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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):
Group enriched (lung cancer, renal cancer, thyroid cancer)
HPA (cell line):
Cell line enhanced (A549, ASC TERT1, RPTEC TERT1)
HPA (normal tissue):
Expressed in all
Protein evidencei
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.
Cytoplasmic expression in several cell types, including pneumocytes and cells in renal tubules.
IMMUNOHISTOCHEMISTRY DATA RELIABILITY
Data reliability descriptioni
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 score - normal tissuesi
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.
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).
TCGA dataseti
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. The cancer types are color-coded according to which type of normal organ the cancer originates from.
RNA cancer category: Group enriched (lung cancer, renal cancer, thyroid cancer)
PROTEIN EXPRESSIONi
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, color-coded bars indicate the percentage of patients (maximum 12 patients) with high and medium protein expression level. The cancer types are color-coded according to which type of normal organ the cancer originates from. Low or not detected protein expression results in a white bar. Mouse-over function shows details about expression level and normal tissue of origin. 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.
A few cases of hepatocellular carcinomas and single cases of renal and thyroid carcinomas were moderately cytoplasmic stained. Remaining cancer tissues were negative.
Cancer tissues showed moderate to strong cytoplasmic and membranous staining.
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
LRRK2 (HGNC Symbol)
Synonyms
DKFZp434H2111, FLJ45829, PARK8, RIPK7, ROCO2
Description
Leucine rich repeat kinase 2 (HGNC Symbol)
Entrez gene summary
This gene is a member of the leucine-rich repeat kinase family and encodes a protein with an ankryin repeat region, a leucine-rich repeat (LRR) domain, a kinase domain, a DFG-like motif, a RAS domain, a GTPase domain, a MLK-like domain, and a WD40 domain. The protein is present largely in the cytoplasm but also associates with the mitochondrial outer membrane. Mutations in this gene have been associated with Parkinson disease-8. [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). 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.
LRRK2-001
LRRK2-002
LRRK2-004
LRRK2-008
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.
SCAMPI predicted membrane proteins Predicted intracellular proteins Cancer-related genes Mutational cancer driver genes Protein evidence (Ezkurdia et al 2014)
Enzymes ENZYME proteins Transferases Kinases TKL Ser/Thr protein kinases SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins Predicted intracellular proteins Cancer-related genes Mutational cancer driver genes Disease related genes Potential drug targets Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000149 [SNARE binding] GO:0000165 [MAPK cascade] GO:0000166 [nucleotide binding] GO:0000186 [activation of MAPKK activity] GO:0000187 [activation of MAPK activity] GO:0001933 [negative regulation of protein phosphorylation] GO:0001934 [positive regulation of protein phosphorylation] GO:0001948 [glycoprotein binding] GO:0003779 [actin binding] GO:0003924 [GTPase activity] GO:0004672 [protein kinase activity] GO:0004674 [protein serine/threonine kinase activity] GO:0004708 [MAP kinase kinase activity] GO:0005096 [GTPase activator activity] GO:0005515 [protein binding] GO:0005524 [ATP binding] GO:0005525 [GTP binding] GO:0005615 [extracellular space] GO:0005622 [intracellular] GO:0005634 [nucleus] GO:0005737 [cytoplasm] GO:0005739 [mitochondrion] GO:0005741 [mitochondrial outer membrane] GO:0005743 [mitochondrial inner membrane] GO:0005759 [mitochondrial matrix] GO:0005764 [lysosome] GO:0005768 [endosome] GO:0005783 [endoplasmic reticulum] GO:0005794 [Golgi apparatus] GO:0005798 [Golgi-associated vesicle] GO:0005802 [trans-Golgi network] GO:0005829 [cytosol] GO:0005886 [plasma membrane] GO:0005902 [microvillus] GO:0006468 [protein phosphorylation] GO:0006897 [endocytosis] GO:0006914 [autophagy] GO:0006979 [response to oxidative stress] GO:0007005 [mitochondrion organization] GO:0007030 [Golgi organization] GO:0007040 [lysosome organization] GO:0007264 [small GTPase mediated signal transduction] GO:0007528 [neuromuscular junction development] GO:0008017 [microtubule binding] GO:0008021 [synaptic vesicle] GO:0008340 [determination of adult lifespan] GO:0009267 [cellular response to starvation] GO:0010506 [regulation of autophagy] GO:0010508 [positive regulation of autophagy] GO:0010738 [regulation of protein kinase A signaling] GO:0010955 [negative regulation of protein processing] GO:0014041 [regulation of neuron maturation] GO:0015631 [tubulin binding] GO:0016020 [membrane] GO:0016234 [inclusion body] GO:0016242 [negative regulation of macroautophagy] GO:0016301 [kinase activity] GO:0016310 [phosphorylation] GO:0016740 [transferase activity] GO:0017048 [Rho GTPase binding] GO:0017075 [syntaxin-1 binding] GO:0018105 [peptidyl-serine phosphorylation] GO:0018107 [peptidyl-threonine phosphorylation] GO:0019722 [calcium-mediated signaling] GO:0021772 [olfactory bulb development] GO:0022028 [tangential migration from the subventricular zone to the olfactory bulb] GO:0030054 [cell junction] GO:0030154 [cell differentiation] GO:0030159 [receptor signaling complex scaffold activity] GO:0030276 [clathrin binding] GO:0030424 [axon] GO:0030425 [dendrite] GO:0030426 [growth cone] GO:0030529 [intracellular ribonucleoprotein complex] GO:0030672 [synaptic vesicle membrane] GO:0031398 [positive regulation of protein ubiquitination] GO:0031410 [cytoplasmic vesicle] GO:0031966 [mitochondrial membrane] GO:0032091 [negative regulation of protein binding] GO:0032092 [positive regulation of protein binding] GO:0032436 [positive regulation of proteasomal ubiquitin-dependent protein catabolic process] GO:0032473 [cytoplasmic side of mitochondrial outer membrane] GO:0032839 [dendrite cytoplasm] GO:0034211 [GTP-dependent protein kinase activity] GO:0034260 [negative regulation of GTPase activity] GO:0034599 [cellular response to oxidative stress] GO:0034613 [cellular protein localization] GO:0035556 [intracellular signal transduction] GO:0035564 [regulation of kidney size] GO:0035640 [exploration behavior] GO:0035641 [locomotory exploration behavior] GO:0035751 [regulation of lysosomal lumen pH] GO:0036479 [peroxidase inhibitor activity] GO:0039706 [co-receptor binding] GO:0040012 [regulation of locomotion] GO:0042391 [regulation of membrane potential] GO:0042802 [identical protein binding] GO:0042803 [protein homodimerization activity] GO:0042995 [cell projection] GO:0043005 [neuron projection] GO:0043025 [neuronal cell body] GO:0043068 [positive regulation of programmed cell death] GO:0043195 [terminal bouton] GO:0043204 [perikaryon] GO:0043231 [intracellular membrane-bounded organelle] GO:0043406 [positive regulation of MAP kinase activity] GO:0043547 [positive regulation of GTPase activity] GO:0044325 [ion channel binding] GO:0044753 [amphisome] GO:0044754 [autolysosome] GO:0045121 [membrane raft] GO:0045202 [synapse] GO:0046039 [GTP metabolic process] GO:0046777 [protein autophosphorylation] GO:0048312 [intracellular distribution of mitochondria] GO:0048812 [neuron projection morphogenesis] GO:0051018 [protein kinase A binding] GO:0051646 [mitochondrion localization] GO:0051900 [regulation of mitochondrial depolarization] GO:0051966 [regulation of synaptic transmission, glutamatergic] GO:0060070 [canonical Wnt signaling pathway] GO:0060079 [excitatory postsynaptic potential] GO:0060159 [regulation of dopamine receptor signaling pathway] GO:0060161 [positive regulation of dopamine receptor signaling pathway] GO:0060828 [regulation of canonical Wnt signaling pathway] GO:0061001 [regulation of dendritic spine morphogenesis] GO:0070062 [extracellular exosome] GO:0070585 [protein localization to mitochondrion] GO:0070997 [neuron death] GO:0071287 [cellular response to manganese ion] GO:0071407 [cellular response to organic cyclic compound] GO:0072593 [reactive oxygen species metabolic process] GO:0090140 [regulation of mitochondrial fission] GO:0090263 [positive regulation of canonical Wnt signaling pathway] GO:0090394 [negative regulation of excitatory postsynaptic potential] GO:0097487 [multivesicular body, internal vesicle] GO:0098794 [postsynapse] GO:0099400 [caveola neck] GO:1901214 [regulation of neuron death] GO:1901215 [negative regulation of neuron death] GO:1902236 [negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway] GO:1902499 [positive regulation of protein autoubiquitination] GO:1902692 [regulation of neuroblast proliferation] GO:1902803 [regulation of synaptic vesicle transport] GO:1902823 [negative regulation of late endosome to lysosome transport] GO:1902902 [negative regulation of autophagosome assembly] GO:1903125 [negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation] GO:1903206 [negative regulation of hydrogen peroxide-induced cell death] GO:1903215 [negative regulation of protein targeting to mitochondrion] GO:1903217 [negative regulation of protein processing involved in protein targeting to mitochondrion] GO:1903351 [cellular response to dopamine] GO:1904713 [beta-catenin destruction complex binding] GO:1904887 [Wnt signalosome assembly] GO:1905279 [regulation of retrograde transport, endosome to Golgi] GO:1905289 [regulation of CAMKK-AMPK signaling cascade] GO:1990909 [Wnt signalosome] GO:2000172 [regulation of branching morphogenesis of a nerve] GO:2000300 [regulation of synaptic vesicle exocytosis]