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| TissGeneSummary for COL25A1 |
 Gene summary |
| Basic gene information | Gene symbol | COL25A1 |
| Gene name | collagen, type XXV, alpha 1 | |
| Synonyms | AMY|CLAC|CLAC-P|CLACP | |
| Cytomap | UCSC genome browser: 4q25 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001256074.1, NM_032518.2,NM_198721.3,NR_045756.2, | |
| Description | alzheimer disease amyloid-associated proteincollagen alpha-1(XXV) chaincollagen-like Alzheimer amyloid plaque componentcollagenous Alzheimer amyloid plaque component | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 610004 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000188517 | ||
| HPRD : 09886 | ||
| Vega : OTTHUMG00000150039 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_COL25A1 | |
| BioGPS: 84570 | ||
| Pathway | NCI Pathway Interaction Database: COL25A1 | |
| KEGG: COL25A1 | ||
| REACTOME: COL25A1 | ||
| Pathway Commons: COL25A1 | ||
| Context | iHOP: COL25A1 | |
| ligand binding site mutation search in PubMed: COL25A1 | ||
| UCL Cancer Institute: COL25A1 | ||
| 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 COL25A1 | ||
| 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 COL25A1 |
| 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 |
| LIHC | -2.059614831 | 0.943113169 | -3.002728 | 1.43E-17 | 7.39E-16 |
| KIRP | -1.611428331 | 1.075199794 | -2.686628125 | 2.68E-14 | 6.46E-13 |
| KICH | -0.647450831 | 1.921277169 | -2.568728 | 1.20E-06 | 4.48E-06 |
| BRCA | -0.853820656 | 2.146489871 | -3.000310526 | 5.44E-51 | 4.23E-49 |
| THCA | 0.280963406 | 2.366370186 | -2.08540678 | 1.32E-12 | 1.13E-11 |
| BLCA | -2.245217147 | -0.660990831 | -1.584226316 | 0.00278 | 0.016755339 |
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| TissGene-miRNA for COL25A1 |
| 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 |
| ACC | hsa-miR-143-3p | MIMAT0000435 | 0.024 | -0.26 | 78 |
| ACC | hsa-miR-143-3p | MIMAT0000435 | 0.024 | -0.26 | 78 |
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| TissGeneMut for COL25A1 |
| TissGeneSNV for COL25A1 |
| 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.R402C | SKCM | 3 |
| p.E366K | SKCM | 2 |
| p.R29G | LUAD | 1 |
| p.D555E | SKCM | 1 |
| p.P352S | UCEC | 1 |
| p.Q457R | LUAD | 1 |
| p.N434T | ESCA | 1 |
| p.D430E | OV | 1 |
| p.R393K | CESC | 1 |
| p.L635V | LUAD | 1 |
| p.G622R | BLCA | 1 |
| p.D644N | HNSC | 1 |
| p.P454H | ESCA | 1 |
| p.E377K | SKCM | 1 |
| p.E614K | BLCA | 1 |
| p.R317H | ACC | 1 |
| p.P469Q | THYM | 1 |
| p.P238L | LUAD | 1 |
| p.E366K | THYM | 1 |
| p.G249R | SKCM | 1 |
| p.G559R | KIRC | 1 |
| p.P624L | LUAD | 1 |
| p.R321H | ACC | 1 |
| p.P525L | SKCM | 1 |
| p.G323V | LUAD | 1 |
| p.P337L | LUAD | 1 |
| p.E91X | STAD | 1 |
| p.G276A | UVM | 1 |
| p.G11R | HNSC | 1 |
| p.G559* | LUAD | 1 |
| p.E477K | SKCM | 1 |
| p.G371R | LUAD | 1 |
| p.L239V | CESC | 1 |
| p.Q158L | LUAD | 1 |
| p.P224T | LUAD | 1 |
| p.Q411* | BLCA | 1 |
| p.S116* | LUSC | 1 |
| p.G210W | LUAD | 1 |
| p.G306* | LUAD | 1 |
| p.A28G | LUAD | 1 |
| p.P316R | LUAD | 1 |
| p.P602T | LUAD | 1 |
| p.P200S | SKCM | 1 |
| p.D215Y | UCEC | 1 |
| p.P305L | BLCA | 1 |
| p.G625E | HNSC | 1 |
| p.T448M | STAD | 1 |
| p.A575V | LGG | 1 |
| p.E623K | SKCM | 1 |
| p.Q259X | COAD | 1 |
| p.I630V | STAD | 1 |
| p.P549L | SKCM | 1 |
| p.R364Q | PAAD | 1 |
| p.P472Q | LUAD | 1 |
| p.P337T | LUAD | 1 |
| p.P148S | BLCA | 1 |
| p.G382R | PRAD | 1 |
| p.L50M | STAD | 1 |
| p.P378L | LUAD | 1 |
| p.H172N | ESCA | 1 |
| p.R364W | OV | 1 |
| p.P32L | SKCM | 1 |
| p.R112T | KICH | 1 |
| p.R184H | UCEC | 1 |
| p.P649R | LUAD | 1 |
| p.D289N | LUAD | 1 |
| p.G264V | LUAD | 1 |
| p.G162A | LUAD | 1 |
| p.Q621K | HNSC | 1 |
| p.S390A | HNSC | 1 |
| p.E91D | UCEC | 1 |
| p.G141* | LUAD | 1 |
| p.N432K | LUAD | 1 |
| p.G376R | LUSC | 1 |
| p.L97V | BRCA | 1 |
| p.G424E | SKCM | 1 |
| p.A7T | COAD | 1 |
| p.R375Q | LUAD | 1 |
| p.A45V | COAD | 1 |
| p.G568E | SARC | 1 |
| p.G604C | LUAD | 1 |
| p.A65T | UCEC | 1 |
| p.G535D | LGG | 1 |
| p.E226* | LUAD | 1 |
| p.G306V | ESCA | 1 |
| p.R16T | BLCA | 1 |
| p.P469A | HNSC | 1 |
| p.G470V | PAAD | 1 |
| p.R128Q | COAD | 1 |
| p.K612R | STAD | 1 |
| p.G461E | PAAD | 1 |
| p.P337L | LGG | 1 |
| p.G394V | LUAD | 1 |
| p.G433C | COAD | 1 |
| p.E301K | SKCM | 1 |
| p.G376V | UCEC | 1 |
| p.H76Y | HNSC | 1 |
| p.P316L | SKCM | 1 |
| p.K615R | STAD | 1 |
| p.P520R | UCEC | 1 |
| p.H625Y | COAD | 1 |
| p.R603Q | SKCM | 1 |
| p.I110L | BRCA | 1 |
| p.R29Q | SKCM | 1 |
| p.L97P | BLCA | 1 |
| p.M220I | ACC | 1 |
| p.K384E | PAAD | 1 |
| p.G494V | LUAD | 1 |
| p.G201V | LUAD | 1 |
| p.H26Y | STAD | 1 |
| p.G162E | CESC | 1 |
| p.E91* | STAD | 1 |
| p.G306V | UCEC | 1 |
| p.P22S | SKCM | 1 |
| p.P450L | SKCM | 1 |
| p.R29W | STAD | 1 |
| p.T21I | LGG | 1 |
| p.G473R | LUSC | 1 |
| p.Q142H | LUAD | 1 |
| p.K573Q | LUAD | 1 |
| p.L435V | GBM | 1 |
| p.G479A | THYM | 1 |
| p.Q158R | LIHC | 1 |
| p.G249E | SKCM | 1 |
| p.G195R | KIRP | 1 |
| p.D215Y | COAD | 1 |
| p.G529C | LUSC | 1 |
| p.G500R | SKCM | 1 |
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| TissGeneCNV for COL25A1 |
| 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 COL25A1 |
| 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-A0CL-01A | COL25A1-CCDC109B | NA | Chr4:109762851 | Chr4:110569640 |
| TCGAfusionPortal | PRADA | BRCA | TCGA-D8-A1X5-01A | PPP3CA-COL25A1 | Out-of-frame | Chr4:102267896 | Chr4:109895715 |
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| TissGeneNet for COL25A1 |
| 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) |
| COL25A1, APP, SNCA, CTSA, IAPP (tumor) | COL25A1, APP, SNCA, CTSA, IAPP (normal) |
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| COAD (tumor) | COAD (normal) |
| COL25A1, APP, SNCA, CTSA, IAPP (tumor) | COL25A1, APP, SNCA, CTSA, IAPP (normal) |
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| HNSC (tumor) | HNSC (normal) |
| COL25A1, APP, SNCA, CTSA, IAPP (tumor) | COL25A1, APP, SNCA, CTSA, IAPP (normal) |
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| KICH (tumor) | KICH (normal) |
| COL25A1, APP, SNCA, CTSA, IAPP (tumor) | COL25A1, APP, SNCA, CTSA, IAPP (normal) |
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| KIRC (tumor) | KIRC (normal) |
| COL25A1, APP, SNCA, CTSA, IAPP (tumor) | COL25A1, APP, SNCA, CTSA, IAPP (normal) |
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| KIRP (tumor) | KIRP (normal) |
| COL25A1, APP, SNCA, CTSA, IAPP (tumor) | COL25A1, APP, SNCA, CTSA, IAPP (normal) |
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| LIHC (tumor) | LIHC (normal) |
| COL25A1, APP, SNCA, CTSA, IAPP (tumor) | COL25A1, APP, SNCA, CTSA, IAPP (normal) |
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| LUAD (tumor) | LUAD (normal) |
| COL25A1, APP, SNCA, CTSA, IAPP (tumor) | COL25A1, APP, SNCA, CTSA, IAPP (normal) |
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| LUSC (tumor) | LUSC (normal) |
| COL25A1, APP, SNCA, CTSA, IAPP (tumor) | COL25A1, APP, SNCA, CTSA, IAPP (normal) |
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| PRAD (tumor) | PRAD (normal) |
| COL25A1, APP, SNCA, CTSA, IAPP (tumor) | COL25A1, APP, SNCA, CTSA, IAPP (normal) |
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| STAD (tumor) | STAD (normal) |
| COL25A1, APP, SNCA, CTSA, IAPP (tumor) | COL25A1, APP, SNCA, CTSA, IAPP (normal) |
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| THCA (tumor) | THCA (normal) |
| COL25A1, APP, SNCA, CTSA, IAPP (tumor) | COL25A1, APP, SNCA, CTSA, IAPP (normal) |
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| TissGeneProg for COL25A1 |
| 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 COL25A1 |
| TissGeneDrug for COL25A1 |
| 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 COL25A1 |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0002395 | Alzheimer's Disease | 5 | BeFree,GAD,LHGDN |
| umls:C0333463 | Senile Plaques | 5 | BeFree |
| umls:C2936349 | Plaque, Amyloid | 3 | BeFree |
| umls:C0001973 | Alcoholic Intoxication, Chronic | 1 | GAD |
| umls:C0003431 | Antisocial Personality Disorder | 1 | BeFree |
| umls:C0003469 | Anxiety Disorders | 1 | BeFree |
| umls:C0013080 | Down Syndrome | 1 | BeFree |
| umls:C0023903 | Liver neoplasms | 1 | BeFree |
| umls:C0038580 | Substance Dependence | 1 | BeFree |
| umls:C0040336 | Tobacco Use Disorder | 1 | GAD |
| umls:C2239176 | Liver carcinoma | 1 | BeFree |
| umls:C4015552 | FIBROSIS OF EXTRAOCULAR MUSCLES, CONGENITAL, 5 | 1 | UNIPROT |
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