We use cookies to enhance the usability of our website. If you continue, we'll assume that you are happy to receive all cookies. More information. Don't show this again.
RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for data imported from The Genotype-Tissue Expression project (GTEX), FANTOM5 Consortium (FANTOM5) and internally generated Human Protein Atlas (HPA) data.
Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.
Evidence at protein level
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.
Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.
Antibody staining mainly consistent with RNA expression data.
Reliability scorei
Reliability score (score description), divided into Enhanced, Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between antibody staining pattern, available RNA-Seq and gene/protein characterization data, as well as similarity between independent antibodies targeting the same protein.
Below is an overview of RNA and protein expression data generated in the Human Protein Atlas project. Analyzed tissues are divided into color-coded groups according to which functional features they have in common. For each group, a list of included tissues is accessed by clicking on group name, group symbol, RNA bar, or protein bar. Subsequent selection of a particular tissue in this list links to the image data page.
Images of selected tissues give a visual summary of the protein expression profile furthest to the right.
The gray human body provides links to a histology dictionary when clicking on any part of the figure.
RNA expression (TPM)i
RNA-seq results generated in HPA are reported as number of transcripts per million (TPM). Each bar represents the highest expression score found in a particular group of tissues. The assay is described more in detail in Assays & Annotation.
Protein expression (score)i
Each bar represents the highest expression score found in a particular group of tissues. Protein expression scores are based on a best estimate of the "true" protein expression from a knowledge-based annotation, described more in detail under Assays & annotation. For genes where more than one antibody has been used, a collective score is set displaying the estimated true protein expression.
Protein expression data is shown for each of the 44 tissues. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. Mouse-over function shows protein score for analyzed cell types in a selected tissue. To access image data click on tissue name or bar. Annotation of protein expression is described in detail in Assays & annotation.
For genes with available protein data for which a knowledge-based annotation gave inconclusive results, no protein expression data is displayed in the protein expression data overview. However, all immunohistochemical images are still available and the annotation data can be found under Primary data.
Organ
Expression
Alphabetical
RNA EXPRESSION OVERVIEWi
RNA expression overview shows RNA-data from three different sources: Internally generated Human Protein Atlas (HPA) RNA-seq data, RNA-seq data from the Genotype-Tissue Expression (GTEx) project and CAGE data from FANTOM5 project. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
HPA dataseti
HPA dataset RNA-seq tissue data is reported as mean TPM (transcripts per million), corresponding to mean values of the different individual samples from each tissue. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar. The RNA-seq assay is described in detail in Assays & Annotation.
RNA tissue category HPA HPA RNA tissue category (category description) is calculated based on mRNA expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
GTEx dataseti
GTEx dataset RNA-seq data is reported as median RPKM (reads per kilobase per million mapped reads), generated by the Genotype-Tissue Expression (GTEx) project. More information can be found in Assays & Annotation.
RNA tissue category GTEx GTEx RNA tissue category (category description) is calculated based on mRNA expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
FANTOM5 dataseti
FANTOM5 dataset Tissue data obtained through Cap Analysis of Gene Expression (CAGE) are reported as Tags Per Million, generated by the FANTOM5 project. More information can be found in Assays & Annotation.
RNA tissue category FANTOM5 FANTOM5 RNA tissue category (category description) is calculated based on gene expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
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
KDM1A (HGNC Symbol)
Synonyms
AOF2, BHC110, KDM1, KIAA0601, LSD1
Description
Lysine demethylase 1A (HGNC Symbol)
Entrez gene summary
This gene encodes a nuclear protein containing a SWIRM domain, a FAD-binding motif, and an amine oxidase domain. This protein is a component of several histone deacetylase complexes, though it silences genes by functioning as a histone demethylase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.
At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.
Under the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more).
The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (read more).
If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.
Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.
KDM1A-001
KDM1A-002
KDM1A-004
KDM1A-005
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.
SPOCTOPUS predicted membrane proteins Predicted secreted proteins Secreted proteins predicted by MDSEC Phobius predicted secreted proteins SPOCTOPUS predicted secreted proteins Disease related genes Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000784 [nuclear chromosome, telomeric region] GO:0000790 [nuclear chromatin] GO:0002039 [p53 binding] GO:0003677 [DNA binding] GO:0003682 [chromatin binding] GO:0004407 [histone deacetylase activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005667 [transcription factor complex] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006357 [regulation of transcription from RNA polymerase II promoter] GO:0006482 [protein demethylation] GO:0007275 [multicellular organism development] GO:0007596 [blood coagulation] GO:0008134 [transcription factor binding] GO:0010569 [regulation of double-strand break repair via homologous recombination] GO:0016491 [oxidoreductase activity] GO:0016569 [covalent chromatin modification] GO:0016575 [histone deacetylation] GO:0019899 [enzyme binding] GO:0030374 [ligand-dependent nuclear receptor transcription coactivator activity] GO:0032091 [negative regulation of protein binding] GO:0032451 [demethylase activity] GO:0032452 [histone demethylase activity] GO:0032453 [histone demethylase activity (H3-K4 specific)] GO:0032454 [histone demethylase activity (H3-K9 specific)] GO:0033169 [histone H3-K9 demethylation] GO:0033184 [positive regulation of histone ubiquitination] GO:0034644 [cellular response to UV] GO:0034648 [histone demethylase activity (H3-dimethyl-K4 specific)] GO:0034720 [histone H3-K4 demethylation] GO:0042162 [telomeric DNA binding] GO:0043234 [protein complex] GO:0043392 [negative regulation of DNA binding] GO:0043426 [MRF binding] GO:0043433 [negative regulation of sequence-specific DNA binding transcription factor activity] GO:0043518 [negative regulation of DNA damage response, signal transduction by p53 class mediator] GO:0044212 [transcription regulatory region DNA binding] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0050660 [flavin adenine dinucleotide binding] GO:0050681 [androgen receptor binding] GO:0051091 [positive regulation of sequence-specific DNA binding transcription factor activity] GO:0055001 [muscle cell development] GO:0055114 [oxidation-reduction process] GO:0061752 [telomeric repeat-containing RNA binding] GO:0071480 [cellular response to gamma radiation] GO:1902166 [negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator] GO:1903827 [regulation of cellular protein localization] GO:1990391 [DNA repair complex]
SPOCTOPUS predicted membrane proteins Predicted secreted proteins Secreted proteins predicted by MDSEC Phobius predicted secreted proteins SPOCTOPUS predicted secreted proteins Disease related genes Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000380 [alternative mRNA splicing, via spliceosome] GO:0000784 [nuclear chromosome, telomeric region] GO:0000790 [nuclear chromatin] GO:0001085 [RNA polymerase II transcription factor binding] GO:0001701 [in utero embryonic development] GO:0002039 [p53 binding] GO:0003677 [DNA binding] GO:0003682 [chromatin binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0004407 [histone deacetylase activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005667 [transcription factor complex] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006357 [regulation of transcription from RNA polymerase II promoter] GO:0006482 [protein demethylation] GO:0007275 [multicellular organism development] GO:0007596 [blood coagulation] GO:0008134 [transcription factor binding] GO:0008283 [cell proliferation] GO:0010569 [regulation of double-strand break repair via homologous recombination] GO:0010725 [regulation of primitive erythrocyte differentiation] GO:0010976 [positive regulation of neuron projection development] GO:0014070 [response to organic cyclic compound] GO:0016491 [oxidoreductase activity] GO:0016569 [covalent chromatin modification] GO:0016575 [histone deacetylation] GO:0019899 [enzyme binding] GO:0021983 [pituitary gland development] GO:0021987 [cerebral cortex development] GO:0030374 [ligand-dependent nuclear receptor transcription coactivator activity] GO:0030851 [granulocyte differentiation] GO:0032091 [negative regulation of protein binding] GO:0032451 [demethylase activity] GO:0032452 [histone demethylase activity] GO:0032453 [histone demethylase activity (H3-K4 specific)] GO:0032454 [histone demethylase activity (H3-K9 specific)] GO:0033169 [histone H3-K9 demethylation] GO:0033184 [positive regulation of histone ubiquitination] GO:0034644 [cellular response to UV] GO:0034648 [histone demethylase activity (H3-dimethyl-K4 specific)] GO:0034720 [histone H3-K4 demethylation] GO:0035563 [positive regulation of chromatin binding] GO:0042162 [telomeric DNA binding] GO:0042551 [neuron maturation] GO:0043234 [protein complex] GO:0043392 [negative regulation of DNA binding] GO:0043426 [MRF binding] GO:0043433 [negative regulation of sequence-specific DNA binding transcription factor activity] GO:0043518 [negative regulation of DNA damage response, signal transduction by p53 class mediator] GO:0044212 [transcription regulatory region DNA binding] GO:0045648 [positive regulation of erythrocyte differentiation] GO:0045654 [positive regulation of megakaryocyte differentiation] GO:0045793 [positive regulation of cell size] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0046098 [guanine metabolic process] GO:0046886 [positive regulation of hormone biosynthetic process] GO:0050660 [flavin adenine dinucleotide binding] GO:0050681 [androgen receptor binding] GO:0050767 [regulation of neurogenesis] GO:0050768 [negative regulation of neurogenesis] GO:0051091 [positive regulation of sequence-specific DNA binding transcription factor activity] GO:0051572 [negative regulation of histone H3-K4 methylation] GO:0051573 [negative regulation of histone H3-K9 methylation] GO:0055001 [muscle cell development] GO:0055114 [oxidation-reduction process] GO:0060992 [response to fungicide] GO:0061752 [telomeric repeat-containing RNA binding] GO:0071320 [cellular response to cAMP] GO:0071480 [cellular response to gamma radiation] GO:1902166 [negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator] GO:1903827 [regulation of cellular protein localization] GO:1990138 [neuron projection extension] GO:1990391 [DNA repair complex] GO:2000179 [positive regulation of neural precursor cell proliferation] GO:2000648 [positive regulation of stem cell proliferation]
The Human Protein Atlas project is funded
MENU
