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 LSM1
Basic gene info.Gene symbolLSM1
Gene nameLSM1, U6 small nuclear RNA associated
SynonymsCASM|YJL124C
CytomapUCSC genome browser: 8p11.2
Genomic locationchr8 :38020838-38034248
Type of geneprotein-coding
RefGenesNM_014462.2,
NR_045492.1,NR_045493.1,
Ensembl idENSG00000175324
DescriptionLSM1 homolog, U6 small nuclear RNA associatedU6 snRNA-associated Sm-like protein LSm1cancer-associated Sm-like proteinsmall nuclear ribonuclear CaSm
Modification date20141207
dbXrefs MIM : 607281
HGNC : HGNC
Ensembl : ENSG00000175324
HPRD : 06281
Vega : OTTHUMG00000164051
ProteinUniProt: O15116
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LSM1
BioGPS: 27257
Gene Expression Atlas: ENSG00000175324
The Human Protein Atlas: ENSG00000175324
PathwayNCI Pathway Interaction Database: LSM1
KEGG: LSM1
REACTOME: LSM1
ConsensusPathDB
Pathway Commons: LSM1
MetabolismMetaCyc: LSM1
HUMANCyc: LSM1
RegulationEnsembl's Regulation: ENSG00000175324
miRBase: chr8 :38,020,838-38,034,248
TargetScan: NM_014462
cisRED: ENSG00000175324
ContextiHOP: LSM1
cancer metabolism search in PubMed: LSM1
UCL Cancer Institute: LSM1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for LSM1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LSM1
Familial Cancer Database: LSM1
* 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 607281; gene.
Orphanet
DiseaseKEGG Disease: LSM1
MedGen: LSM1 (Human Medical Genetics with Condition)
ClinVar: LSM1
PhenotypeMGI: LSM1 (International Mouse Phenotyping Consortium)
PhenomicDB: LSM1

Mutations for LSM1
* 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 LSM1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA501557LPP12843188138333188434852LSM18525383802093538021103

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample4 1     4        
GAIN (# sample)4 1     4        
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=10)
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
chr8:38027405-38027405p.R49H1
chr8:38021254-38021254p.L112L1
chr8:38027409-38027409p.E48*1
chr8:38021327-38021327p.Q88R1
chr8:38029500-38029500p.R33K1
chr8:38027330-38027330p.L74P1
chr8:38029512-38029512p.I29T1
chr8:38027332-38027332p.L73L1
chr8:38029515-38029515p.L28P1
chr8:38027335-38027335p.V72V1

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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
# sample11 5  1 2  12   12 1
# mutation11 4  1 2  12   12 1
nonsynonymous SNV   3  1 1  12   11 1
synonymous SNV11 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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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
chr8:38021226p.L122I2
chr8:38027405p.E132Q1
chr8:38021254p.L112L1
chr8:38029512p.Q88R1
chr8:38021327p.L87I1
chr8:38029515p.L73L1
chr8:38021331p.V72V1
chr8:38033806p.G62V1
chr8:38027332p.I59S1
chr8:38027335p.D58H1

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 LSM1 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 LSM1

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

ADAM9,ASH2L,BAG4,BRF2,C12orf60,SMIM19,C8orf86,
DDHD2,EIF4EBP1,ERLIN2,FGFR1,GOLGA7,LETM2,LOC728024,
LSM1,PPAPDC1B,PROSC,RAB11FIP1,TM2D2,WHSC1L1,ZNF703
ATP5E,ATP6V1E1,EMC7,COPRS,DNAJC8,EIF2S2,ENY2,
GTF3A,LSM1,NEDD8,POP4,PPP1R7,PSMA4,PSMA6,
PSMB1,PTPMT1,STX8,TRAPPC3,TTC1,UBE2F,ZBTB8OS

ACN9,AIMP1,ASH2L,BAG4,BRF2,EMC7,EIF4EBP1,
ERLIN2,GEMIN6,LAMTOR5,HSPE1,LSM1,MRPL13,MYEOV2,
NOP10,OSTC,PPAPDC1B,PROSC,SEP15,TM2D2,EMC4
EMC7,COA6,CALM2,CKLF,DPM1,DYNLT1,LAMTOR5,
HSBP1,LSM1,MYEOV2,NDUFB6,NDUFV2,PHF5A,PSMB1,
PSMD13,PTS,RBX1,SELK,TRAPPC3,VPS29,ZNF410
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 LSM1


There's no related Drug.
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Cross referenced IDs for LSM1
* 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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