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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 not 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: Mixed
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: Tissue enhanced (ovary)
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: Mixed
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
GATA6
Synonyms
Description
GATA binding protein 6 (HGNC Symbol)
Entrez gene summary
This gene is a member of a small family of zinc finger transcription factors that play an important role in the regulation of cellular differentiation and organogenesis during vertebrate development. This gene is expressed during early embryogenesis and localizes to endo- and mesodermally derived cells during later embryogenesis and thereby plays an important role in gut, lung, and heart development. Mutations in this gene are associated with several congenital defects. [provided by RefSeq, Mar 2012]
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.
GATA6-001
GATA6-002
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.
Predicted intracellular proteins Transcription factors Zinc-coordinating DNA-binding domains 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:0000977 [RNA polymerase II regulatory region sequence-specific DNA binding] GO:0000979 [RNA polymerase II core promoter sequence-specific DNA binding] GO:0000981 [RNA polymerase II transcription factor activity, sequence-specific DNA binding] GO:0001085 [RNA polymerase II transcription factor binding] GO:0001103 [RNA polymerase II repressing transcription factor binding] GO:0001228 [transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding] GO:0001701 [in utero embryonic development] GO:0001889 [liver development] GO:0003148 [outflow tract septum morphogenesis] GO:0003309 [type B pancreatic cell differentiation] GO:0003310 [pancreatic A cell differentiation] GO:0003677 [DNA binding] GO:0003682 [chromatin binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0003705 [transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding] 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:0006366 [transcription from RNA polymerase II promoter] GO:0006644 [phospholipid metabolic process] GO:0007493 [endodermal cell fate determination] GO:0007596 [blood coagulation] GO:0008134 [transcription factor binding] GO:0008270 [zinc ion binding] GO:0008584 [male gonad development] GO:0010468 [regulation of gene expression] GO:0014898 [cardiac muscle hypertrophy in response to stress] GO:0019901 [protein kinase binding] GO:0030513 [positive regulation of BMP signaling pathway] GO:0030855 [epithelial cell differentiation] GO:0031016 [pancreas development] GO:0031965 [nuclear membrane] GO:0032911 [negative regulation of transforming growth factor beta1 production] GO:0032912 [negative regulation of transforming growth factor beta2 production] GO:0035239 [tube morphogenesis] GO:0035987 [endodermal cell differentiation] GO:0042493 [response to drug] GO:0043066 [negative regulation of apoptotic process] GO:0043565 [sequence-specific DNA binding] GO:0043627 [response to estrogen] GO:0044212 [transcription regulatory region DNA binding] GO:0044267 [cellular protein metabolic process] GO:0045766 [positive regulation of angiogenesis] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0046872 [metal ion binding] GO:0048645 [animal organ formation] GO:0048738 [cardiac muscle tissue development] GO:0051145 [smooth muscle cell differentiation] GO:0051891 [positive regulation of cardioblast differentiation] GO:0055007 [cardiac muscle cell differentiation] GO:0060045 [positive regulation of cardiac muscle cell proliferation] GO:0060430 [lung saccule development] GO:0060486 [Clara cell differentiation] GO:0060510 [Type II pneumocyte differentiation] GO:0060575 [intestinal epithelial cell differentiation] GO:0060947 [cardiac vascular smooth muscle cell differentiation] GO:0070848 [response to growth factor] GO:0071158 [positive regulation of cell cycle arrest] GO:0071371 [cellular response to gonadotropin stimulus] GO:0071456 [cellular response to hypoxia] GO:0071773 [cellular response to BMP stimulus]
Predicted intracellular proteins Transcription factors Zinc-coordinating DNA-binding domains Disease related genes Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000977 [RNA polymerase II regulatory region sequence-specific DNA binding] GO:0000981 [RNA polymerase II transcription factor activity, sequence-specific DNA binding] GO:0001085 [RNA polymerase II transcription factor binding] GO:0001228 [transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding] GO:0003148 [outflow tract septum morphogenesis] GO:0003677 [DNA binding] GO:0003682 [chromatin binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] 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:0006366 [transcription from RNA polymerase II promoter] GO:0007596 [blood coagulation] GO:0008134 [transcription factor binding] GO:0008270 [zinc ion binding] GO:0008584 [male gonad development] GO:0019901 [protein kinase binding] GO:0030513 [positive regulation of BMP signaling pathway] GO:0031965 [nuclear membrane] GO:0032911 [negative regulation of transforming growth factor beta1 production] GO:0032912 [negative regulation of transforming growth factor beta2 production] GO:0042493 [response to drug] GO:0043066 [negative regulation of apoptotic process] GO:0043565 [sequence-specific DNA binding] GO:0044212 [transcription regulatory region DNA binding] GO:0044267 [cellular protein metabolic process] GO:0045766 [positive regulation of angiogenesis] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0046872 [metal ion binding] GO:0051145 [smooth muscle cell differentiation] GO:0060575 [intestinal epithelial cell differentiation] GO:0060947 [cardiac vascular smooth muscle cell differentiation] GO:0070848 [response to growth factor] GO:0071158 [positive regulation of cell cycle arrest] GO:0071456 [cellular response to hypoxia]
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