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| TissGeneSummary for APOF |
 Gene summary |
| Basic gene information | Gene symbol | APOF |
| Gene name | apolipoprotein F | |
| Synonyms | Apo-F|LTIP | |
| Cytomap | UCSC genome browser: 12q13.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001638.2, | |
| Description | lipid transfer inhibitor protein | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 107760 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000175336 | ||
| HPRD : 00137 | ||
| Vega : OTTHUMG00000170715 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_APOF | |
| BioGPS: 319 | ||
| Pathway | NCI Pathway Interaction Database: APOF | |
| KEGG: APOF | ||
| REACTOME: APOF | ||
| Pathway Commons: APOF | ||
| Context | iHOP: APOF | |
| ligand binding site mutation search in PubMed: APOF | ||
| UCL Cancer Institute: APOF | ||
| 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) | Liver | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | LIHC | |
| Reference showing the relevant tissue of APOF | ||
| 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 APOF |
| 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 | 5.326591555 | 10.07206356 | -4.745472 | 3.19E-15 | 9.84E-14 |
| PRAD | 3.800429555 | 0.704314171 | 3.096115385 | 4.45E-15 | 5.87E-13 |
| KICH | -3.244932445 | -2.101160445 | -1.143772 | 2.63E-07 | 1.10E-06 |
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| TissGene-miRNA for APOF |
| 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 APOF |
| TissGeneSNV for APOF |
| 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.Q42E | ACC | 1 |
| p.P50S | SKCM | 1 |
| p.Y306C | STAD | 1 |
| p.R215* | SARC | 1 |
| p.P50L | SKCM | 1 |
| p.A266T | GBM | 1 |
| p.P50L | LUSC | 1 |
| p.A80P | GBM | 1 |
| p.A280T | THYM | 1 |
| p.I219M | UCEC | 1 |
| p.S55F | SKCM | 1 |
| p.A230S | THYM | 1 |
| p.E172Q | CESC | 1 |
| p.L245F | PAAD | 1 |
| p.T273I | LIHC | 1 |
| p.D265H | BRCA | 1 |
| p.D216N | SKCM | 1 |
| p.D316A | UCEC | 1 |
| p.S59F | SKCM | 1 |
| p.P271L | SKCM | 1 |
| p.L245F | SKCM | 1 |
| p.G252W | SKCM | 1 |
| p.M232I | GBM | 1 |
| p.K209N | BLCA | 1 |
| p.L207M | UCEC | 1 |
| p.L166F | SKCM | 1 |
| p.R128* | UCEC | 1 |
| p.A119V | SARC | 1 |
| p.Q157K | BRCA | 1 |
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| TissGeneCNV for APOF |
| 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 APOF |
| 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 |
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| TissGeneNet for APOF |
| 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) |
| APOF, APOA1, APOA2 (tumor) | APOF, APOA1, APOA2 (normal) |
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| COAD (tumor) | COAD (normal) |
| APOF, APOA1, APOA2 (tumor) | APOF, APOA1, APOA2 (normal) |
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| HNSC (tumor) | HNSC (normal) |
| APOF, APOA1, APOA2 (tumor) | APOF, APOA1, APOA2 (normal) |
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| KICH (tumor) | KICH (normal) |
| APOF, APOA1, APOA2 (tumor) | APOF, APOA1, APOA2 (normal) |
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| KIRC (tumor) | KIRC (normal) |
| APOF, APOA1, APOA2 (tumor) | APOF, APOA1, APOA2 (normal) |
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| KIRP (tumor) | KIRP (normal) |
| APOF, APOA1, APOA2 (tumor) | APOF, APOA1, APOA2 (normal) |
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| LIHC (tumor) | LIHC (normal) |
| APOF, APOA1, APOA2 (tumor) | APOF, APOA1, APOA2 (normal) |
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| LUAD (tumor) | LUAD (normal) |
| APOF, APOA1, APOA2 (tumor) | APOF, APOA1, APOA2 (normal) |
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| LUSC (tumor) | LUSC (normal) |
| APOF, APOA1, APOA2 (tumor) | APOF, APOA1, APOA2 (normal) |
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| PRAD (tumor) | PRAD (normal) |
| APOF, APOA1, APOA2 (tumor) | APOF, APOA1, APOA2 (normal) |
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| STAD (tumor) | STAD (normal) |
| APOF, APOA1, APOA2 (tumor) | APOF, APOA1, APOA2 (normal) |
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| THCA (tumor) | THCA (normal) |
| APOF, APOA1, APOA2 (tumor) | APOF, APOA1, APOA2 (normal) |
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| TissGeneProg for APOF |
| 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 APOF |
| TissGeneDrug for APOF |
| 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 APOF |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0002395 | Alzheimer's Disease | 1 | GAD |
| umls:C0010068 | Coronary heart disease | 1 | GAD |
| umls:C0019196 | Hepatitis C | 1 | GAD |
| umls:C0020443 | Hypercholesterolemia | 1 | BeFree |
| umls:C0020473 | Hyperlipidemia | 1 | BeFree |
| umls:C0021368 | Inflammation | 1 | GAD |
| umls:C0021655 | Insulin Resistance | 1 | GAD |
| umls:C0023903 | Liver neoplasms | 1 | BeFree |
| umls:C1956346 | Coronary Artery Disease | 1 | GAD |
| umls:C2239176 | Liver carcinoma | 1 | BeFree |
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