Details for: LINC01558

Gene ID: 26238

Gene Type:  ncRNA (Non-coding RNA)  - A functional RNA molecule that is transcribed from DNA but not translated into a protein. Includes classes like miRNA and lncRNA.

Symbol: LINC01558

Ensembl ID: ENSG00000198221

Description: long intergenic non-protein coding RNA 1558

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • progenitor cell CL0011026
    CSI 4.97
    rCSI 10.57%
    PRS 97.97
  • neuroblast (sensu Nematoda and Protostomia) CL0000338
    CSI 3.71
    rCSI 4.29%
    PRS 98.06
  • radial glial cell CL0000681
    CSI 2.79
    rCSI 3.88%
    PRS 99.34
  • amacrine cell CL0000561
    CSI 2.76
    rCSI 8.01%
    PRS 97.48
  • neuroblast (sensu Vertebrata) CL0000031
    CSI 2.76
    rCSI 3.54%
    PRS 98.63
  • cerebral cortex GABAergic interneuron CL0010011
    CSI 2.46
    rCSI 7.26%
    PRS 99.32

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

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Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [LINC01558](/details-gene/26238) is a long non-coding RNA (lncRNA) located on human chromosome 6q27. While its molecular function is currently poorly characterized, its expression profile provides strong evidence for a specialized role in the nervous system. **Overall**, [LINC01558](/details-gene/26238) shows highly significant expression in neural precursor populations, including [progenitor cell](/details-cell/CL0011026)s, [neuroblast](/details-cell/CL0000031)s, and [radial glial cell](/details-cell/CL0000681)s. This pattern suggests a potential function in regulating neurogenesis, cellular differentiation, or the maintenance of neural stem cell identity. ## Cellular Roles and Expression Landscape The expression landscape of [LINC01558](/details-gene/26238) is prominently skewed towards cells of the developing and mature nervous system. Its highest cell significance index (CSI) is observed in [progenitor cell](/details-cell/CL0011026)s (CSI: 4.97), indicating it may serve as a key marker or functional regulator in this undifferentiated population. This association with neurodevelopment is further substantiated by its high significance in other neural precursor types: * [neuroblast (sensu Nematoda and Protostomia)](/details-cell/CL0000338) (CSI: 3.71) * [radial glial cell](/details-cell/CL0000681) (CSI: 2.79) * [neuroblast (sensu Vertebrata)](/details-cell/CL0000031) (CSI: 2.76) Collectively, this evidence suggests that [LINC01558](/details-gene/26238) is most active during the early stages of nervous system formation. The gene also maintains significant expression in more differentiated neuronal subtypes, such as the [amacrine cell](/details-cell/CL0000561) of the retina and the [cerebral cortex GABAergic interneuron](/details-cell/CL0010011), suggesting a sustained role in the function or maintenance of specific mature neural circuits. ## Pathways and Molecular Function The functional annotation for [LINC01558](/details-gene/26238) is currently limited to high-level, general Gene Ontology (GO) terms, which do not specify a precise molecular activity. The assigned terms include: * **Biological Process:** [Biological_process (GO:0008150)](https://www.ebi.ac.uk/QuickGO/term/GO:0008150) * **Molecular Function:** [Molecular_function (GO:0003674)](https://www.ebi.ac.uk/QuickGO/term/GO:0003674) * **Cellular Component:** [Cellular_component (GO:0005575)](https://www.ebi.ac.uk/QuickGO/term/GO:0005575) Despite the lack of specific annotations, the highly restricted expression of [LINC01558](/details-gene/26238) in neural progenitor cells strongly implies its involvement in biological pathways governing neurogenesis, cell fate determination, and nervous system development. As a lncRNA, it may function by regulating gene expression at the epigenetic or transcriptional level, or by scaffolding protein complexes. ## Research Directions The specific expression pattern of [LINC01558](/details-gene/26238) in neural precursors makes it a compelling candidate for further investigation into the mechanisms of neurodevelopment and related pathologies. **Proposed Hypotheses:** 1. [LINC01558](/details-gene/26238) is a crucial regulator for maintaining the pluripotency or undifferentiated state of neural progenitor cells. Its downregulation may be a prerequisite for terminal differentiation. 2. [LINC01558](/details-gene/26238) controls the specification of neuronal lineages, potentially promoting a GABAergic fate, as suggested by its expression in [cerebral cortex GABAergic interneuron](/details-cell/CL0010011)s. **Experimental Approach:** To test the hypothesis that [LINC01558](/details-gene/26238) is essential for neural progenitor cell maintenance, a loss-of-function study could be performed. Using CRISPR-Cas9 or antisense oligonucleotides (ASOs) to deplete [LINC01558](/details-gene/26238) in a human induced pluripotent stem cell (iPSC)-derived neural rosette model, researchers could assess the impact on progenitor self-renewal and differentiation. Subsequent single-cell RNA sequencing (scRNA-seq) would reveal shifts in cell population dynamics and identify downstream transcriptional targets, clarifying its role in developmental trajectories. **Therapeutic Potential:** Given its non-coding nature, [LINC01558](/details-gene/26238) is not a conventional drug target. However, its high specificity for neural progenitor cells could make it a target for therapeutic intervention in diseases characterized by aberrant progenitor cell activity, such as glioblastoma or other neurodevelopmental disorders. If [LINC01558](/details-gene/26238) is found to drive proliferation in a cancer context, therapeutic strategies would likely focus on **inhibition**. Modalities such as ASOs designed to target and degrade the [LINC01558](/details-gene/26238) transcript could offer a precise way to modulate its activity, though delivery across the blood-brain barrier would be a critical challenge.