TissGeneSummary for SAA2 |
Gene summary |
Basic gene information | Gene symbol | SAA2 |
Gene name | serum amyloid A2 | |
Synonyms | - | |
Cytomap | UCSC genome browser: 11p15.1-p14 | |
Type of gene | protein-coding | |
RefGenes | NM_001127380.2, NM_030754.4, | |
Description | serum amyloid A-2 protein | |
Modification date | 20141207 | |
dbXrefs | MIM : 104751 | |
HGNC : HGNC | ||
Ensembl : ENSG00000134339 | ||
HPRD : 00098 | ||
Vega : OTTHUMG00000166484 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SAA2 | |
BioGPS: 6289 | ||
Pathway | NCI Pathway Interaction Database: SAA2 | |
KEGG: SAA2 | ||
REACTOME: SAA2 | ||
Pathway Commons: SAA2 | ||
Context | iHOP: SAA2 | |
ligand binding site mutation search in PubMed: SAA2 | ||
UCL Cancer Institute: SAA2 | ||
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) | Liver | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | LIHC | |
Reference showing the relevant tissue of SAA2 | ||
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 SAA2 |
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 | 1.295354945 | 6.08710319 | -4.791748246 | 7.70E-37 | 1.61E-35 |
LIHC | 4.971120524 | 8.683810524 | -3.71269 | 2.53E-07 | 1.57E-06 |
KIRP | -0.111100976 | -1.827804101 | 1.716703125 | 0.0176 | 0.036201101 |
COAD | -0.421901938 | -1.890598092 | 1.468696154 | 0.0148 | 0.031060153 |
KIRC | -0.409070421 | -1.714724588 | 1.305654167 | 0.00695 | 0.011971522 |
LUAD | 0.961876179 | -0.454422097 | 1.416298276 | 0.00239 | 0.00491363 |
THCA | -2.507640595 | -3.635723646 | 1.128083051 | 0.000715 | 0.001724412 |
ESCA | 2.825577433 | -2.566031658 | 5.391609091 | 1.40E-07 | 0.0003058 |
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TissGene-miRNA for SAA2 |
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 SAA2 |
TissGeneSNV for SAA2 |
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.S23L | SKCM | 2 |
p.K102E | BLCA | 2 |
p.K102E | CESC | 2 |
p.L4F | SKCM | 1 |
p.R114* | STAD | 1 |
p.Q98E | BLCA | 1 |
p.D97N | STAD | 1 |
p.W103* | SKCM | 1 |
p.K64E | LIHC | 1 |
p.S40C | BLCA | 1 |
p.E120K | SKCM | 1 |
p.K102E | UVM | 1 |
p.G88C | LGG | 1 |
p.R108K | CESC | 1 |
p.W103X | SKCM | 1 |
p.K102E | PCPG | 1 |
p.S23L | LGG | 1 |
p.R114X | STAD | 1 |
p.D97N | SKCM | 1 |
p.A96V | LGG | 1 |
p.L14V | LUAD | 1 |
p.K102E | HNSC | 1 |
p.A70S | LUAD | 1 |
p.K102E | THCA | 1 |
p.R57W | CESC | 1 |
p.L25F | SKCM | 1 |
p.K102E | LUAD | 1 |
p.R114Q | PRAD | 1 |
p.A63V | SKCM | 1 |
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TissGeneCNV for SAA2 |
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 SAA2 |
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 SAA2 |
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 SAA2 |
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 SAA2 |
TissGeneDrug for SAA2 |
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 SAA2 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0002726 | Amyloidosis | 5 | BeFree,GAD |
umls:C0221014 | Reactive systemic amyloidosis | 3 | BeFree |
umls:C0003873 | Rheumatoid Arthritis | 2 | BeFree |
umls:C0031069 | Familial Mediterranean Fever | 2 | BeFree,GAD |
umls:C0268382 | Amyloid nephropathy | 2 | BeFree |
umls:C3536715 | AA amyloidosis | 2 | BeFree |
umls:C0002395 | Alzheimer's Disease | 1 | GAD |
umls:C0004936 | Mental disorders | 1 | GAD |
umls:C0007222 | Cardiovascular Diseases | 1 | GAD |
umls:C0017601 | Glaucoma | 1 | BeFree |
umls:C0036983 | Septic Shock | 1 | LHGDN |
umls:C0040336 | Tobacco Use Disorder | 1 | GAD |
umls:C0206669 | Hepatocellular Adenoma | 1 | BeFree |