Details for: LINC00426

Gene ID: 100188949

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: LINC00426

Ensembl ID: ENSG00000238121

Description: long intergenic non-protein coding RNA 426

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

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

  • late pro-B cell CL0002048
    CSI 7.67
    rCSI 19.21%
    PRS 96
  • lymphoid lineage restricted progenitor cell CL0000838
    CSI 4.59
    rCSI 17.87%
    PRS 97.2
  • early lymphoid progenitor CL0000936
    CSI 3.74
    rCSI 3.28%
    PRS 92.21
  • double negative thymocyte CL0002489
    CSI 3.67
    rCSI 2.55%
    PRS 96.33
  • small pre-B-II cell CL0000954
    CSI 3.37
    rCSI 3.24%
    PRS 96.05
  • plasmablast CL0000980
    CSI 2.95
    rCSI 2.32%
    PRS 91.4
  • mature T cell CL0002419
    CSI 2.82
    rCSI 2.19%
    PRS 96.47
  • precursor B cell CL0000817
    CSI 2.67
    rCSI 2.34%
    PRS 93.14
  • CD4-positive, CD25-positive, alpha-beta regulatory T cell CL0000792
    CSI 2.47
    rCSI 2.43%
    PRS 96.93
  • double-positive, alpha-beta thymocyte CL0000809
    CSI 2.45
    rCSI 2.5%
    PRS 94.34
  • fraction A pre-pro B cell CL0002045
    CSI 2.45
    rCSI 2.8%
    PRS 93.82
  • pro-B cell CL0000826
    CSI 2.45
    rCSI 2.03%
    PRS 90.5
  • effector memory CD8-positive, alpha-beta T cell CL0000913
    CSI 2.4
    rCSI 2.19%
    PRS 96.12
  • T follicular helper cell CL0002038
    CSI 2.32
    rCSI 1.73%
    PRS 96.19
  • effector CD4-positive, alpha-beta T cell CL0001044
    CSI 1.57
    rCSI 4.5%
    PRS 98.01
  • common lymphoid progenitor CL0000051
    CSI 1.56
    rCSI 2.09%
    PRS 97.15

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.

Comma-separated if multiple.
Comma-separated if multiple.
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 [LINC00426](/details-gene/100188949), or Long Intergenic Non-Protein Coding RNA 426, is a non-coding RNA gene located on chromosome 13. Expression data indicates that [LINC00426](/details-gene/100188949) is a highly specific marker of the lymphoid lineage within the hematopoietic system. Its significance is particularly pronounced during the early stages of B lymphocyte development, with the highest expression observed in [late pro-B cell](/details-cell/CL0002048)s. The gene also shows notable expression across various stages of T cell development and in mature T cell subsets, suggesting a fundamental regulatory role in the adaptive immune system. ## Cellular Roles and Expression Landscape The expression profile of [LINC00426](/details-gene/100188949) points to a specialized function in lymphopoiesis. **Overall**, the data reveals its highest significance in developing B lymphocytes, positioning it as a key molecular player in this process. It is most prominent in [late pro-B cell](/details-cell/CL0002048) (CSI: 7.67), a critical stage of B cell commitment, and also shows high significance in upstream progenitors like the [lymphoid lineage restricted progenitor cell](/details-cell/CL0000838) (CSI: 4.59) and [early lymphoid progenitor](/details-cell/CL0000936) (CSI: 3.74). This pattern of expression across the B cell developmental trajectory, including [fraction A pre-pro B cell](/details-cell/CL0002045), [pro-B cell](/details-cell/CL0000826), and [small pre-B-II cell](/details-cell/CL0000954), suggests its involvement in establishing B cell identity. Beyond the B cell lineage, [LINC00426](/details-gene/100188949) is also consistently expressed in T cells. Its significance is noted in early thymic precursors, such as the [double negative thymocyte](/details-cell/CL0002489), as well as in more mature populations like [mature T cell](/details-cell/CL0002419)s, [effector memory CD8-positive, alpha-beta T cell](/details-cell/CL0000913)s, and [CD4-positive, CD25-positive, alpha-beta regulatory T cell](/details-cell/CL0000792)s. This broader expression across the lymphoid compartment suggests that its function may not be exclusively restricted to B cells but may encompass shared regulatory networks governing the development and function of all lymphocytes. ## Pathways and Molecular Function While detailed functional annotations for [LINC00426](/details-gene/100188949) are not specified in the provided data, its distinct expression pattern allows for functional inference. As a long non-coding RNA highly expressed during early lymphocyte development, it is likely involved in the epigenetic or transcriptional regulation of key developmental genes. Its peak expression in pro-B and pre-B cells suggests a potential role in processes central to this stage, such as the regulation of transcription factors (e.g., EBF1, PAX5), or the control of V(D)J recombination of the immunoglobulin heavy chain locus. Its presence in T cell progenitors similarly implies a possible role in T cell receptor gene rearrangement or lineage commitment within the thymus. ## Research Directions The highly specific expression of [LINC00426](/details-gene/100188949) in lymphoid progenitors warrants further investigation to elucidate its precise molecular functions and clinical relevance. **Proposed Hypotheses:** 1. [LINC00426](/details-gene/100188949) is an essential regulator for the pro-B to pre-B cell transition. Its knockdown or knockout would be expected to cause a developmental block at the [pro-B cell](/details-cell/CL0000826) stage, preventing the successful rearrangement and expression of the pre-B cell receptor. 2. The expression of [LINC00426](/details-gene/100188949) is aberrantly regulated in B-cell acute lymphoblastic leukemia (B-ALL), where it may act as an oncogene by promoting the proliferation or survival of malignant B cell precursors. 3. In T cells, [LINC00426](/details-gene/100188949) may be involved in the maintenance of cellular identity or the regulation of effector functions, particularly in subsets like [T follicular helper cell](/details-cell/CL0002038)s where it is significantly expressed. **Key Experimental Approach:** To test the hypothesis that [LINC00426](/details-gene/100188949) is critical for B cell development (Hypothesis 1), a CRISPR-Cas9-mediated knockout could be performed in primary murine or human hematopoietic stem and progenitor cells (HSPCs). These genetically modified HSPCs would then be co-cultured on stromal cells (e.g., OP9) that support *in vitro* B-lymphopoiesis. The developmental progression of B cells from control versus knockout HSPCs would be tracked over time using flow cytometry to quantify distinct populations based on surface markers (e.g., B220, CD43, CD19, BP-1, IgM). A significant accumulation of cells at the [pro-B cell](/details-cell/CL0000826) stage in the knockout condition would provide strong evidence for its essential role. Subsequent RNA-sequencing on sorted progenitor populations could then identify the downstream gene networks regulated by [LINC00426](/details-gene/100188949). **Therapeutic Potential:** As a non-coding RNA, [LINC00426](/details-gene/100188949) is not a conventional drug target. However, its high specificity for lymphoid progenitors makes it an attractive candidate for novel therapeutic strategies. If its function is proven to be oncogenic in lymphoid malignancies, therapies based on antisense oligonucleotides (ASOs) or siRNAs could be developed to specifically inhibit its expression in cancerous cells. This approach would offer high target specificity, potentially minimizing off-target effects on non-hematopoietic tissues. Furthermore, its restricted expression profile suggests it could serve as a highly sensitive biomarker for the detection of minimal residual disease in B-ALL patients following treatment.