Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	LSM1
	Gene name	LSM1, U6 small nuclear RNA associated
	Synonyms	CASM\|YJL124C
	Cytomap	UCSC genome browser: 8p11.2
	Genomic location	chr8 :38020838-38034248
	Type of gene	protein-coding
	RefGenes	NM_014462.2, NR_045492.1,NR_045493.1,
	Ensembl id	ENSG00000175324
	Description	LSM1 homolog, U6 small nuclear RNA associatedU6 snRNA-associated Sm-like protein LSm1cancer-associated Sm-like proteinsmall nuclear ribonuclear CaSm
	Modification date	20141207
dbXrefs	MIM : 607281
	HGNC : HGNC
	Ensembl : ENSG00000175324
	HPRD : 06281
	Vega : OTTHUMG00000164051
Protein	UniProt: O15116 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_LSM1
	BioGPS: 27257
	Gene Expression Atlas: ENSG00000175324
	The Human Protein Atlas: ENSG00000175324
Pathway	NCI Pathway Interaction Database: LSM1
	KEGG: LSM1
	REACTOME: LSM1
	ConsensusPathDB
	Pathway Commons: LSM1
Metabolism	MetaCyc: LSM1
	HUMANCyc: LSM1
Regulation	Ensembl's Regulation: ENSG00000175324
	miRBase: chr8 :38,020,838-38,034,248
	TargetScan: NM_014462
	cisRED: ENSG00000175324
Context	iHOP: LSM1
	cancer metabolism search in PubMed: LSM1
	UCL Cancer Institute: LSM1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for LSM1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	607281; gene.
Orphanet
Disease	KEGG Disease: LSM1
	MedGen: LSM1 (Human Medical Genetics with Condition)
	ClinVar: LSM1
Phenotype	MGI: LSM1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LSM1 related fusion information.

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

AA501557

LPP

188138333

188434852

LSM1

253

38020935

38021103

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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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
chr8:38027359-38027359	p.F64fs*11	1
chr8:38027366-38027366	p.G62V	1
chr8:38027375-38027375	p.I59S	1
chr8:38027383-38027383	p.Y56Y	1
chr8:38021196-38021196	p.E132Q	1
chr8:38027393-38027393	p.G53D	1
chr8:38021226-38021226	p.L122I	1
chr8:38027405-38027405	p.R49H	1
chr8:38021254-38021254	p.L112L	1
chr8:38027409-38027409	p.E48*	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		5			1		2			1	2				1	2		1
# mutation	1	1		4			1		2			1	2				1	2		1
nonsynonymous SNV				3			1		1			1	2				1	1		1
synonymous SNV	1	1		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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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
chr8:38021226	p.L122I	2
chr8:38027366	p.D58H	1
chr8:38027375	p.Y56Y	1
chr8:38027379	p.G53D	1
chr8:38027383	p.R49H	1
chr8:38021196	p.I29T	1
chr8:38027393	p.L28P	1
chr8:38027405	p.I11I	1
chr8:38021254	p.E132Q	1
chr8:38029512	p.L112L	1

Other 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

Copy 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

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))

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CNV 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

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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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