Ensembl id | ENSG00000082014 | |
Description | 60 kDa BRG-1/Brm-associated factor subunit CBRG1-associated factor 60CSWI/SNF complex 60 kDa subunit CSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3Swp73-like proteinchromatin remodeling complex BAF60C s | |
Modification date | 20141207 | |
dbXrefs | MIM : 601737 | |
HGNC : HGNC | ||
Ensembl : ENSG00000082014 | ||
HPRD : 03440 | ||
Vega : OTTHUMG00000157431 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SMARCD3 | |
BioGPS: 6604 | ||
Gene Expression Atlas: ENSG00000082014 | ||
The Human Protein Atlas: ENSG00000082014 | ||
Pathway | NCI Pathway Interaction Database: SMARCD3 | |
KEGG: SMARCD3 | ||
REACTOME: SMARCD3 | ||
ConsensusPathDB | ||
Pathway Commons: SMARCD3 | ||
Metabolism | MetaCyc: SMARCD3 | |
HUMANCyc: SMARCD3 | ||
Regulation | Ensembl's Regulation: ENSG00000082014 | |
miRBase: chr7 :150,936,058-150,945,749 | ||
TargetScan: NM_001003801 | ||
cisRED: ENSG00000082014 | ||
Context | iHOP: SMARCD3 | |
cancer metabolism search in PubMed: SMARCD3 | ||
UCL Cancer Institute: SMARCD3 | ||
Assigned class in ccmGDB | C |
Top |
Phenotypic Information for SMARCD3(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SMARCD3 |
Familial Cancer Database: SMARCD3 |
* This gene is included in those cancer gene databases. |
. | ||||||||||||||||||||
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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Mutations for SMARCD3 |
* 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 | Top |
- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | SMARCD3 | chr7 | 150942539 | 150942559 | SMARCD3 | chr7 | 150943207 | 150943227 |
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 SMARCD3 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 |
BP276382 | SMARCD3 | 1 | 257 | 7 | 150942569 | 150946275 | NPIPB7 | 251 | 580 | 16 | 28592375 | 28596473 | |
CA427258 | EPAS1 | 18 | 284 | 2 | 46613570 | 46613836 | SMARCD3 | 284 | 742 | 7 | 150936172 | 150937539 | |
AL532622 | SMARCD3 | 28 | 589 | 7 | 150939048 | 150974198 | LRP11 | 580 | 646 | 6 | 150184590 | 150184656 |
Other DBs for Structural Variants |
Top |
Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=41) | (# total SNVs=13) |
(# total SNVs=3) | (# total SNVs=0) |
Top |
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 |
chr7:150939642-150939642 | p.A155A | 4 |
chr7:150938634-150938634 | p.R282G | 3 |
chr7:150937320-150937320 | p.D338N | 2 |
chr7:150939905-150939905 | p.Q107K | 2 |
chr7:150939626-150939626 | p.D161H | 2 |
chr7:150939032-150939032 | p.D223D | 2 |
chr7:150938678-150938678 | p.R267H | 2 |
chr7:150936822-150936822 | p.T382M | 1 |
chr7:150939290-150939290 | p.S190Y | 1 |
chr7:150939826-150939826 | p.A133V | 1 |
Top |
SNV Counts per Each Loci in TCGA data |
|
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 | 11 | 1 |   | 4 |   | 1 |   |   | 3 | 1 | 2 |   |   | 3 | 3 |   | 9 |
# mutation | 1 | 2 | 1 | 9 | 1 |   | 4 |   | 1 |   |   | 3 | 1 | 2 |   |   | 3 | 3 |   | 10 |
nonsynonymous SNV | 1 | 2 | 1 | 6 | 1 |   | 2 |   | 1 |   |   | 3 |   | 2 |   |   | 2 | 2 |   | 7 |
synonymous SNV |   |   |   | 3 |   |   | 2 |   |   |   |   |   | 1 |   |   |   | 1 | 1 |   | 3 |
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]) |
Top |
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 |
chr7:150939642 | p.A168A,SMARCD3 | 3 |
chr7:150938634 | p.R295G,SMARCD3 | 3 |
chr7:150945617 | p.R11H | 2 |
chr7:150937310 | p.S398P,SMARCD3 | 1 |
chr7:150939031 | p.D245E,SMARCD3 | 1 |
chr7:150936544 | p.G237S,SMARCD3 | 1 |
chr7:150939810 | p.T395T,SMARCD3 | 1 |
chr7:150937513 | p.K206N,SMARCD3 | 1 |
chr7:150939280 | p.T395M,SMARCD3 | 1 |
chr7:150936546 | p.S202F,SMARCD3 | 1 |
Other DBs for Point Mutations |
Copy Number for SMARCD3 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] |
Top |
Gene Expression for SMARCD3 |
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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
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 |
A1BG,ABHD14A,AES,AGAP3,BRSK1,F12,FBXO44, ARHGEF25,GSTK1,KCTD17,LRRC29,LRRC61,MST1,MYL6B, ORM2,ROM1,SAT2,SLC45A1,SMARCD3,TMUB1,ZNHIT1 | ATP5G1,ATP5SL,ATPIF1,BANF1,C15orf52,C19orf47,FLJ37453, CPTP,MRPL14,NEURL2,NXN,PACSIN3,PCBP4,PRMT1, PTGES2,RBM38,SMARCD3,TIAF1,TMEM201,ZNF672,ZNF784 |
ANKRD35,CLIP3,CNRIP1,COPZ2,DZIP1,FAM110B,FERMT2, FEZ1,ARHGEF25,GYPC,HSPB2,JAM3,JAZF1,KCNJ8, LOC399959,MEIS1,NLGN2,PLEKHO1,SMARCD3,TGFB1I1,ZNF667 | COPZ2,CRTAP,DNAJC18,FEZ1,GUCY1B3,HSPB2,LOC644538, RAB23,RAB34,IFT22,RHOQ,SELM,SGCE,SMARCD3, SPG20,ST3GAL3,TCEA2,TEAD2,TMEM55A,TNFSF12,ZNF25 |
Co-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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for SMARCD3 |
There's no related Drug. |
Top |
Cross referenced IDs for SMARCD3 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |