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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for LSM2 |
Basic gene info. | Gene symbol | LSM2 |
Gene name | LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) | |
Synonyms | C6orf28|G7B|YBL026W|snRNP | |
Cytomap | UCSC genome browser: 6p21.3 | |
Genomic location | chr6_mcf_hap5 :3144865-3154459 | |
Type of gene | protein-coding | |
RefGenes | NM_021177.4, | |
Ensembl id | ENSG00000204392 | |
Description | U6 snRNA-associated Sm-like protein LSm2protein G7bsmall nuclear ribonuclear protein D homologsnRNP core Sm-like protein Sm-x5 | |
Modification date | 20141207 | |
dbXrefs | MIM : 607282 | |
HGNC : HGNC | ||
Ensembl : ENSG00000204392 | ||
HPRD : 06282 | ||
Vega : OTTHUMG00000031121 | ||
Protein | UniProt: Q9Y333 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LSM2 | |
BioGPS: 57819 | ||
Gene Expression Atlas: ENSG00000204392 | ||
The Human Protein Atlas: ENSG00000204392 | ||
Pathway | NCI Pathway Interaction Database: LSM2 | |
KEGG: LSM2 | ||
REACTOME: LSM2 | ||
ConsensusPathDB | ||
Pathway Commons: LSM2 | ||
Metabolism | MetaCyc: LSM2 | |
HUMANCyc: LSM2 | ||
Regulation | Ensembl's Regulation: ENSG00000204392 | |
miRBase: chr6_mcf_hap5 :3,144,865-3,154,459 | ||
TargetScan: NM_021177 | ||
cisRED: ENSG00000204392 | ||
Context | iHOP: LSM2 | |
cancer metabolism search in PubMed: LSM2 | ||
UCL Cancer Institute: LSM2 | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
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Phenotypic Information for LSM2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: LSM2 |
Familial Cancer Database: LSM2 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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 | 607282; gene. |
Orphanet | |
Disease | KEGG Disease: LSM2 |
MedGen: LSM2 (Human Medical Genetics with Condition) | |
ClinVar: LSM2 | |
Phenotype | MGI: 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. |
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 LSM2 related fusion information. |
ID | 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 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=8) | (# total SNVs=3) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr6:31765563-31765563 | p.R87G | 3 |
chr6:31765567-31765567 | p.A85A | 2 |
chr6:31765565-31765565 | p.A86V | 2 |
chr6:31765628-31765628 | p.S65L | 1 |
chr6:31765635-31765635 | p.R63W | 1 |
chr6:31765646-31765646 | p.N59S | 1 |
chr6:31766264-31766264 | p.S31F | 1 |
chr6:31773857-31773857 | p.D22D | 1 |
chr6:31773919-31773919 | p.L2V | 1 |
chr6:31773924-31773924 | p.? | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   |   | 1 |   |   |   |   | 1 |   |   |   |   | 1 |   |   |   |
# mutation | 1 |   |   | 1 |   |   | 1 |   |   |   |   | 1 |   |   |   |   | 1 |   |   |   |
nonsynonymous SNV | 1 |   |   | 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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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 |
chr6:31765774 | p.S31F | 1 |
chr6:31766264 | p.L2V | 1 |
chr6:31773919 | p.Y69Y | 1 |
chr6:31765615 | p.S56L | 1 |
chr6:31765655 | p.P52H | 1 |
Other DBs for Point Mutations |
Copy 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 |
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. |
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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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for LSM2 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Organism-specific databases | PharmGKB | PA25929; -. |
Organism-specific databases | CTD | 57819; -. |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00564 | LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) | approved; investigational | Carbamazepine |
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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 |
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