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 LSM5
Basic gene info.Gene symbolLSM5
Gene nameLSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae)
SynonymsYER146W
CytomapUCSC genome browser: 7p14.3
Genomic locationchr7 :32524944-32534870
Type of geneprotein-coding
RefGenesNM_001130710.1,
NM_001139499.1,NM_012322.2,NR_024466.1,
Ensembl idENSG00000106355
DescriptionU6 snRNA-associated Sm-like protein LSm5
Modification date20141207
dbXrefs MIM : 607285
HGNC : HGNC
Ensembl : ENSG00000106355
HPRD : 06285
Vega : OTTHUMG00000022913
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LSM5
BioGPS: 23658
Gene Expression Atlas: ENSG00000106355
The Human Protein Atlas: ENSG00000106355
PathwayNCI Pathway Interaction Database: LSM5
KEGG: LSM5
REACTOME: LSM5
ConsensusPathDB
Pathway Commons: LSM5
MetabolismMetaCyc: LSM5
HUMANCyc: LSM5
RegulationEnsembl's Regulation: ENSG00000106355
miRBase: chr7 :32,524,944-32,534,870
TargetScan: NM_001130710
cisRED: ENSG00000106355
ContextiHOP: LSM5
cancer metabolism search in PubMed: LSM5
UCL Cancer Institute: LSM5
Assigned class in ccmGDBC

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Phenotypic Information for LSM5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LSM5
Familial Cancer Database: LSM5
* 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
Orphanet
DiseaseKEGG Disease: LSM5
MedGen: LSM5 (Human Medical Genetics with Condition)
ClinVar: LSM5
PhenotypeMGI: LSM5 (International Mouse Phenotyping Consortium)
PhenomicDB: LSM5

Mutations for LSM5
* 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 LSM5 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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=9)
Stat. for Synonymous SNVs
(# total SNVs=2)
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
chr7:32529936-32529936p.P14P2
chr7:32529949-32529949p.S10L2
chr7:32529974-32529974p.A2S2
chr7:32528879-32528879p.G42R2
chr7:32528908-32528908p.S32T1
chr7:32528913-32528913p.M30I1
chr7:32528929-32528929p.R25I1
chr7:32529929-32529929p.?1
chr7:32529942-32529942p.L12L1
chr7:32528860-32528860p.?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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 21        1       1
# mutation 21        1       1
nonsynonymous SNV 21                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
chr7:32529949p.S10L2
chr7:32529942p.M1I,LSM51
chr7:32528913p.R25I1
chr7:32528929p.L12L1

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 LSM5 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 LSM5

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

FAM213A,CCDC172,MALSU1,CBX3,CDCA7L,CYCS,GARS,
GGCT,HIBADH,KLHL7,LOC285954,LSM5,NOD1,NUPL2,
OR4D6,OR5A1,RP9,RP9P,SH2D4B,TOMM7,TRA2A
METTL23,C18orf21,CISD2,COX16,GTF2A2,H3F3A,IER3IP1,
LSM5,PIGY,C7orf73,PTGES3,TRMT10C,RSL24D1,RWDD4,
SNRPE,SPCS2,SRP9,SUMO2,TPRKB,UBE2D2,UBE2E1

AIMP2,BZW2,MPLKIP,MALSU1,COA1,CBX3,CCDC58,
CHCHD2,CYCS,GGCT,H2AFV,LSM5,MRPL32,MRPS17,
MRPS24,NDUFA4,NUPL2,PPIA,PSMA2,RPA3,SSBP1
DPM1,EEF1E1,EMG1,ENOPH1,GLMN,HSPE1,LSM5,
MRPL1,MRPL50,SNRNP40,SNRPD1,SNRPE,SNRPG,SRP9,
SSBP1,TAF9,THOC7,TOMM5,TOMM6,UBE2N,VBP1
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 LSM5


There's no related Drug.
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Cross referenced IDs for LSM5
* 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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