RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue/cell line enriched, group enriched, tissue/cell line enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for The Cancer Genome Atlas (TCGA) data from cancer tissues and internally generated Human Protein Atlas (HPA) data from normal tissues and cell lines.
TCGA (cancer tissue):
HPA (cell line):
Cell line enhanced (AN3-CA, HEK93)
HPA (normal tissue):
Tissue enhanced (adrenal gland, epididymis)
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 expression normal tissuei
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.
Estimation of protein expression could not be performed. View primary data.
ANTIBODY IHC RELIABILITY
Data reliability descriptioni
Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.
RNA-based expert annotation gave inconclusive results. Pending reevaluation.
Reliability score (score description), divided into Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between the staining pattern of one antibody or several antibodies with RNA-seq data and available gene/protein characterization data.
Kaplan-Meier plots for all cancers where high expression of this gene has significant (p<0.001) association with patient survival are shown in this summary. Whether the prognosis is favourable or unfavourable is indicated in brackets. Each Kaplan-Meier plot is clickable and redirects to a detailed page that includes individual expression and survival data for patients with the selected cancer.
RNA expression overview shows RNA-seq data from The Cancer Genome Atlas (TCGA).
RNA-seq data in 17 cancer types are reported as median FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA). RNA cancer tissue category is calculated based on mRNA expression levels across all 17 cancer tissues and include: cancer tissue enriched, cancer group enriched, cancer tissue enhanced, expressed in all, mixed and not detected. To access cancer specific RNA and prognostic data, click on the cancer name.
Antibody staining in 20 different cancers is summarized by a selection of four standard cancer tissue samples representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional fifth image can be added as a complement. The assay and annotation is described here. Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset.
For each cancer, the fraction of samples with protein expression level high, medium, low, or not detected are provided by the blue-scale color-coding (as described by the color-coding scale in the box to the left). The length of the bar represents the number of patient samples analyzed (max=12 patients). The images and annotations can be accessed by clicking on the cancer name or protein expression bar. If more than one antibody is analyzed, the tabs at the top of the staining summary section can be used to toggle between the different antibodies. The mouse-over function displays additional data for the features in the staining summary view.
Next to the cancer staining data, the protein expression data of normal tissues or specific cell types corresponding to each cancer are shown and protein expression levels are indicated by the blue-scale color coding.
A manually written summary of the overall protein expression pattern across the analyzed cancer tissues.
All cancer tissues were weak to moderate cytoplasmic stained.
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.
HOXA5 (HGNC Symbol)
Homeobox A5 (HGNC Symbol)
Entrez gene summary
In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. Methylation of this gene may result in the loss of its expression and, since the encoded protein upregulates the tumor suppressor p53, this protein may play an important role in tumorigenesis. [provided by RefSeq, Jul 2008]
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) (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.
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 Helix-turn-helix domains Cancer-related genes Candidate cancer biomarkers Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
GO:0000978 [RNA polymerase II core promoter proximal region sequence-specific DNA binding] GO:0001077 [transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding] GO:0001501 [skeletal system development] GO:0002009 [morphogenesis of an epithelium] GO:0003016 [respiratory system process] GO:0003677 [DNA binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0006355 [regulation of transcription, DNA-templated] GO:0006366 [transcription from RNA polymerase II promoter] GO:0007389 [pattern specification process] GO:0007585 [respiratory gaseous exchange] GO:0009952 [anterior/posterior pattern specification] GO:0010870 [positive regulation of receptor biosynthetic process] GO:0016477 [cell migration] GO:0016525 [negative regulation of angiogenesis] GO:0030324 [lung development] GO:0030878 [thyroid gland development] GO:0033599 [regulation of mammary gland epithelial cell proliferation] GO:0035264 [multicellular organism growth] GO:0043065 [positive regulation of apoptotic process] GO:0043565 [sequence-specific DNA binding] GO:0045639 [positive regulation of myeloid cell differentiation] GO:0045647 [negative regulation of erythrocyte differentiation] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0048286 [lung alveolus development] GO:0048704 [embryonic skeletal system morphogenesis] GO:0048706 [embryonic skeletal system development] GO:0060435 [bronchiole development] GO:0060439 [trachea morphogenesis] GO:0060441 [epithelial tube branching involved in lung morphogenesis] GO:0060480 [lung goblet cell differentiation] GO:0060481 [lobar bronchus epithelium development] GO:0060484 [lung-associated mesenchyme development] GO:0060535 [trachea cartilage morphogenesis] GO:0060536 [cartilage morphogenesis] GO:0060574 [intestinal epithelial cell maturation] GO:0060638 [mesenchymal-epithelial cell signaling] GO:0060644 [mammary gland epithelial cell differentiation] GO:0060749 [mammary gland alveolus development] GO:0060764 [cell-cell signaling involved in mammary gland development]