Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 LSM2
Basic gene info.Gene symbolLSM2
Gene nameLSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae)
SynonymsC6orf28|G7B|YBL026W|snRNP
CytomapUCSC genome browser: 6p21.3
Genomic locationchr6_mcf_hap5 :3144865-3154459
Type of geneprotein-coding
RefGenesNM_021177.4,
Ensembl idENSG00000204392
DescriptionU6 snRNA-associated Sm-like protein LSm2protein G7bsmall nuclear ribonuclear protein D homologsnRNP core Sm-like protein Sm-x5
Modification date20141207
dbXrefs MIM : 607282
HGNC : HGNC
Ensembl : ENSG00000204392
HPRD : 06282
Vega : OTTHUMG00000031121
ProteinUniProt: Q9Y333
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LSM2
BioGPS: 57819
Gene Expression Atlas: ENSG00000204392
The Human Protein Atlas: ENSG00000204392
PathwayNCI Pathway Interaction Database: LSM2
KEGG: LSM2
REACTOME: LSM2
ConsensusPathDB
Pathway Commons: LSM2
MetabolismMetaCyc: LSM2
HUMANCyc: LSM2
RegulationEnsembl's Regulation: ENSG00000204392
miRBase: chr6_mcf_hap5 :3,144,865-3,154,459
TargetScan: NM_021177
cisRED: ENSG00000204392
ContextiHOP: LSM2
cancer metabolism search in PubMed: LSM2
UCL Cancer Institute: LSM2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for LSM2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LSM2
Familial Cancer Database: LSM2
* 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_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 607282; gene.
Orphanet
DiseaseKEGG Disease: LSM2
MedGen: LSM2 (Human Medical Genetics with Condition)
ClinVar: LSM2
PhenotypeMGI: LSM2 (International Mouse Phenotyping Consortium)
PhenomicDB: LSM2

Mutations for LSM2
* 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 LSM2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=8)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr6:31765563-31765563p.R87G3
chr6:31765565-31765565p.A86V2
chr6:31765567-31765567p.A85A2
chr6:31765628-31765628p.S65L1
chr6:31765635-31765635p.R63W1
chr6:31765646-31765646p.N59S1
chr6:31766264-31766264p.S31F1
chr6:31773857-31773857p.D22D1
chr6:31773919-31773919p.L2V1
chr6:31773924-31773924p.?1

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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
# sample1  1  1    1    1   
# mutation1  1  1    1    1   
nonsynonymous SNV1  1  1         1   
synonymous SNV           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
chr6:31766264p.Y69Y1
chr6:31773919p.S56L1
chr6:31765615p.P52H1
chr6:31765655p.S31F1
chr6:31765774p.L2V1

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 LSM2 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 LSM2

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

ABCF1,ABT1,CCDC167,CSNK2B,FKBPL,GTF2H4,HMGA1,
LSM2,NDUFAF4,NPM3,NUDT3,NELFE,RPP21,SNRPC,
SNRPD1,SNRPG,TAF11,TUBB,UQCRH,WDR46,ZNRD1
C17orf49,CSNK2B,CUTA,DGUOK,DPM2,DYRK4,LSM2,
PDCD6,PFDN5,POLR2G,PPIA,PPIH,RPL27A,RPS24,
SF3B14,SNRPD2,SNRPF,SSR2,SUPT4H1,UBE2I,UXT

CKS2,COX7A2,GADD45GIP1,LSM2,LSM3,MRPL11,MRPL14,
MRPL22,MRPL54,MYEOV2,NDUFA11,NDUFA13,PPIL1,RPL35,
RPS10,RPS18,SF3B5,SRSF3,SNRPC,SNRPG,TIMM8B
ADSL,ELP6,TMEM261,GEMIN6,LSM2,MRPL11,MRPL49,
MRPL52,MRPS14,MRPS15,MRPS7,NHP2,NUDCD2,POLE3,
POLR2G,RPL35,RPSAP58,SNRPC,SNRPD2,STOML2,TOMM6
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 LSM2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA25929; -.
Organism-specific databasesCTD 57819; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00564LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae)approved; investigationalCarbamazepine


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Cross referenced IDs for LSM2
* 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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