Blood atlas - LIMS1 - The Human Protein Atlas

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LIMS1

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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.	LIMS1
Gene descriptionⁱ Full gene name according to HGNC.	LIM zinc finger domain containing 1
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

HUMAN PROTEIN ATLAS INFORMATION
RNA blood cell lineage specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: lineage enriched, group enriched, lineage enhanced, low lineage specificity and not detected. Lineages include B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells. Read more	Low lineage specificity
RNA blood cell lineage distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Lineages include B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells. Read more	Detected in all
RNA blood cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Low cell type specificity
RNA blood cell type distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Blood-based immunoassayⁱ The blood-based immunoassay category applies to actively secreted proteins and is based on plasma or serum protein concentrations established with enzyme-linked immunosorbent assays, compiled from a literature search. The categories include: detected and not detected, where detection refers to a concentration found in the literature search. Read more	Not analysed since only proteins predicted to be actively secreted to blood is analysed here
Mass spectrometryⁱ Detection or not of the gene in blood, based on spectral count estimations from a publicly available mass spectrometry-based plasma proteomics data set obtained from the PeptideAtlas.	Detected

BLOOD CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
Consensus datasetⁱ The resulting transcript expression values, denoted Normalized eXpression (NX), resulting from the internal normalization pipeline for 18 blood cell types and total peripheral blood mononuclear cells (PBMC). Read more Lineage Expression Alphabetical RNA cell type specificity: Low cell type specificity
HPA scaled datasetⁱ pTPM values are calculated by scaling all TPM values per sample to a sum of 1 million TPM to compensate for the previously removed non-coding transcripts and are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC). Read more Lineage Expression Alphabetical
Monaco scaled datasetⁱ pTPM values are calculated by scaling all TPM values per sample to a sum of 1 million TPM to compensate for the previously removed non-coding transcripts and are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Read more Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Read more Lineage Expression Alphabetical

PROTEIN CONCENTRATION IN BLOOD - IMMUNOASSAYⁱ

Protein target not predicted to be actively secreted to blood and therefore not analyzed here

PROTEIN CONCENTRATION IN PLASMA - MASS SPECTROMETRYⁱ The protein concentration in blood is quantified by mass spectrometry-based plasma proteomics and estimated from spectral counts in a publicly available data set obtained from the PeptideAtlas. Read more
Detected in plasma by mass spectrometry 130 µg/L, PeptideAtlas

PROTEIN DETECTED IN PLASMA - PROXIMITY EXTENSION ASSAYⁱ The protein profiling results based on proximity extension assays (Olink) for a longitudinal wellness study covering 86 individuals with four visits during one year at three months intervals. Protein expression levels are reported as Normalized Protein Expression (NPX). Read more
Pending analysis

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.