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| TissGeneSummary for SMC1B |
 Gene summary |
| Basic gene information | Gene symbol | SMC1B |
| Gene name | structural maintenance of chromosomes 1B | |
| Synonyms | SMC1BETA|SMC1L2 | |
| Cytomap | UCSC genome browser: 22q13.31 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001291501.1, NM_148674.4, | |
| Description | SMC protein 1BSMC1 (structural maintenance of chromosomes 1, yeast)-like 1SMC1 structural maintenance of chromosomes 1-like 2mitosis-specific chromosome segregation protein like protein betastructural maintenance of chromosomes protein 1B | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 608685 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000077935 | ||
| HPRD : 10564 | ||
| Vega : OTTHUMG00000151334 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_SMC1B | |
| BioGPS: 27127 | ||
| Pathway | NCI Pathway Interaction Database: SMC1B | |
| KEGG: SMC1B | ||
| REACTOME: SMC1B | ||
| Pathway Commons: SMC1B | ||
| Context | iHOP: SMC1B | |
| ligand binding site mutation search in PubMed: SMC1B | ||
| UCL Cancer Institute: SMC1B | ||
| Assigned class in TissGDB* | C | |
| Included tissue-specific gene expression resources | HPA,GTEx | |
| Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | Testis | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | TGCT | |
| Reference showing the relevant tissue of SMC1B | ||
| Description by TissGene annotations | Fused withTSGene | |
| * Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C. |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO term | PubMed ID |
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| TissGeneExp for SMC1B |
| Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
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| Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01) |
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| Gene expressions across normal tissues of GTEx data (GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct) - Here, we shows the matched tissue types only among our 28 cancer types. |
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| Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
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| - Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
| Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
| LUAD | 0.245094001 | -2.094376689 | 2.33947069 | 1.17E-09 | 6.13E-09 |
| BRCA | 0.269355888 | -0.974352884 | 1.243708772 | 1.81E-07 | 5.30E-07 |
| LIHC | -0.503823586 | -2.270987586 | 1.767164 | 9.07E-07 | 4.87E-06 |
| LUSC | 0.27035465 | -2.086884566 | 2.357239216 | 1.15E-08 | 3.61E-08 |
| STAD | -0.255474211 | -1.510871086 | 1.255396875 | 0.00261 | 0.011331834 |
| HNSC | -0.576775446 | -1.980596376 | 1.40382093 | 0.000825 | 0.002860169 |
| BLCA | 1.21960852 | -1.378270428 | 2.597878947 | 0.000233 | 0.002205072 |
| KICH | -0.770409586 | -2.199529586 | 1.42912 | 0.000458 | 0.001056997 |
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| TissGene-miRNA for SMC1B |
| Significantly anti-correlated miRNAs of TissGene across 28 cancer types (Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016) (TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21) (TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16) (Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25)) |
| Cancer type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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| TissGeneMut for SMC1B |
| TissGeneSNV for SMC1B |
| nsSNV counts per each loci. Different colors of circles represent different cancer types. Circle size denotes number of samples. (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) * Click on the image to enlarge it in a new window. |
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| Somatic nucleotide variants of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of mutated samples) The numbers in parentheses are numbers of samples with mutation (nsSNVs). (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) |
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| - nsSNVs sorted by frequency. |
| AAchange | Cancer type | # samples |
| p.E303* | UCEC | 2 |
| p.E356K | SKCM | 2 |
| p.E464* | BLCA | 1 |
| p.A193T | LUAD | 1 |
| p.R16Q | STAD | 1 |
| p.L479V | LUSC | 1 |
| p.A997V | SKCM | 1 |
| p.E587K | SKCM | 1 |
| p.R25Q | UCEC | 1 |
| p.V594A | BRCA | 1 |
| p.Q1177L | DLBC | 1 |
| p.D1152E | KIRC | 1 |
| p.K268R | ESCA | 1 |
| p.A68V | PAAD | 1 |
| p.E269K | SKCM | 1 |
| p.I789V | HNSC | 1 |
| p.L290P | CHOL | 1 |
| p.N1110D | BLCA | 1 |
| p.K1028E | LUAD | 1 |
| p.E1097D | UCEC | 1 |
| p.L1050M | COAD | 1 |
| p.K662E | HNSC | 1 |
| p.R363L | LUSC | 1 |
| p.H1141Q | KIRP | 1 |
| p.E141K | HNSC | 1 |
| p.I165M | LGG | 1 |
| p.E1153* | BLCA | 1 |
| p.G101* | LUSC | 1 |
| p.I83L | OV | 1 |
| p.L1158V | SARC | 1 |
| p.G687D | SKCM | 1 |
| p.G166R | BLCA | 1 |
| p.E1056K | UCEC | 1 |
| p.E505K | SKCM | 1 |
| p.F24L | ESCA | 1 |
| p.G67R | SKCM | 1 |
| p.L45I | BLCA | 1 |
| p.K551N | UCEC | 1 |
| p.R434Q | SKCM | 1 |
| p.K174T | COAD | 1 |
| p.R1210* | PRAD | 1 |
| p.R799W | HNSC | 1 |
| p.I1075T | SKCM | 1 |
| p.F765C | READ | 1 |
| p.P23L | SKCM | 1 |
| p.T917N | UCEC | 1 |
| p.R895Q | SKCM | 1 |
| p.L585P | UCEC | 1 |
| p.A1139V | COAD | 1 |
| p.Q1068E | SKCM | 1 |
| p.D949Y | STAD | 1 |
| p.M272R | SKCM | 1 |
| p.N132K | COAD | 1 |
| p.A565T | KIRP | 1 |
| p.F570L | SKCM | 1 |
| p.T458I | LGG | 1 |
| p.L692H | LUSC | 1 |
| p.H524Y | BLCA | 1 |
| p.N1162Y | HNSC | 1 |
| p.E330Q | LUSC | 1 |
| p.Q916L | LUAD | 1 |
| p.R807G | COAD | 1 |
| p.R558* | SKCM | 1 |
| p.L242X | COAD | 1 |
| p.I940M | COAD | 1 |
| p.R586K | HNSC | 1 |
| p.E911Q | BLCA | 1 |
| p.S1074* | BLCA | 1 |
| p.F730V | SKCM | 1 |
| p.Q1035E | GBM | 1 |
| p.R790C | SKCM | 1 |
| p.R758X | READ | 1 |
| p.L943S | SKCM | 1 |
| p.P148S | SKCM | 1 |
| p.E357D | UCEC | 1 |
| p.R496C | PRAD | 1 |
| p.R678* | STAD | 1 |
| p.C523F | KIRC | 1 |
| p.S649F | SKCM | 1 |
| p.G35S | STAD | 1 |
| p.R106C | READ | 1 |
| p.D642N | LUSC | 1 |
| p.R114H | COAD | 1 |
| p.E303K | SKCM | 1 |
| p.E764K | SKCM | 1 |
| p.S657R | KIRC | 1 |
| p.E670* | LUSC | 1 |
| p.A565G | KIRP | 1 |
| p.K589T | COAD | 1 |
| p.R496C | UCEC | 1 |
| p.D1064N | UCEC | 1 |
| p.F1055L | COAD | 1 |
| p.K171N | UCEC | 1 |
| p.K723N | CESC | 1 |
| p.F1034C | UCEC | 1 |
| p.K844T | UCEC | 1 |
| p.H524N | BRCA | 1 |
| p.N34K | LIHC | 1 |
| p.E568D | UCEC | 1 |
| p.D875E | THYM | 1 |
| p.E91D | UCEC | 1 |
| p.I842L | HNSC | 1 |
| p.T703S | STAD | 1 |
| p.R816Q | STAD | 1 |
| p.E356A | SKCM | 1 |
| p.N1110K | LUAD | 1 |
| p.E169K | SKCM | 1 |
| p.L576V | SARC | 1 |
| p.T491I | DLBC | 1 |
| p.S715L | BLCA | 1 |
| p.E668A | STAD | 1 |
| p.R558Q | SKCM | 1 |
| p.L685I | ESCA | 1 |
| p.G494E | LUSC | 1 |
| p.L641I | LGG | 1 |
| p.S250R | THYM | 1 |
| p.N304Y | SKCM | 1 |
| p.E893D | COAD | 1 |
| p.E323K | SKCM | 1 |
| p.R173T | CESC | 1 |
| p.I545T | LGG | 1 |
| p.D1011N | SKCM | 1 |
| p.A193V | CESC | 1 |
| p.R760* | STAD | 1 |
| p.Q1009K | SKCM | 1 |
| p.A1156S | LUAD | 1 |
| p.T703N | UCEC | 1 |
| p.K669T | UCEC | 1 |
| p.S286L | UCEC | 1 |
| p.E1223K | THYM | 1 |
| p.R363* | LUAD | 1 |
| p.S482I | OV | 1 |
| p.R760X | STAD | 1 |
| p.I124V | LIHC | 1 |
| p.A387T | COAD | 1 |
| p.K853N | COAD | 1 |
| p.E303D | SKCM | 1 |
| p.R558X | SKCM | 1 |
| p.R678X | STAD | 1 |
| p.V887A | LGG | 1 |
| p.Q610L | STAD | 1 |
| p.T957I | GBM | 1 |
| p.R496H | COAD | 1 |
| p.S746F | PAAD | 1 |
| p.E954K | BRCA | 1 |
| p.E179K | STAD | 1 |
| p.D775N | SKCM | 1 |
| p.E911* | UCEC | 1 |
| p.T815S | LUAD | 1 |
| p.L982I | SKCM | 1 |
| p.R678* | UCEC | 1 |
| p.T28A | UCEC | 1 |
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| TissGeneCNV for SMC1B |
| Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples) (TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16) |
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| TissGeneFusions for SMC1B |
| Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
| Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
| Chimerdb3.0 | FusionScan | CESC | TCGA-DS-A3LQ-01A | KIAA0930-SMC1B | In-Frame | chr22:45607836 | chr22:45741450 |
| Chimerdb3.0 | TopHat-Fusion | BLCA | TCGA-E7-A5KE-01A | SMC1B-FBLN1 | In-Frame | chr22:45805755 | chr22:45946494 |
| TCGAfusionPortal | PRADA | PRAD | TCGA-KK-A7AU-01A | KPNA1-SMC1B | Out-of-frame | Chr3:122215284 | Chr22:45804779 |
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| TissGeneNet for SMC1B |
| Co-expressed gene networks based on protein-protein interaction data (CePIN) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (PINA2 ppi data) |
| BRCA (tumor) | BRCA (normal) |
| SMC1B, SUMO1, SMC3 (tumor) | SMC1B, SUMO1, SMC3 (normal) |
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| COAD (tumor) | COAD (normal) |
| SMC1B, SUMO1, SMC3 (tumor) | SMC1B, SUMO1, SMC3 (normal) |
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| HNSC (tumor) | HNSC (normal) |
| SMC1B, SUMO1, SMC3 (tumor) | SMC1B, SUMO1, SMC3 (normal) |
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| KICH (tumor) | KICH (normal) |
| SMC1B, SUMO1, SMC3 (tumor) | SMC1B, SUMO1, SMC3 (normal) |
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| KIRC (tumor) | KIRC (normal) |
| SMC1B, SUMO1, SMC3 (tumor) | SMC1B, SUMO1, SMC3 (normal) |
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| KIRP (tumor) | KIRP (normal) |
| SMC1B, SUMO1, SMC3 (tumor) | SMC1B, SUMO1, SMC3 (normal) |
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| LIHC (tumor) | LIHC (normal) |
| SMC1B, SUMO1, SMC3 (tumor) | SMC1B, SUMO1, SMC3 (normal) |
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| LUAD (tumor) | LUAD (normal) |
| SMC1B, SUMO1, SMC3 (tumor) | SMC1B, SUMO1, SMC3 (normal) |
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| LUSC (tumor) | LUSC (normal) |
| SMC1B, SUMO1, SMC3 (tumor) | SMC1B, SUMO1, SMC3 (normal) |
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| PRAD (tumor) | PRAD (normal) |
| SMC1B, SUMO1, SMC3 (tumor) | SMC1B, SUMO1, SMC3 (normal) |
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| STAD (tumor) | STAD (normal) |
| SMC1B, SUMO1, SMC3 (tumor) | SMC1B, SUMO1, SMC3 (normal) |
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| THCA (tumor) | THCA (normal) |
| SMC1B, SUMO1, SMC3 (tumor) | SMC1B, SUMO1, SMC3 (normal) |
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| TissGeneProg for SMC1B |
| Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image to enlarge it in a new window. |
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| Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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| Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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| Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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| TissGeneClin for SMC1B |
| TissGeneDrug for SMC1B |
| Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
| DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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| TissGeneDisease for SMC1B |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0004509 | Azoospermia | 1 | GAD |
| umls:C0005695 | Bladder Neoplasm | 1 | CTD_human |
| umls:C0018671 | Head and Neck Neoplasms | 1 | GAD |
| umls:C0027643 | Neoplasm Recurrence, Local | 1 | GAD |
| umls:C0028960 | Oligospermia | 1 | GAD |
| umls:C0085183 | Neoplasms, Second Primary | 1 | GAD |
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