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 SMARCD3
Basic gene info.Gene symbolSMARCD3
Gene nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3
SynonymsBAF60C|CRACD3|Rsc6p
CytomapUCSC genome browser: 7q35-q36
Genomic locationchr7 :150936058-150945749
Type of geneprotein-coding
RefGenesNM_001003801.1,
NM_001003802.1,NM_003078.3,
Ensembl idENSG00000082014
Description60 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 date20141207
dbXrefs MIM : 601737
HGNC : HGNC
Ensembl : ENSG00000082014
HPRD : 03440
Vega : OTTHUMG00000157431
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SMARCD3
BioGPS: 6604
Gene Expression Atlas: ENSG00000082014
The Human Protein Atlas: ENSG00000082014
PathwayNCI Pathway Interaction Database: SMARCD3
KEGG: SMARCD3
REACTOME: SMARCD3
ConsensusPathDB
Pathway Commons: SMARCD3
MetabolismMetaCyc: SMARCD3
HUMANCyc: SMARCD3
RegulationEnsembl's Regulation: ENSG00000082014
miRBase: chr7 :150,936,058-150,945,749
TargetScan: NM_001003801
cisRED: ENSG00000082014
ContextiHOP: SMARCD3
cancer metabolism search in PubMed: SMARCD3
UCL Cancer Institute: SMARCD3
Assigned class in ccmGDBC

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Phenotypic Information for SMARCD3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SMARCD3
Familial Cancer Database: SMARCD3
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SMARCD3
MedGen: SMARCD3 (Human Medical Genetics with Condition)
ClinVar: SMARCD3
PhenotypeMGI: SMARCD3 (International Mouse Phenotyping Consortium)
PhenomicDB: SMARCD3

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.

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

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovarySMARCD3chr7150942539150942559SMARCD3chr7150943207150943227
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 SMARCD3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP276382SMARCD312577150942569150946275NPIPB7251580162859237528596473
CA427258EPAS11828424661357046613836SMARCD32847427150936172150937539
AL532622SMARCD3285897150939048150974198LRP115806466150184590150184656

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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=41)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=3)
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
chr7:150939642-150939642p.A155A4
chr7:150938634-150938634p.R282G3
chr7:150938678-150938678p.R267H2
chr7:150937320-150937320p.D338N2
chr7:150939905-150939905p.Q107K2
chr7:150939626-150939626p.D161H2
chr7:150939032-150939032p.D223D2
chr7:150937254-150937254p.S360C1
chr7:150939644-150939644p.A155S1
chr7:150937577-150937577p.E311G1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample121111 4 1  312  33 9
# mutation12191 4 1  312  33 10
nonsynonymous SNV12161 2 1  3 2  22 7
synonymous SNV   3  2     1   11 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])

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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
chr7:150939642p.R295G,SMARCD33
chr7:150938634p.A168A,SMARCD33
chr7:150945617p.R11H2
chr7:150937577p.A458A,SMARCD31
chr7:150939621p.Q327H,SMARCD31
chr7:150936822p.R155W,SMARCD31
chr7:150938597p.R446W,SMARCD31
chr7:150937202p.E324G,SMARCD31
chr7:150939644p.M151I,SMARCD31
chr7:150937304p.R445H,SMARCD31

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 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]

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Gene Expression for SMARCD3

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

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
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 SMARCD3


There's no related Drug.
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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

: Open all cross reference information



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