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| TissGeneSummary for MKS1 |
 Gene summary |
| Basic gene information | Gene symbol | MKS1 |
| Gene name | Meckel syndrome, type 1 | |
| Synonyms | BBS13|MES|MKS|POC12 | |
| Cytomap | UCSC genome browser: 17q22 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001165927.1, NM_017777.3, | |
| Description | FABB proteome-like proteinMeckel syndrome type 1 proteinPOC12 centriolar protein homolog | |
| Modification date | 20141219 | |
| dbXrefs | MIM : 609883 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000011143 | ||
| HPRD : 07900 | ||
| Vega : OTTHUMG00000133714 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_MKS1 | |
| BioGPS: 54903 | ||
| Pathway | NCI Pathway Interaction Database: MKS1 | |
| KEGG: MKS1 | ||
| REACTOME: MKS1 | ||
| Pathway Commons: MKS1 | ||
| Context | iHOP: MKS1 | |
| ligand binding site mutation search in PubMed: MKS1 | ||
| UCL Cancer Institute: MKS1 | ||
| Assigned class in TissGDB* | C | |
| Included tissue-specific gene expression resources | TiGER,GTEx | |
| Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | CervixTestis | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | CESCTGCT | |
| Reference showing the relevant tissue of MKS1 | ||
| Description by TissGene annotations | TissgsLTS Fused withOncogene | |
| * 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 MKS1 |
| 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 |
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| TissGene-miRNA for MKS1 |
| 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 MKS1 |
| TissGeneSNV for MKS1 |
| 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.R536W | ESCA | 1 |
| p.P102S | SKCM | 1 |
| p.S321L | BLCA | 1 |
| p.P212L | SKCM | 1 |
| p.R58M | UCEC | 1 |
| p.N194S | STAD | 1 |
| p.G255R | OV | 1 |
| p.R158L | MESO | 1 |
| p.S372F | LUSC | 1 |
| p.V332I | GBM | 1 |
| p.V354G | PRAD | 1 |
| p.G518W | LUAD | 1 |
| p.E304Q | HNSC | 1 |
| p.V196L | LUAD | 1 |
| p.V5I | ESCA | 1 |
| p.L39I | UCEC | 1 |
| p.T253M | CESC | 1 |
| p.G317E | SKCM | 1 |
| p.S362F | READ | 1 |
| p.A208T | STAD | 1 |
| p.M365V | BRCA | 1 |
| p.R514G | THYM | 1 |
| p.R282P | LUAD | 1 |
| p.Q60* | LUAD | 1 |
| p.Q522H | BLCA | 1 |
| p.E304Q | BLCA | 1 |
| p.S362F | SKCM | 1 |
| p.A208T | THYM | 1 |
| p.R163M | LUAD | 1 |
| p.P102L | SKCM | 1 |
| p.E69X | THYM | 1 |
| p.R510W | COAD | 1 |
| p.P270L | SKCM | 1 |
| p.R533H | KIRC | 1 |
| p.Q495* | UCEC | 1 |
| p.Q548* | OV | 1 |
| p.D71E | DLBC | 1 |
| p.I236M | PRAD | 1 |
| p.R180C | STAD | 1 |
| p.G79V | LUAD | 1 |
| p.R124Q | UCEC | 1 |
| p.H356P | BRCA | 1 |
| p.G65E | SKCM | 1 |
| p.E337K | LUAD | 1 |
| p.R281Q | COAD | 1 |
| p.R536L | LUAD | 1 |
| p.R475C | SKCM | 1 |
| p.G440D | STAD | 1 |
| p.R108H | STAD | 1 |
| p.E72K | GBM | 1 |
| p.E277K | BLCA | 1 |
| p.Q60K | CESC | 1 |
| p.R537C | COAD | 1 |
| p.K469E | STAD | 1 |
| p.S117L | UCEC | 1 |
| p.H342Y | SKCM | 1 |
| p.R164S | COAD | 1 |
| p.G438A | CESC | 1 |
| p.R312Q | STAD | 1 |
| p.E252G | LIHC | 1 |
| p.R290W | COAD | 1 |
| p.E115K | SKCM | 1 |
| p.L54S | UCEC | 1 |
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| TissGeneCNV for MKS1 |
| 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 MKS1 |
| 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 |
| TCGAfusionPortal | PRADA | BRCA | TCGA-A2-A1FW-01A | MKS1-SPAG9 | Out-of-frame | Chr17:56288020 | Chr17:49109083 |
| TCGAfusionPortal | PRADA | BRCA | TCGA-E2-A14V-01A | MKS1-KSR1 | Out-of-frame | Chr17:56293449 | Chr17:25909672 |
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| TissGeneNet for MKS1 |
| 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) |
| MKS1, SMAD2, DDX24, TMEM67 (tumor) | MKS1, SMAD2, DDX24, TMEM67 (normal) |
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| COAD (tumor) | COAD (normal) |
| MKS1, SMAD2, DDX24, TMEM67 (tumor) | MKS1, SMAD2, DDX24, TMEM67 (normal) |
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| HNSC (tumor) | HNSC (normal) |
| MKS1, SMAD2, DDX24, TMEM67 (tumor) | MKS1, SMAD2, DDX24, TMEM67 (normal) |
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| KICH (tumor) | KICH (normal) |
| MKS1, SMAD2, DDX24, TMEM67 (tumor) | MKS1, SMAD2, DDX24, TMEM67 (normal) |
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| KIRC (tumor) | KIRC (normal) |
| MKS1, SMAD2, DDX24, TMEM67 (tumor) | MKS1, SMAD2, DDX24, TMEM67 (normal) |
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| KIRP (tumor) | KIRP (normal) |
| MKS1, SMAD2, DDX24, TMEM67 (tumor) | MKS1, SMAD2, DDX24, TMEM67 (normal) |
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| LIHC (tumor) | LIHC (normal) |
| MKS1, SMAD2, DDX24, TMEM67 (tumor) | MKS1, SMAD2, DDX24, TMEM67 (normal) |
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| LUAD (tumor) | LUAD (normal) |
| MKS1, SMAD2, DDX24, TMEM67 (tumor) | MKS1, SMAD2, DDX24, TMEM67 (normal) |
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| LUSC (tumor) | LUSC (normal) |
| MKS1, SMAD2, DDX24, TMEM67 (tumor) | MKS1, SMAD2, DDX24, TMEM67 (normal) |
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| PRAD (tumor) | PRAD (normal) |
| MKS1, SMAD2, DDX24, TMEM67 (tumor) | MKS1, SMAD2, DDX24, TMEM67 (normal) |
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| STAD (tumor) | STAD (normal) |
| MKS1, SMAD2, DDX24, TMEM67 (tumor) | MKS1, SMAD2, DDX24, TMEM67 (normal) |
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| THCA (tumor) | THCA (normal) |
| MKS1, SMAD2, DDX24, TMEM67 (tumor) | MKS1, SMAD2, DDX24, TMEM67 (normal) |
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| TissGeneProg for MKS1 |
| 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 MKS1 |
| TissGeneDrug for MKS1 |
| 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 MKS1 |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C3714506 | Meckel syndrome type 1 | 11 | BeFree,CLINVAR,CTD_human,GAD,MGD |
| umls:C0152427 | Polydactyly | 4 | BeFree,GAD,LHGDN |
| umls:C0752166 | Bardet-Biedl Syndrome | 4 | BeFree,CTD_human,LHGDN,ORPHANET |
| umls:C1261473 | Sarcoma | 4 | BeFree |
| umls:C0265215 | Meckel-Gruber syndrome | 3 | BeFree,CLINVAR,ORPHANET |
| umls:C0338113 | Uterine Corpus Sarcoma | 3 | BeFree |
| umls:C0431399 | Familial aplasia of the vermis | 3 | BeFree |
| umls:C0017638 | Glioma | 2 | BeFree |
| umls:C0242379 | Malignant neoplasm of lung | 2 | BeFree |
| umls:C0684249 | Carcinoma of lung | 2 | BeFree |
| umls:C0687120 | Nephronophthisis | 2 | BeFree |
| umls:C0000768 | Congenital Abnormality | 1 | GAD |
| umls:C0006142 | Malignant neoplasm of breast | 1 | BeFree |
| umls:C0007131 | Non-Small Cell Lung Carcinoma | 1 | BeFree |
| umls:C0007137 | Squamous cell carcinoma | 1 | BeFree |
| umls:C0007789 | Cerebral Palsy | 1 | BeFree |
| umls:C0010964 | Dandy-Walker Syndrome | 1 | BeFree |
| umls:C0014065 | Congenital cerebral hernia | 1 | BeFree |
| umls:C0017636 | Glioblastoma | 1 | BeFree |
| umls:C0022679 | Cystic kidney | 1 | BeFree |
| umls:C0149782 | Squamous cell carcinoma of lung | 1 | BeFree |
| umls:C0343401 | MRSA - Methicillin resistant Staphylococcus aureus infection | 1 | BeFree |
| umls:C0678222 | Breast Carcinoma | 1 | BeFree |
| umls:C0847097 | Heartburn acidity | 1 | BeFree |
| umls:C2673873 | BARDET-BIEDL SYNDROME 13 | 1 | CLINVAR,UNIPROT |
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