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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for SAA1
check button Gene summary
Basic gene informationGene symbolSAA1
Gene nameserum amyloid A1
SynonymsPIG4|SAA|SAA2|TP53I4
CytomapUCSC genome browser: 11p15.1
Type of geneprotein-coding
RefGenesNM_000331.4,
NM_001178006.1,NM_199161.3,
Descriptionserum amyloid A proteinserum amyloid A-1 proteintumor protein p53 inducible protein 4
Modification date20141222
dbXrefs MIM : 104750
HGNC : HGNC
Ensembl : ENSG00000173432
HPRD : 00097
Vega : OTTHUMG00000166147
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SAA1
BioGPS: 6288
PathwayNCI Pathway Interaction Database: SAA1
KEGG: SAA1
REACTOME: SAA1
Pathway Commons: SAA1
ContextiHOP: SAA1
ligand binding site mutation search in PubMed: SAA1
UCL Cancer Institute: SAA1
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,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 SAA1
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.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0007204positive regulation of cytosolic calcium ion concentration9892621
GO:0045785positive regulation of cell adhesion11830469
GO:0048246macrophage chemotaxis7561109
GO:0048247lymphocyte chemotaxis7636186
GO:0050715positive regulation of cytokine secretion12857601
GO:0007204positive regulation of cytosolic calcium ion concentration9892621
GO:0045785positive regulation of cell adhesion11830469
GO:0048246macrophage chemotaxis7561109
GO:0048247lymphocyte chemotaxis7636186
GO:0050715positive regulation of cytokine secretion12857601


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TissGeneExp for SAA1

check button 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 exp


check button 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 isoform exp


check button 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.
normal gene exp


check button 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)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
LIHC5.2145423878.730812387-3.516275.49E-073.13E-06
BRCA2.0660669136.853001124-4.7869342111.05E-362.15E-35
LUAD0.884265008-0.4566315441.3408965520.001620.00342475
KICH-3.867567613-1.974675613-1.8928920.000820.001798289
ESCA2.955347296-2.1334799775.0888272736.95E-060.000913862
KIRC-0.10579778-2.0532575021.9474597220.0004530.000887389


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TissGene-miRNA for SAA1

check button 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 typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for SAA1
TissGeneSNV for SAA1

check button 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.
SNV lollipop
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check button 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)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.S23LSKCM3
p.I83MBLCA1
p.E27KBRCA1
p.D41NSKCM1
p.R19*SKCM1
p.G117DUCEC1
p.E120DUCEC1
p.E74DPAAD1
p.A100VCOAD1
p.E120QBLCA1
p.R80TCESC1
p.R19*UCEC1
p.A99TSKCM1
p.S18RSKCM1
p.R57WCESC1


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TissGeneCNV for SAA1

check button 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)
CNV


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TissGeneFusions for SAA1

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0ChiTaRsNABC070311SAA1-GYS2chr11:18291274chr12:21689127
Chimerdb3.0ChiTaRsNABG562889SAA1-APOA2chr11:18290879chr1:161192152
Chimerdb3.0ChiTaRsNABP384371SAA1-CRIP2chr11:18291465chr14:105946164
Chimerdb3.0FusionScanBRCATCGA-BH-A0BZ-11ARNF214-SAA1Out-of-Framechr11:117105095chr11:18290741


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TissGeneNet for SAA1

check button 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)
SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (tumor)SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (normal)
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COAD (tumor)COAD (normal)
SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (tumor)SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (normal)
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HNSC (tumor)HNSC (normal)
SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (tumor)SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (normal)
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KICH (tumor)KICH (normal)
SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (tumor)SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (normal)
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KIRC (tumor)KIRC (normal)
SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (tumor)SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (normal)
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KIRP (tumor)KIRP (normal)
SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (tumor)SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (normal)
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LIHC (tumor)LIHC (normal)
SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (tumor)SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (normal)
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LUAD (tumor)LUAD (normal)
SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (tumor)SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (normal)
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LUSC (tumor)LUSC (normal)
SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (tumor)SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (normal)
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PRAD (tumor)PRAD (normal)
SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (tumor)SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (normal)
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STAD (tumor)STAD (normal)
SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (tumor)SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (normal)
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THCA (tumor)THCA (normal)
SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (tumor)SAA1, HNF4A, PITX3, FPR1, ICAM1, COL4A1, APOA1, COL4A2, COL4A4, LAMA1, GLUD2 (normal)
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TissGeneProg for SAA1

check button 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.
survival 1

check button 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.
survival 2

check button 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.
survival 3

check button 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.
survival 4

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TissGeneClin for SAA1
TissGeneDrug for SAA1

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for SAA1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0002726Amyloidosis31BeFree,GAD,LHGDN
umls:C0221014Reactive systemic amyloidosis31BeFree,ORPHANET
umls:C3536715AA amyloidosis26BeFree
umls:C0003873Rheumatoid Arthritis24BeFree,GAD,LHGDN
umls:C0031069Familial Mediterranean Fever15BeFree,GAD
umls:C0003850Arteriosclerosis8BeFree
umls:C0004153Atherosclerosis8BeFree
umls:C0268382Amyloid nephropathy6BeFree
umls:C0007222Cardiovascular Diseases5BeFree,GAD,LHGDN
umls:C0028754Obesity5BeFree
umls:C0003864Arthritis3BeFree,LHGDN
umls:C0021368Inflammation2LHGDN
umls:C0178874Tumor Progression2BeFree
umls:C0243026Sepsis2BeFree
umls:C0375023Respiratory syncytial virus (RSV) infection in conditions classified elsewhere and of unspecified site2BeFree
umls:C1956346Coronary Artery Disease2BeFree
umls:C2239176Liver carcinoma2BeFree
umls:C2931822Nasopharyngeal carcinoma2BeFree
umls:C3714514Infection2LHGDN
umls:C0002395Alzheimer's Disease1GAD
umls:C0004623Bacterial Infections1BeFree
umls:C0007102Malignant tumor of colon1BeFree
umls:C0009324Ulcerative Colitis1BeFree
umls:C0009375Colonic Neoplasms1LHGDN
umls:C0010054Coronary Arteriosclerosis1BeFree
umls:C0010068Coronary heart disease1BeFree
umls:C0011616Contact Dermatitis1CTD_human
umls:C0011881Diabetic Nephropathy1BeFree
umls:C0011991Diarrhea1BeFree
umls:C0015625Fanconi Anemia1BeFree
umls:C0015695Fatty Liver1BeFree
umls:C0017601Glaucoma1BeFree
umls:C0019061Hemolytic-Uremic Syndrome1BeFree
umls:C0019196Hepatitis C1LHGDN
umls:C0020473Hyperlipidemia1BeFree
umls:C0020507Hyperplasia1LHGDN
umls:C0020538Hypertensive disease1GAD
umls:C0022661Kidney Failure, Chronic1BeFree
umls:C0027627Neoplasm Metastasis1BeFree
umls:C0027819Neuroblastoma1BeFree
umls:C0029408Degenerative polyarthritis1BeFree
umls:C0033860Psoriasis1BeFree
umls:C0035435Rheumatism1BeFree
umls:C0036983Septic Shock1LHGDN
umls:C0038013Ankylosing spondylitis1LHGDN
umls:C0079772T-Cell Lymphoma1BeFree
umls:C0151594Hemorrhagic diarrhea1BeFree
umls:C0153392Malignant neoplasm of nasopharynx1BeFree
umls:C0206669Hepatocellular Adenoma1BeFree
umls:C0238301Cancer of Nasopharynx1BeFree
umls:C0265219Miller Dieker syndrome1BeFree
umls:C0268380Systemic amyloidosis1BeFree
umls:C0268381Primary amyloidosis1BeFree
umls:C0281479Primary Systemic Amyloidosis1BeFree
umls:C0302810Uremia syndrome1BeFree
umls:C0699790Colon Carcinoma1BeFree
umls:C0700095Central neuroblastoma1BeFree
umls:C0740394Hyperuricemia1BeFree
umls:C0993582Arthritis, Experimental1CTD_human
umls:C1270972Mild cognitive disorder1BeFree
umls:C2316212Cryopyrin-Associated Periodic Syndromes1BeFree
umls:C2936349Plaque, Amyloid1BeFree
umls:C2939462Immunoglobulin deposition disease1BeFree
umls:C3495559Juvenile arthritis1BeFree
umls:C3714757Juvenile rheumatoid arthritis1BeFree