KDM1B protein expression summary - The Human Protein Atlas

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KDM1B

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HUMAN PROTEIN ATLAS SUMMARYⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Proteinⁱ Full gene name according to HGNC.	Lysine demethylase 1B
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	KDM1B (AOF1, bA204B7.3, C6orf193, dJ298J15.2, FLJ33898, FLJ34109, FLJ43328, LSD2)
Tissue specificityⁱ ??The RNA specificity category is based on mRNA expression levels in the consensus dataset which is calculated from the RNA expression levels in samples from HPA and GTEX. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. Read more	Low tissue specificity
Tissue expression clusterⁱ The RNA data was used to cluster genes according to their expression across tissues. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Bone marrow - mRNA splicing & Cell cycle (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Low cell type specificity
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Monocytes & Neutrophils - Innate immune response (mainly)
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed blood cell samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Low immune cell specificity
Brain specificityⁱ The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category Read more	Low human brain regional specificity
Cancer prognostic summary	Prognostic marker in colorectal cancer (favorable)
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location. Read more	Intracellular
Subcellular summaryⁱ Describes the main and potential additional location(s) of the encoded protein according to ICC-IF resukt in the Cell Atlas, as well as potential data regarding cell cycle depency (CCD) for the RNA and/or protein expression.	Located in Nucleoplasm
Protein function (UniProt)ⁱ Useful information about the protein provided by UniProt.	Histone demethylase that demethylates 'Lys-4' of histone H3, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Required for de novo DNA methylation of a subset of imprinted genes during oogenesis. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Demethylates both mono- and di-methylated 'Lys-4' of histone H3. Has no effect on tri-methylated 'Lys-4', mono-, di-or tri-methylated 'Lys-9', mono-, di-or tri-methylated 'Lys-27', mono-, di-or tri-methylated 'Lys-36' of histone H3, or on mono-, di-or tri-methylated 'Lys-20' of histone H4.... show less
Molecular function (UniProt)ⁱ Keywords assigned by UniProt to proteins due to their particular molecular function.	Chromatin regulator, Developmental protein, Oxidoreductase, Repressor
Biological process (UniProt)ⁱ Keywords assigned by UniProt to proteins because they are involved in a particular biological process.	Transcription, Transcription regulation
Ligand (UniProt)ⁱ Keywords assigned by UniProt to proteins because they bind, are associated with, or whose activity is dependent of some molecule.	FAD, Flavoprotein, Metal-binding, Zinc
Gene summary (Entrez)ⁱ Useful information about the gene from Entrez	Flavin-dependent histone demethylases, such as KDM1B, regulate histone lysine methylation, an epigenetic mark that regulates gene expression and chromatin function (Karytinos et al., 2009).[supplied by OMIM, Oct 2009]... show less

TISSUEⁱ Summary of data presented in the Tissue section, with a representative image of protein expression (left) and an interactive chart showing the tissue-specific mRNA expression (right). The image and the chart are clickable and will redirect to more Tissue data. This section contains information regarding the expression profiles of protein-coding genes in normal human tissue, both on the mRNA and protein level. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry. Read more

Tissue expression clusterⁱ The RNA data was used to cluster genes according to their expression across tissues. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Bone marrow - mRNA splicing & Cell cycle (mainly)
Tissue specificityⁱ The RNA specificity category is based on mRNA expression levels in the consensus dataset which is calculated from the RNA expression levels in samples from HPA and GTEX. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. Read more	Low tissue specificity
Tissue distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA and GTEX. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Protein expressionⁱ A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation. "Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile. Read more	Cytoplasmic and nuclear expression in most tissues.

BRAINⁱ Summary of data presented in the Brain Atlas and a representative image of mRNA expression in the human brain. The image is clickable and will redirect to more Brain Atlas data. The Brain Atlas explores the protein expression in the mammalian brain by visualization and integration of data from three mammalian species (human, pig and mouse). Transcriptomics data combined with affinity-based protein in situ localization down to single cell level is available in a brain-centric sub atlas of the Human Protein Atlas. Read more

Human regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low region specificity
Pig regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low region specificity
Mouse regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analysed brain samples, grouped into 13 main brain regions and calculated for the three different species. All brain expression profiles are based on data from HPA. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low region specificity

SINGLE CELL TYPEⁱ Summary of data presented in the Single cell Type section, with an interactive chart showing the cell type-specific mRNA expression. The chart is clickable and will redirect to more Cell Type data. This section contains information about single cell type RNA expression based on scRNAseq of human tissues. The data also covers transcriptomics analysis of human blood and cultured cell lines. Read more

Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Monocytes & Neutrophils - Innate immune response (mainly)
Cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Low cell type specificity

TISSUE CELL TYPEⁱ

Keratinocyte (other)

Thyroid glandular cells

Classificationⁱ

Cell type enriched in 3 tissues

PATHOLOGYⁱ Summary of data presented in the Pathology section, with representative images of protein expression in cancer (left) and correlation between mRNA expression and patient survival (right). Images are clickable and redirect to pages with more Pathology data. This section contains mRNA and protein expression data from 17 different forms of human cancer, as well as correlation analysis of mRNA expression and patient survival. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry. Read more
	Colorectal cancer p<0.001
Prognostic summary	Prognostic marker in colorectal cancer (favorable)
Cancer specificityⁱ Specificity of RNA expression in 17 cancer types is categorized as either cancer enriched, group enriched, cancer enhanced, low cancer specificity and not detected. Read more	Low cancer specificity
Cancer distributionⁱ Distribution of RNA expression in 17 cancer types is categorized as either detected in single, detected in some, detected in many, detected in all, or not detected. Read more	Detected in all

IMMUNE CELLⁱ Summary of data presented in the Immune Cell section and a representative image of mRNA expression in immune cells in the blood. The image is clickable and will redirect to more immune cell related data. The Immune Cell section contains information regarding single cell type mRNA expression profiles of protein-coding genes in various immune cells in the blood, e.g. B-cells and granulocytes. Read more

Immune cell expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Eosinophils - Transcription (mainly)
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Low immune cell specificity

BLOOD PROTEINⁱ Summary of data presented in the Blood proteins section and a representative image of the concentration in plasma and related function for the protein in plasma. The image is clickable and will redirect to more data. The Blood proteins section contains plasma levels of proteins detected in human blood and an analysis of the human secretome (including annotation of the genes predicted to be actively secreted to human blood) is also presented. Read more
Detected in blood by immunoassayⁱ The blood-based immunoassay category applies to actively secreted proteins and is based on plasma or serum protein concentrations established with enzyme-linked immunosorbent assays, compiled from a literature search. The categories include: detected and not detected, where detection refers to a concentration found in the literature search. Read more	No (not applicable)
Detected in blood by mass spectrometryⁱ Detection or not of the gene in blood, based on spectral count estimations from a publicly available mass spectrometry-based plasma proteomics data set obtained from the PeptideAtlas.	No
Detected in blood by proximity extension assayⁱ Detection or not of the gene in blood, based on proximity extension assays (Olink) for a longitudinal wellness study covering 76 individuals with three visits during two years. Read more	No

SUBCELLULARⁱ Summary of data presented in the Cell Atlas and a representative image of subcellular localization. The Cell Atlas provides RNA expression data derived from RNA sequencing of a large panel of cell lines and protein localization data derived from antibody-based profiling by immunofluorescence confocal microscopy, using a subset of cell lines selected based on RNA expression. Read more

Main locationⁱ Main subcellular location(s) and reliability score(s) for the encoded protein(s) in human cells. The main location(s) may be characterized by presence in all tested cell lines and/or ihigher staining intensity compared to the potential additional location(s). If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively. Read more	Localized to the Nucleoplasm

CELL LINEⁱ Summary of data presented in the Cell Line section and a representative image of mRNA expression across different human cell lines. The image is clickable and will redirect to more cell line data. This section contains information regarding mRNA expression profiles of human protein-coding genes for a large variety of cell lines. Read more

Cell line expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	OE19 - Mitochondria (mainly)
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Low cell line specificity
Cell type distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many

METABOLIC

Metabolic info	Not available

GENE INFORMATIONⁱ Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.
Gene name	KDM1B (HGNC Symbol)
Synonyms	AOF1, bA204B7.3, C6orf193, dJ298J15.2, FLJ33898, FLJ34109, FLJ43328, LSD2
Description	Lysine demethylase 1B (HGNC Symbol)
Chromosome	6
Cytoband	p22.3
Chromosome location (bp)	18155329 - 18223854
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4
Protein evidence	Evidence at protein level (all genes)
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes
Ensembl	ENSG00000165097 (version 103.38)
Entrez gene	221656
UniProt	Q8NB78 (UniProt - Evidence at protein level)
neXtProt	NX_Q8NB78
Antibodypedia	KDM1B antibodies

PROTEIN BROWSERⁱ

KDM1B-201

KDM1B-202

KDM1B-203

KDM1B-205

PROTEIN INFORMATIONⁱ The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database. The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein. The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class. The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Splice variant	UniProt	Protein class	Gene ontology	Length & mass	Signal peptide (predicted)	Transmembrane regions (predicted)
KDM1B-201 ENSP00000297792 ENST00000297792	Q8NB78 [Direct mapping] Lysine-specific histone demethylase 1B Show all	Enzymes ENZYME proteins Oxidoreductases SPOCTOPUS predicted membrane proteins Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014) Show all	GO:0000122 [negative regulation of transcription by RNA polymerase II] GO:0000785 [chromatin] GO:0000786 [nucleosome] GO:0003682 [chromatin binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0006325 [chromatin organization] GO:0006349 [regulation of gene expression by genetic imprinting] GO:0007275 [multicellular organism development] GO:0008134 [transcription factor binding] GO:0008270 [zinc ion binding] GO:0016491 [oxidoreductase activity] GO:0016579 [protein deubiquitination] GO:0034648 [histone demethylase activity (H3-dimethyl-K4 specific)] GO:0034649 [histone demethylase activity (H3-monomethyl-K4 specific)] GO:0034720 [histone H3-K4 demethylation] GO:0042393 [histone binding] GO:0044030 [regulation of DNA methylation] GO:0045944 [positive regulation of transcription by RNA polymerase II] GO:0046872 [metal ion binding] GO:0050660 [flavin adenine dinucleotide binding] GO:0055114 [oxidation-reduction process] GO:0071949 [FAD binding] Show all	590 aa 65.7 kDa	No	0
KDM1B-202 ENSP00000405669 ENST00000449850	H0Y6H0 [Direct mapping] Lysine-specific histone demethylase 1B Show all	SPOCTOPUS predicted membrane proteins Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Protein evidence (Ezkurdia et al 2014) Show all	GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0006349 [regulation of gene expression by genetic imprinting] GO:0008270 [zinc ion binding] GO:0016491 [oxidoreductase activity] GO:0034648 [histone demethylase activity (H3-dimethyl-K4 specific)] GO:0034649 [histone demethylase activity (H3-monomethyl-K4 specific)] GO:0034720 [histone H3-K4 demethylation] GO:0043046 [DNA methylation involved in gamete generation] GO:0044030 [regulation of DNA methylation] GO:0046872 [metal ion binding] GO:0050660 [flavin adenine dinucleotide binding] GO:0055114 [oxidation-reduction process] Show all	823 aa 92.2 kDa	No	0
KDM1B-203 ENSP00000442670 ENST00000546309	Q08EI0 [Direct mapping] AOF1 protein; Lysine-specific histone demethylase 1B Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Protein evidence (Ezkurdia et al 2014) Show all	GO:0016491 [oxidoreductase activity] GO:0055114 [oxidation-reduction process] Show all	113 aa 12.5 kDa	No	0
KDM1B-205 ENSP00000499208 ENST00000650836	Q8NB78 [Direct mapping] Lysine-specific histone demethylase 1B Show all	Enzymes ENZYME proteins Oxidoreductases SPOCTOPUS predicted membrane proteins Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Ezkurdia et al 2014) Show all	GO:0000122 [negative regulation of transcription by RNA polymerase II] GO:0000785 [chromatin] GO:0000786 [nucleosome] GO:0003682 [chromatin binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0006325 [chromatin organization] GO:0006349 [regulation of gene expression by genetic imprinting] GO:0007275 [multicellular organism development] GO:0008134 [transcription factor binding] GO:0008270 [zinc ion binding] GO:0016491 [oxidoreductase activity] GO:0016579 [protein deubiquitination] GO:0034648 [histone demethylase activity (H3-dimethyl-K4 specific)] GO:0034649 [histone demethylase activity (H3-monomethyl-K4 specific)] GO:0034720 [histone H3-K4 demethylation] GO:0042393 [histone binding] GO:0044030 [regulation of DNA methylation] GO:0045944 [positive regulation of transcription by RNA polymerase II] GO:0046872 [metal ion binding] GO:0050660 [flavin adenine dinucleotide binding] GO:0055114 [oxidation-reduction process] GO:0071949 [FAD binding] Show all	822 aa 92.1 kDa	No	0

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