TissGeneSummary for KDM5B |
Gene summary |
Basic gene information | Gene symbol | KDM5B |
Gene name | lysine (K)-specific demethylase 5B | |
Synonyms | CT31|JARID1B|PLU-1|PLU1|PPP1R98|PUT1|RBBP2H1A | |
Cytomap | UCSC genome browser: 1q32.1 | |
Type of gene | protein-coding | |
RefGenes | NM_006618.3, | |
Description | RBP2-H1cancer/testis antigen 31histone demethylase JARID1Bjumonji, AT rich interactive domain 1Bjumonji/ARID domain-containing protein 1Blysine-specific demethylase 5Bprotein phosphatase 1, regulatory subunit 98putative DNA/chromatin binding motif | |
Modification date | 20141207 | |
dbXrefs | MIM : 605393 | |
HGNC : HGNC | ||
Ensembl : ENSG00000117139 | ||
HPRD : 09251 | ||
Vega : OTTHUMG00000041401 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_KDM5B | |
BioGPS: 10765 | ||
Pathway | NCI Pathway Interaction Database: KDM5B | |
KEGG: KDM5B | ||
REACTOME: KDM5B | ||
Pathway Commons: KDM5B | ||
Context | iHOP: KDM5B | |
ligand binding site mutation search in PubMed: KDM5B | ||
UCL Cancer Institute: KDM5B | ||
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 KDM5B | ||
Description by TissGene annotations | Cancer gene TissgsLTS Fused withTSGene |
* 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 | GO:0034720 | histone H3-K4 demethylation | 20228790 | GO:0034721 | histone H3-K4 demethylation, trimethyl-H3-K4-specific | 20228790 | GO:0045892 | negative regulation of transcription, DNA-templated | 12657635 | GO:0034720 | histone H3-K4 demethylation | 20228790 | GO:0034721 | histone H3-K4 demethylation, trimethyl-H3-K4-specific | 20228790 | GO:0045892 | negative regulation of transcription, DNA-templated | 12657635 |
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TissGeneExp for KDM5B |
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 |
LUSC | 1.082734447 | -0.210306729 | 1.293041176 | 9.06E-19 | 9.11E-18 |
BRCA | 1.513379752 | 0.483625366 | 1.029754386 | 1.19E-33 | 1.97E-32 |
LUAD | 0.836171161 | -0.237418494 | 1.073589655 | 6.54E-20 | 1.28E-18 |
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TissGene-miRNA for KDM5B |
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 |
ACC | hsa-miR-6835-3p | MIMAT0027571 | 0.019 | -0.27 | 78 |
ACC | hsa-miR-6835-3p | MIMAT0027571 | 0.019 | -0.27 | 78 |
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TissGeneMut for KDM5B |
TissGeneSNV for KDM5B |
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.L461F | PAAD | 2 |
p.R1461C | UCEC | 2 |
p.R323L | STAD | 1 |
p.A1205E | UVM | 1 |
p.R411W | LUSC | 1 |
p.L837* | SARC | 1 |
p.R1534H | PRAD | 1 |
p.Y1325X | KIRP | 1 |
p.S1126G | STAD | 1 |
p.S470F | SKCM | 1 |
p.R1423G | LUAD | 1 |
p.V533A | HNSC | 1 |
p.E1101K | LUSC | 1 |
p.R177Q | HNSC | 1 |
p.R258C | KIRC | 1 |
p.P296L | SKCM | 1 |
p.L979I | SKCM | 1 |
p.W459C | HNSC | 1 |
p.D687N | LGG | 1 |
p.Q1303* | LUSC | 1 |
p.S812F | SKCM | 1 |
p.D690Y | GBM | 1 |
p.Q816H | SKCM | 1 |
p.M482I | BLCA | 1 |
p.S1331* | BLCA | 1 |
p.E1381D | UCEC | 1 |
p.R918C | STAD | 1 |
p.D661N | BLCA | 1 |
p.Q925P | STAD | 1 |
p.W1262C | LUAD | 1 |
p.P539L | SKCM | 1 |
p.K297N | HNSC | 1 |
p.L1086V | COAD | 1 |
p.L1356F | UCEC | 1 |
p.R1253Q | LUAD | 1 |
p.S1324L | BLCA | 1 |
p.R1412T | UCEC | 1 |
p.T1465A | PAAD | 1 |
p.P28L | SKCM | 1 |
p.R570Q | SKCM | 1 |
p.Q132* | CESC | 1 |
p.R670H | UCEC | 1 |
p.T1061I | SKCM | 1 |
p.G1309D | UCEC | 1 |
p.F1199Y | SARC | 1 |
p.H1200N | STAD | 1 |
p.L1356I | ESCA | 1 |
p.N756S | SKCM | 1 |
p.Q1357* | PAAD | 1 |
p.I243M | LUAD | 1 |
p.T884M | STAD | 1 |
p.S664F | LUSC | 1 |
p.R125G | BLCA | 1 |
p.Q961R | UCEC | 1 |
p.A367S | UCEC | 1 |
p.D442H | HNSC | 1 |
p.R940H | STAD | 1 |
p.R1461C | SKCM | 1 |
p.M780I | LUSC | 1 |
p.P1247R | LUAD | 1 |
p.F627L | LUAD | 1 |
p.R380H | UCEC | 1 |
p.V566L | LUAD | 1 |
p.R1281X | READ | 1 |
p.R1534C | BLCA | 1 |
p.L552V | BRCA | 1 |
p.R86H | BRCA | 1 |
p.P1001S | SKCM | 1 |
p.Q1191* | HNSC | 1 |
p.R177Q | READ | 1 |
p.P1308S | SKCM | 1 |
p.T668N | LGG | 1 |
p.S1470* | HNSC | 1 |
p.V1174A | SARC | 1 |
p.R1245C | SKCM | 1 |
p.Q1028* | STAD | 1 |
p.A1008V | ESCA | 1 |
p.Q844X | STAD | 1 |
p.Y736C | STAD | 1 |
p.S218C | SKCM | 1 |
p.E1173Q | LUSC | 1 |
p.S828Y | THYM | 1 |
p.N255S | HNSC | 1 |
p.R1047Q | LGG | 1 |
p.L1366F | STAD | 1 |
p.P1316L | SKCM | 1 |
p.A1198G | LUAD | 1 |
p.L865I | UCEC | 1 |
p.E1425Q | LUAD | 1 |
p.R801C | UCS | 1 |
p.P727L | DLBC | 1 |
p.P1092L | SKCM | 1 |
p.K1121E | UCEC | 1 |
p.D376H | READ | 1 |
p.Q925R | UCEC | 1 |
p.R172S | LUAD | 1 |
p.I155N | READ | 1 |
p.P1338L | SKCM | 1 |
p.S457N | COAD | 1 |
p.R913C | SKCM | 1 |
p.Q1051H | LUSC | 1 |
p.F1077L | UCEC | 1 |
p.Q195R | BRCA | 1 |
p.A1413D | LUSC | 1 |
p.R570* | LGG | 1 |
p.P1219A | SKCM | 1 |
p.R960L | SARC | 1 |
p.L777I | OV | 1 |
p.H122R | BRCA | 1 |
p.Y208F | LUAD | 1 |
p.R1334Q | BLCA | 1 |
p.V406F | KIRC | 1 |
p.V1074A | UCEC | 1 |
p.P1034S | PAAD | 1 |
p.R868H | UCEC | 1 |
p.W971C | ESCA | 1 |
p.E246K | BLCA | 1 |
p.Y886H | LUSC | 1 |
p.G1212V | LIHC | 1 |
p.G1212C | PAAD | 1 |
p.E1230D | BLCA | 1 |
p.E577K | THYM | 1 |
p.E1458* | BLCA | 1 |
p.E139K | LGG | 1 |
p.S1470* | CESC | 1 |
p.V1490L | SKCM | 1 |
p.C298Y | UCEC | 1 |
p.L1236F | UCEC | 1 |
p.Q1267K | SKCM | 1 |
p.S1289N | UCEC | 1 |
p.R1032C | STAD | 1 |
p.S1462F | HNSC | 1 |
p.D356N | LUSC | 1 |
p.E531* | BLCA | 1 |
p.D806H | LUAD | 1 |
p.R1448T | UCEC | 1 |
p.Y506F | HNSC | 1 |
p.V813L | BLCA | 1 |
p.T737M | STAD | 1 |
p.S1082Y | UCEC | 1 |
p.H1220Y | SKCM | 1 |
p.P1219T | SKCM | 1 |
p.R1423W | COAD | 1 |
p.S505N | KIRP | 1 |
p.R1543Q | STAD | 1 |
p.R1387T | CESC | 1 |
p.K109N | KIRC | 1 |
p.Y546C | LUSC | 1 |
p.S1360L | LUSC | 1 |
p.E140K | PAAD | 1 |
p.G947E | BLCA | 1 |
p.R1461C | COAD | 1 |
p.K749N | ACC | 1 |
p.R86H | UCEC | 1 |
p.R996Q | UCEC | 1 |
p.L256V | STAD | 1 |
p.P1234S | STAD | 1 |
p.P281H | PAAD | 1 |
p.R233C | UCEC | 1 |
p.E1417* | LUAD | 1 |
p.Q844* | STAD | 1 |
p.R619H | COAD | 1 |
p.D972G | PRAD | 1 |
p.P1005L | SKCM | 1 |
p.R380H | LGG | 1 |
p.W519* | UCEC | 1 |
p.R1047* | UCEC | 1 |
p.A648T | LGG | 1 |
p.Y1361* | KIRP | 1 |
p.E250K | COAD | 1 |
p.P29S | SKCM | 1 |
p.R1253Q | STAD | 1 |
p.Q1357X | PAAD | 1 |
p.P1185L | LIHC | 1 |
p.R125K | LUAD | 1 |
p.Q1028X | STAD | 1 |
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TissGeneCNV for KDM5B |
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 KDM5B |
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 |
Chimerdb3.0 | ChiTaRs | NA | BP208834 | KDM5B-OXR1 | chr1:202777547 | chr8:107749747 | |
Chimerdb3.0 | ChiTaRs | NA | BG009982 | CANX-KDM5B | chr5:179156146 | chr1:202712054 | |
Chimerdb3.0 | ChiTaRs | NA | CV330182 | KDM5B-KDM5B | chr1:202740413 | chr1:202738858 | |
Chimerdb3.0 | ChiTaRs | NA | BF840350 | HSPB8-KDM5B | chr12:119631687 | chr1:202698111 | |
Chimerdb3.0 | FusionScan | LGG | TCGA-DU-6542-01A | KDM5B-UAP1 | CDS-5'UTR | chr1:202777229 | chr1:162535801 |
Chimerdb3.0 | FusionScan | LGG | TCGA-FG-5965-02B | KDM5B-PPP1R12B | In-Frame | chr1:202743740 | chr1:202385914 |
Chimerdb3.0 | TopHat-Fusion | BRCA | TCGA-A2-A1FW-01A | DHX9-KDM5B | 5'UTR-CDS | chr1:182809245 | chr1:202745982 |
Chimerdb3.0 | TopHat-Fusion | LGG | TCGA-CS-5395-01A | KDM5B-SYT14 | Out-of-Frame | chr1:202721725 | chr1:210267743 |
Chimerdb3.0 | TopHat-Fusion | UCEC | TCGA-EO-A3B1-01A | KDM5B-SLC25A39 | In-Frame | chr1:202765541 | chr17:42399851 |
TCGAfusionPortal | PRADA | BRCA | TCGA-A2-A1FW-01A | KDM5B-RABGAP1L | Out-of-frame | Chr1:202742246 | Chr1:174340117 |
TCGAfusionPortal | PRADA | LGG | TCGA-CS-5395-01A | LIN9-KDM5B | Out-of-frame | Chr1:226465476 | Chr1:202746222 |
TCGAfusionPortal | PRADA | LGG | TCGA-DU-6542-01A | KDM5B-UAP1 | CDS-5UTR | Chr1:202777230 | Chr1:162535802 |
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TissGeneNet for KDM5B |
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 KDM5B |
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 KDM5B |
TissGeneDrug for KDM5B |
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 KDM5B |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0006142 | Malignant neoplasm of breast | 10 | BeFree |
umls:C0678222 | Breast Carcinoma | 10 | BeFree |
umls:C0025202 | melanoma | 6 | BeFree |
umls:C0027627 | Neoplasm Metastasis | 3 | BeFree |
umls:C0596263 | Carcinogenesis | 3 | BeFree |
umls:C1458155 | Mammary Neoplasms | 3 | BeFree,LHGDN |
umls:C0027962 | Melanocytic nevus | 2 | BeFree |
umls:C0033578 | Prostatic Neoplasms | 2 | BeFree,LHGDN |
umls:C0153594 | Malignant neoplasm of testis | 2 | BeFree |
umls:C0178874 | Tumor Progression | 2 | BeFree |
umls:C0242379 | Malignant neoplasm of lung | 2 | BeFree |
umls:C0376358 | Malignant neoplasm of prostate | 2 | BeFree |
umls:C0600139 | Prostate carcinoma | 2 | BeFree |
umls:C0684249 | Carcinoma of lung | 2 | BeFree |
umls:C0004997 | Benign Ovarian Neoplasm | 1 | BeFree |
umls:C0005684 | Malignant neoplasm of urinary bladder | 1 | BeFree |
umls:C0007114 | Malignant neoplasm of skin | 1 | BeFree |
umls:C0007137 | Squamous cell carcinoma | 1 | BeFree |
umls:C0009402 | Colorectal Carcinoma | 1 | BeFree |
umls:C0017638 | Glioma | 1 | BeFree |
umls:C0018802 | Congestive heart failure | 1 | BeFree |
umls:C0020538 | Hypertensive disease | 1 | GAD |
umls:C0021051 | Immunologic Deficiency Syndromes | 1 | BeFree |
umls:C0085669 | Acute leukemia | 1 | BeFree |
umls:C0151546 | Oral Cavity Carcinoma | 1 | BeFree |
umls:C0206664 | Teratocarcinoma | 1 | BeFree |
umls:C0220641 | Lip and Oral Cavity Carcinoma | 1 | BeFree |
umls:C0280141 | Acute Undifferentiated Leukemia | 1 | BeFree |
umls:C0334634 | Malignant lymphoma, lymphocytic, intermediate differentiation, diffuse | 1 | BeFree |
umls:C0598766 | Leukemogenesis | 1 | BeFree |
umls:C0677886 | Epithelial ovarian cancer | 1 | BeFree |
umls:C0699885 | Carcinoma of bladder | 1 | BeFree |
umls:C0747845 | early pregnancy | 1 | BeFree |
umls:C1168401 | Squamous cell carcinoma of the head and neck | 1 | BeFree |
umls:C1378511 | Undifferentiated leukemia | 1 | BeFree |
umls:C1527249 | Colorectal Cancer | 1 | BeFree |
umls:C1535926 | Neurodevelopmental Disorders | 1 | BeFree |
umls:C1709246 | Non-Neoplastic Disorder | 1 | BeFree |
umls:C3539878 | Triple Negative Breast Neoplasms | 1 | BeFree |