Tissue expression of LY9 - Summary - The Human Protein Atlas

GENERAL INFORMATIONⁱ 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.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	LY9
Gene descriptionⁱ Full gene name according to HGNC.	Lymphocyte antigen 9
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	CD markers
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,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	5

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of data presented in the Tissue Atlas and representative images of protein expression (left) and mRNA expression (right). The images are clickable and will redirect to more Tissue Atlas data. The Tissue Atlas 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
RNA tissue specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA, GTEX and FANTOM5. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. Read more	Group enriched (blood, intestine, lymphoid tissue, urinary bladder)
RNA tissue distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA, GTEX and FANTOM5. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	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. Read more	Cytoplasmic expression mainly in subsets of lymphoid cells.

IMMUNOHISTOCHEMISTRY DATA RELIABILITY
Data reliability descriptionⁱ Standardized explanatory sentences with additional information required for full understanding of the protein expression profile, based on knowledge-based and secretome-based annotation.	Medium consistency between antibody staining and RNA expression data. Pending external verification.
Reliability scoreⁱ A reliability score is manually set for all genes and indicates the level of reliability of the analyzed protein expression pattern based on available RNA-seq data, protein/gene characterization data and immunohistochemical data from one or several antibodies with non-overlapping epitopes. The reliability score is based on the 44 normal tissues analyzed, and if there is available data from more than one antibody, the staining patterns of all antibodies are taken into consideration during evaluation. The reliability score is divided into Enhanced, Supported, Approved, or Uncertain, and is displayed on both Tissue Atlas and Pathology Atlas. Read more	Approved
Antibodiesⁱ Antibodies used for this assay. Click on an antibody for more information.	HPA050917
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RNA AND PROTEIN EXPRESSION SUMMARYⁱ

Expression

Detection

All organs

RNA expression (NX)ⁱ

Protein expression (score)ⁱ

Brain

Cerebral cortex
Olfactory region			N/A
Hippocampal formation
Amygdala			N/A
Basal ganglia
Thalamus			N/A
Hypothalamus			N/A
Midbrain			N/A
Pons and medulla			N/A
Cerebellum
Corpus callosum			N/A
Spinal cord			N/A

Eye

Retina

N/A

Endocrine tissues

Thyroid gland
Parathyroid gland
Adrenal gland
Pituitary gland			N/A

Lung

Nasopharynx	N/A
Bronchus	N/A
Lung

Proximal digestive tract

Tongue		N/A
Oral mucosa	N/A
Salivary gland
Esophagus

Gastrointestinal tract

Stomach
Duodenum
Small intestine
Colon
Rectum

Liver & gallbladder

Liver
Gallbladder

Pancreas

Kidney & urinary bladder

Kidney
Urinary bladder

Male tissues

Ductus deferens			N/A
Testis
Epididymis
Seminal vesicle
Prostate

Female tissues

Vagina
Ovary
Fallopian tube
Endometrium
Cervix, uterine
Placenta
Breast

Muscle tissues

Heart muscle
Smooth muscle
Skeletal muscle

Adipose & soft tissue

Adipose tissue
Soft tissue	N/A

Skin

Bone marrow & lymphoid tissues

Thymus			N/A
Appendix
Spleen
Lymph node
Tonsil
Bone marrow

Blood

Granulocytes			N/A
Monocytes			N/A
T-cells			N/A
B-cells			N/A
NK-cells			N/A
Dendritic cells			N/A
Total PBMC			N/A

PROTEIN EXPRESSION OVERVIEWⁱ 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, respectively: 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, as well as the consensus dataset which is based on a combination of all three sources. 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. Read more
Consensus datasetⁱ Consensus dataset Consensus Normalized eXpression (NX) levels for 55 tissue types and 6 blood cell types, created by combining the data from the three transcriptomics datasets (HPA, GTEx and FANTOM5) using the internal normalization pipeline. 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. Read more about how the datasets were combined into consensus normalized expression levels in Assays & Annotation. Organ Expression Alphabetical RNA tissue specificity: Group enriched (blood, intestine, lymphoid tissue, urinary bladder)
HPA datasetⁱ HPA dataset HPA RNA-seq tissue data is reported as mean pTPM (protein-coding 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 HPA RNA-seq assay is described in detail in Assays & Annotation. Organ Expression Alphabetical
GTEx datasetⁱ GTEx dataset RNA-seq tissue data generated by the Genotype-Tissue Expression (GTEx) project is reported as mean pTPM (protein-coding 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 GTEx RNA-seq assay is described in detail in Assays & Annotation. Organ Expression Alphabetical
FANTOM5 datasetⁱ FANTOM5 dataset Tissue data for RNA expression obtained through Cap Analysis of Gene Expression (CAGE) generated by the FANTOM5 project are reported as Scaled Tags Per Million. 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 CAGE method is described in detail in Assays & Annotation. Organ Expression Alphabetical