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| TissGeneSummary for HMGB4 |
 Gene summary |
| Basic gene information | Gene symbol | HMGB4 |
| Gene name | high mobility group box 4 | |
| Synonyms | dJ1007G16.5 | |
| Cytomap | UCSC genome browser: 1p35.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_145205.5, NR_033264.1, | |
| Description | HMG2 likehigh mobility group protein B4 | |
| Modification date | 20141207 | |
| dbXrefs | HGNC : HGNC | |
| Ensembl : ENSG00000176256 | ||
| HPRD : 14038 | ||
| Vega : OTTHUMG00000013143 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_HMGB4 | |
| BioGPS: 127540 | ||
| Pathway | NCI Pathway Interaction Database: HMGB4 | |
| KEGG: HMGB4 | ||
| REACTOME: HMGB4 | ||
| Pathway Commons: HMGB4 | ||
| Context | iHOP: HMGB4 | |
| ligand binding site mutation search in PubMed: HMGB4 | ||
| UCL Cancer Institute: HMGB4 | ||
| 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) | Testis | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | TGCT | |
| Reference showing the relevant tissue of HMGB4 | ||
| Description by TissGene annotations | TissgsKTS | |
| * 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 HMGB4 |
| 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 |
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| TissGene-miRNA for HMGB4 |
| 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 HMGB4 |
| TissGeneSNV for HMGB4 |
| 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.D89N | SKCM | 2 |
| p.E56K | SKCM | 2 |
| p.S119L | SKCM | 2 |
| p.G180R | SKCM | 1 |
| p.R179K | SKCM | 1 |
| p.E138K | SKCM | 1 |
| p.H55Q | SKCM | 1 |
| p.Q30L | LUAD | 1 |
| p.L7V | SKCM | 1 |
| p.R85Q | SKCM | 1 |
| p.W118S | LUSC | 1 |
| p.P97S | LUAD | 1 |
| p.S186N | UCEC | 1 |
| p.W118L | LUAD | 1 |
| p.K81N | LUSC | 1 |
| p.I5N | ACC | 1 |
| p.K87E | LIHC | 1 |
| p.A62V | KIRP | 1 |
| p.K48* | UCEC | 1 |
| p.A62D | LIHC | 1 |
| p.R161C | GBM | 1 |
| p.D67N | PAAD | 1 |
| p.P90S | SKCM | 1 |
| p.V17I | STAD | 1 |
| p.R167M | ESCA | 1 |
| p.S99F | SKCM | 1 |
| p.W118L | COAD | 1 |
| p.R145G | ESCA | 1 |
| p.S53* | BLCA | 1 |
| p.R150G | COAD | 1 |
| p.D67E | STAD | 1 |
| p.E73D | ESCA | 1 |
| p.R70Q | LIHC | 1 |
| p.R24G | LUSC | 1 |
| p.R88G | SKCM | 1 |
| p.P141L | SKCM | 1 |
| p.I52V | UCEC | 1 |
| p.E138A | SKCM | 1 |
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| TissGeneCNV for HMGB4 |
| 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 HMGB4 |
| 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 HMGB4 |
| 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 HMGB4 |
| 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 HMGB4 |
| TissGeneDrug for HMGB4 |
| 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 HMGB4 |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0007131 | Non-Small Cell Lung Carcinoma | 1 | BeFree |
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