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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):
Expressed in all
HPA (cell line):
Expressed in all
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.
Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.
Antibody staining mainly consistent with RNA expression data. Caution, targets protein from more than one gene.
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.
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.
Most cancer tissues showed weak to moderate cytoplasmic and membranous immunoreactivity. Lymphomas and renal cancers along with several gliomas, ovarian, lung and liver cancers were negative.
Most malignancies showed moderate cytoplasmic staining. A few cases of breast cancers showed strong immunoreactivity. Many cases of gliomas, lymphomas and renal cancers were weakly stained.
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
CALM1 (HGNC Symbol)
Synonyms
CALML2, CAMI, DD132, PHKD
Description
Calmodulin 1 (HGNC Symbol)
Entrez gene summary
This gene encodes a member of the EF-hand calcium-binding protein family. It is one of three genes which encode an identical calcium binding protein which is one of the four subunits of phosphorylase kinase. Two pseudogenes have been identified on chromosome 7 and X. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 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.
CALM1-001
CALM1-004
CALM1-006
CALM1-007
CALM1-012
CALM1-201
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.
P62158 [Direct mapping] Calmodulin B4DJ51 [Target identity:100%; Query identity:100%] Calmodulin 1 (Phosphorylase kinase, delta), isoform CRA_a; Calmodulin 3 (Phosphorylase kinase, delta), isoform CRA_b; Epididymis secretory protein Li 72; cDNA FLJ61744, highly similar to Calmodulin
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Transporters Accessory Factors Involved in Transport Predicted intracellular proteins Plasma proteins RAS pathway related proteins Cancer-related genes Candidate cancer biomarkers
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GO:0000165 [MAPK cascade] GO:0000922 [spindle pole] GO:0001975 [response to amphetamine] GO:0002027 [regulation of heart rate] GO:0002576 [platelet degranulation] GO:0005088 [Ras guanyl-nucleotide exchange factor activity] GO:0005509 [calcium ion binding] GO:0005513 [detection of calcium ion] GO:0005515 [protein binding] GO:0005576 [extracellular region] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005737 [cytoplasm] GO:0005813 [centrosome] GO:0005819 [spindle] GO:0005829 [cytosol] GO:0005856 [cytoskeleton] GO:0005876 [spindle microtubule] GO:0005886 [plasma membrane] GO:0005980 [glycogen catabolic process] GO:0006479 [protein methylation] GO:0006936 [muscle contraction] GO:0007186 [G-protein coupled receptor signaling pathway] GO:0007190 [activation of adenylate cyclase activity] GO:0007223 [Wnt signaling pathway, calcium modulating pathway] GO:0008179 [adenylate cyclase binding] GO:0008440 [inositol-1,4,5-trisphosphate 3-kinase activity] GO:0010800 [positive regulation of peptidyl-threonine phosphorylation] GO:0010801 [negative regulation of peptidyl-threonine phosphorylation] GO:0010880 [regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum] GO:0010881 [regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion] GO:0014069 [postsynaptic density] GO:0015276 [ligand-gated ion channel activity] GO:0016301 [kinase activity] GO:0016310 [phosphorylation] GO:0019722 [calcium-mediated signaling] GO:0019901 [protein kinase binding] GO:0019904 [protein domain specific binding] GO:0021762 [substantia nigra development] GO:0022400 [regulation of rhodopsin mediated signaling pathway] GO:0030017 [sarcomere] GO:0030234 [enzyme regulator activity] GO:0030235 [nitric-oxide synthase regulator activity] GO:0030426 [growth cone] GO:0030801 [positive regulation of cyclic nucleotide metabolic process] GO:0031432 [titin binding] GO:0031800 [type 3 metabotropic glutamate receptor binding] GO:0031954 [positive regulation of protein autophosphorylation] GO:0031982 [vesicle] GO:0031996 [thioesterase binding] GO:0031997 [N-terminal myristoylation domain binding] GO:0032465 [regulation of cytokinesis] GO:0032516 [positive regulation of phosphoprotein phosphatase activity] GO:0034220 [ion transmembrane transport] GO:0034704 [calcium channel complex] GO:0035307 [positive regulation of protein dephosphorylation] GO:0038095 [Fc-epsilon receptor signaling pathway] GO:0043005 [neuron projection] GO:0043274 [phospholipase binding] GO:0043539 [protein serine/threonine kinase activator activity] GO:0043547 [positive regulation of GTPase activity] GO:0043548 [phosphatidylinositol 3-kinase binding] GO:0043647 [inositol phosphate metabolic process] GO:0044325 [ion channel binding] GO:0046872 [metal ion binding] GO:0047485 [protein N-terminus binding] GO:0048306 [calcium-dependent protein binding] GO:0050998 [nitric-oxide synthase binding] GO:0050999 [regulation of nitric-oxide synthase activity] GO:0051000 [positive regulation of nitric-oxide synthase activity] GO:0051343 [positive regulation of cyclic-nucleotide phosphodiesterase activity] GO:0051412 [response to corticosterone] GO:0051592 [response to calcium ion] GO:0055117 [regulation of cardiac muscle contraction] GO:0060314 [regulation of ryanodine-sensitive calcium-release channel activity] GO:0060315 [negative regulation of ryanodine-sensitive calcium-release channel activity] GO:0060316 [positive regulation of ryanodine-sensitive calcium-release channel activity] GO:0070062 [extracellular exosome] GO:0071902 [positive regulation of protein serine/threonine kinase activity] GO:0072542 [protein phosphatase activator activity] GO:1901841 [regulation of high voltage-gated calcium channel activity] GO:1901844 [regulation of cell communication by electrical coupling involved in cardiac conduction]
The Human Protein Atlas project is funded
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