TissGeneSummary for CLGN |
Gene summary |
Basic gene information | Gene symbol | CLGN |
Gene name | calmegin | |
Synonyms | - | |
Cytomap | UCSC genome browser: 4q28.3-q31.1 | |
Type of gene | protein-coding | |
RefGenes | NM_001130675.1, NM_004362.2, | |
Description | - | |
Modification date | 20141207 | |
dbXrefs | MIM : 601858 | |
HGNC : HGNC | ||
Ensembl : ENSG00000153132 | ||
HPRD : 03513 | ||
Vega : OTTHUMG00000133414 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_CLGN | |
BioGPS: 1047 | ||
Pathway | NCI Pathway Interaction Database: CLGN | |
KEGG: CLGN | ||
REACTOME: CLGN | ||
Pathway Commons: CLGN | ||
Context | iHOP: CLGN | |
ligand binding site mutation search in PubMed: CLGN | ||
UCL Cancer Institute: CLGN | ||
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) | Testis | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | TGCT | |
Reference showing the relevant tissue of CLGN | ||
Description by TissGene annotations |
* 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 CLGN |
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) |
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) |
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. |
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) |
- 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 |
BRCA | 2.409316602 | 0.330687654 | 2.078628947 | 2.03E-13 | 9.45E-13 |
HNSC | -2.344659938 | -0.241501799 | -2.10315814 | 8.47E-07 | 6.55E-06 |
COAD | -2.499417541 | -0.39537908 | -2.104038462 | 8.47E-06 | 3.97E-05 |
KICH | 3.401707689 | -1.404192311 | 4.8059 | 2.35E-12 | 2.59E-11 |
KIRP | 1.157504814 | -1.955373311 | 3.112878125 | 2.64E-09 | 2.27E-08 |
LUSC | 0.557343846 | -0.49829733 | 1.055641176 | 0.00218 | 0.003850478 |
STAD | -1.619220186 | 0.267967314 | -1.8871875 | 0.000493 | 0.002996641 |
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TissGene-miRNA for CLGN |
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 |
UCS | hsa-miR-92a-3p | MIMAT0000092 | 0.038 | -0.28 | 56 |
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TissGeneMut for CLGN |
TissGeneSNV for CLGN |
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. |
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) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.R389Q | SKCM | 3 |
p.F220L | UCEC | 2 |
p.F220L | COAD | 2 |
p.E398K | SKCM | 2 |
p.I17T | LUAD | 1 |
p.D269N | SKCM | 1 |
p.K218E | KIRC | 1 |
p.A312V | PAAD | 1 |
p.D223V | STAD | 1 |
p.D425A | SKCM | 1 |
p.R608Q | SKCM | 1 |
p.R373K | UCEC | 1 |
p.N18D | UCEC | 1 |
p.W372* | SKCM | 1 |
p.P394S | SKCM | 1 |
p.W372X | SKCM | 1 |
p.E318K | SKCM | 1 |
p.A327V | COAD | 1 |
p.S431L | UCEC | 1 |
p.S252G | LIHC | 1 |
p.G58R | SKCM | 1 |
p.G110R | SKCM | 1 |
p.A485E | LUAD | 1 |
p.E539G | HNSC | 1 |
p.E268Q | BLCA | 1 |
p.E37K | SKCM | 1 |
p.E304K | SKCM | 1 |
p.D305N | SKCM | 1 |
p.P470S | SKCM | 1 |
p.M84I | SKCM | 1 |
p.S579F | OV | 1 |
p.E398K | LUAD | 1 |
p.P260T | THYM | 1 |
p.H120Y | SKCM | 1 |
p.Y155C | STAD | 1 |
p.L217R | COAD | 1 |
p.Y155C | LIHC | 1 |
p.S581* | UCEC | 1 |
p.D296Y | ESCA | 1 |
p.D296N | PRAD | 1 |
p.W278* | LUSC | 1 |
p.R608* | PAAD | 1 |
p.E280K | HNSC | 1 |
p.K559R | STAD | 1 |
p.F490C | UCEC | 1 |
p.M362I | SKCM | 1 |
p.I97N | UCEC | 1 |
p.S46F | SKCM | 1 |
p.L137F | BLCA | 1 |
p.P325L | SKCM | 1 |
p.E86K | SKCM | 1 |
p.E558K | SKCM | 1 |
p.D279N | SKCM | 1 |
p.K578Q | SKCM | 1 |
p.E538K | SKCM | 1 |
p.G339E | HNSC | 1 |
p.G203R | SKCM | 1 |
p.P264S | SKCM | 1 |
p.T238I | LGG | 1 |
p.E64K | BLCA | 1 |
p.D147N | BLCA | 1 |
p.E87K | SKCM | 1 |
p.P556H | UCEC | 1 |
p.A410V | READ | 1 |
p.R352W | COAD | 1 |
p.K559N | CESC | 1 |
p.D30Y | UCS | 1 |
p.A301V | STAD | 1 |
p.P182R | OV | 1 |
p.D400N | SKCM | 1 |
p.P54H | UCEC | 1 |
p.G595E | BLCA | 1 |
p.R603C | READ | 1 |
p.P323H | UCEC | 1 |
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TissGeneCNV for CLGN |
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 CLGN |
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 | ChiTaRs | NA | BU568984 | MALAT1-CLGN | chr11:65267423 | chr4:141310240 | |
TCGAfusionPortal | PRADA | BRCA | TCGA-A2-A0SX-01A | MAML3-CLGN | Out-of-frame | Chr4:141074014 | Chr4:141327237 |
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TissGeneNet for CLGN |
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) |
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TissGeneProg for CLGN |
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. |
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. |
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. |
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 CLGN |
TissGeneDrug for CLGN |
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 CLGN |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0040336 | Tobacco Use Disorder | 1 | GAD |
umls:C0346429 | Multiple malignancy | 1 | BeFree |