TissGeneSummary for SAA4 |
Gene summary |
Basic gene information | Gene symbol | SAA4 |
Gene name | ||
Synonyms | ||
Cytomap | UCSC genome browser: | |
Type of gene | ||
RefGenes | ||
Description | ||
Modification date | ||
dbXrefs | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SAA4 | |
BioGPS: 100528017 | ||
Pathway | NCI Pathway Interaction Database: SAA4 | |
KEGG: SAA4 | ||
REACTOME: SAA4 | ||
Pathway Commons: SAA4 | ||
Context | iHOP: SAA4 | |
ligand binding site mutation search in PubMed: SAA4 | ||
UCL Cancer Institute: SAA4 | ||
Assigned class in TissGDB* | B | |
Included tissue-specific gene expression resources | HPA,TiGER,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 SAA4 | ||
Description by TissGene annotations | Significant down-regulated DEG TissgsKTS CNV lost TissGeneKTS |
* 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 SAA4 |
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 | -1.549138422 | 1.724171227 | -3.273309649 | 4.41E-36 | 8.72E-35 |
LIHC | 7.332296947 | 10.51611295 | -3.183816 | 3.31E-10 | 3.97E-09 |
STAD | -1.100784803 | -2.600894178 | 1.500109375 | 0.00809 | 0.029064553 |
ESCA | 0.587658947 | -3.357150144 | 3.944809091 | 3.99E-05 | 0.001706492 |
LUAD | -1.194325536 | -2.44047726 | 1.246151724 | 0.000271 | 0.000639172 |
KIRC | -2.155714665 | -3.247431331 | 1.091716667 | 0.000264 | 0.000532995 |
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TissGene-miRNA for SAA4 |
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 SAA4 |
TissGeneSNV for SAA4 |
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.A72T | STAD | 1 |
p.G68E | COAD | 1 |
p.I7F | BLCA | 1 |
p.R120H | UCEC | 1 |
p.G15X | READ | 1 |
p.K74E | LIHC | 1 |
p.D88Y | UCEC | 1 |
p.R78H | LGG | 1 |
p.S104F | BLCA | 1 |
p.N49H | READ | 1 |
p.R78H | BLCA | 1 |
p.M43I | HNSC | 1 |
p.G69C | LUAD | 1 |
p.Q84* | SKCM | 1 |
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TissGeneCNV for SAA4 |
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 SAA4 |
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 SAA4 |
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 SAA4 |
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 SAA4 |
TissGeneDrug for SAA4 |
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 SAA4 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0010068 | Coronary heart disease | 1 | GAD |
umls:C0017638 | Glioma | 1 | BeFree |
umls:C0021368 | Inflammation | 1 | GAD |
umls:C0021655 | Insulin Resistance | 1 | GAD |
umls:C0029463 | Osteosarcoma | 1 | BeFree |
umls:C0221014 | Reactive systemic amyloidosis | 1 | BeFree |
umls:C0585442 | Osteosarcoma of bone | 1 | BeFree |
umls:C3536715 | AA amyloidosis | 1 | BeFree |