Details for: CL0000767

Cell ID: CL0000767

Cell Name: basophil

Description: Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive.

Synonyms: basophilic leucocyte, basophilic leukocyte, polymorphonuclear leucocyte, polymorphonuclear leukocyte

Selected Context(s): Overall

Gene Significance Landscape

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Genes

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Cell Significance Index (CSI) is uniquely calculated to reveal cell-specific gene markers. More info here

Significant Genes List

Genes with the highest and lowest Percentile Rank Scores (PRS) for basophil within the selected context(s).

Gene ID: A unique numerical identifier for this specific gene.
Symbol: Shortened abbreviation or name that represents this gene.
Ensembl Gene ID: A unique identifier assigned by Ensembl for genomic data mapping.
CSI Score: A combined effect size and statistical significance measure for basophil. Higher scores indicate a stronger, more significant difference in expression.
(Previously described as "Fold Change", but now represents Cliff's Delta × –log10(p).)

Gene ID: A unique numerical identifier for this specific gene.
Symbol: Shortened abbreviation or name that represents this gene.
Ensembl Gene ID: A unique identifier assigned by Ensembl for genomic data mapping.
CSI Score: A combined effect size and statistical significance measure for basophil. Higher scores indicate a stronger, more significant difference in expression.
Average CSI: csi sum / gene count
Cell network configuration

This network visualizes key genes for basophil. It primarily includes:
1. Top genes highly significant for this cell (Num. Top Cell Genes - based on the 'Min. CSI' setting).
2. Any additional specific 'Context Genes' you add below.
The final network is a combined view. Choose an Interaction Source (pathways or protein interactions) and optionally compare CSI scores with a Baseline Cell Type.

Maximum number of selected genes.
Select a context for the baseline cell.
Select a context for the target cell.
Target Cell for CSI:  basophil (CL0000767)

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Node size also reflects Target Cell CSI magnitude.
Node Color (Target Cell CSI in specific network):
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 N/A or Not Sig.
Edges (Interactions):
 STRING (Protein-Protein)
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 Colors vary by pathway category; default arrow applies.

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## Summary The [basophil](/details-cell/CL0000767), a rare polymorphonuclear granulocyte originating in the bone marrow, is defined by a unique and striking transcriptional signature. **Overall**, analysis of its gene expression specificity reveals a profile dominated by genes involved in mitochondrial bioenergetics, suggesting an exceptionally high metabolic capacity. Top markers include numerous components of the electron transport chain, such as [ND3](/details-gene/4537) and [TPT1](/details-gene/7178), a protein involved in calcium binding and translation. This molecular fingerprint points to a cell that is metabolically primed for its critical roles in initiating and modulating allergic and inflammatory responses. ## Key Characteristics and Function The functional identity of the [basophil](/details-cell/CL0000767) is underscored by several distinct clusters of highly specific genes. * **Mitochondrial Bioenergetics:** A remarkable number of the top markers are mitochondrial-encoded genes essential for oxidative phosphorylation. These include multiple subunits of NADH dehydrogenase ([ND1](/details-gene/4535), [ND2](/details-gene/4536), [ND3](/details-gene/4537), [ND4](/details-gene/4538), [ND5](/details-gene/4540)), cytochrome c oxidase ([COX1](/details-gene/4512), [COX2](/details-gene/4513)), ATP synthase ([ATP6](/details-gene/4508)), and cytochrome b ([CYTB](/details-gene/4519)). The high specificity (CSI Z-SCORE) of these genes suggests that basophils possess a uniquely high or specialized capacity for aerobic respiration compared to other hematopoietic cells, likely to fuel their energy-demanding functions such as degranulation and mediator synthesis. * **Iron Homeostasis and Cellular Metabolism:** The ferritin heavy and light chain genes, [FTH1](/details-gene/2495) and [FTL](/details-gene/2512), are also highly specific markers. This indicates a specialized role for basophils in iron sequestration and management, which can be crucial for both host defense and regulating inflammatory processes. Additionally, the top marker [TPT1](/details-gene/7178), a translationally controlled tumor protein, points towards robust protein synthesis and calcium-dependent signaling pathways. * **Immune Signaling and Regulation:** The transcriptional profile highlights genes involved in rapid cellular activation and its subsequent control. The immediate early gene [FOS](/details-gene/2353), a component of the AP-1 transcription factor, suggests basophils are poised for swift response to stimuli. The high specificity of [B2M](/details-gene/567), a component of MHC class I molecules, is consistent with a role in interacting with other immune cells. Furthermore, the expression of [ZFP36](/details-gene/7538), an RNA-binding protein that promotes the degradation of inflammatory mRNA, suggests the presence of potent intrinsic negative feedback loops to temper the basophil's pro-inflammatory output. * **Lineage Distinction:** The anti-marker profile helps to define what this cell is not. The low significance for [KLRG1](/details-gene/10219), a marker for late-differentiated NK and T cells, confirms the basophil's distinct lineage from cytotoxic lymphocytes. Similarly, the low scores for various other lineage-specific markers underscore the unique identity of this granulocyte population. ## Clinical Significance and Contextual Roles **Overall**, the gene significance landscape of basophils points to their central role as potent initiators and regulators of type 2 immunity and allergic inflammation. The pronounced metabolic signature, driven by mitochondrial gene expression, is likely a prerequisite for the rapid synthesis and release of pre-formed mediators like histamine and de novo synthesized leukotrienes and cytokines upon activation, such as through IgE receptor cross-linking. The specific expression of the [FOS](/details-gene/2353) oncogene highlights their capacity for rapid transcriptional reprogramming in response to allergic or inflammatory triggers. This positions them as key early sensors in the immune system. Concurrently, the expression of regulatory molecules like [ZFP36](/details-gene/7538) is critical for homeostasis. By destabilizing the mRNAs of pro-inflammatory cytokines, ZFP36 may act as a crucial brake on the basophil's own effector functions, preventing excessive inflammation that could lead to tissue damage. Dysregulation of this balance could contribute to the pathophysiology of chronic allergic diseases such as asthma and atopic dermatitis. The prominent role of ferritin genes ([FTH1](/details-gene/2495), [FTL](/details-gene/2512)) suggests a potential, and perhaps underappreciated, link between basophil function and iron metabolism in the context of inflammation and host defense against pathogens. ## Potential Mechanisms and Research Directions 1. **The functional necessity of the unique mitochondrial signature.** * **Hypothesis:** The highly specific expression profile of mitochondrial-encoded genes in basophils is a functional adaptation to support the massive and rapid energy demands of degranulation and the synthesis of inflammatory mediators. This heightened capacity for oxidative phosphorylation may be a defining feature that enables their potent effector functions in allergic responses. * **Surprising Findings:** It is highly unusual for core metabolic genes, particularly those encoded by the mitochondrial genome, to serve as top *specificity* markers (`csi_z`). This suggests that other immune cell types in the reference dataset have a significantly lower reliance on or expression of these specific oxidative phosphorylation components, making it a distinguishing characteristic of the [basophil](/details-cell/CL0000767) lineage. * **Testable Questions:** How does pharmacological inhibition of the mitochondrial electron transport chain affect IgE-mediated degranulation and leukotriene synthesis in basophils compared to other granulocytes, such as eosinophils or neutrophils? 2. **Basophils as regulators of local iron microenvironments.** * **Hypothesis:** The specific, high-level expression of ferritin subunits [FTH1](/details-gene/2495) and [FTL](/details-gene/2512) indicates that basophils actively participate in iron sequestration at sites of inflammation. This may serve a dual purpose: limiting the availability of this essential nutrient to invading pathogens and modulating the function of other local immune cells, whose activities can be iron-dependent. * **Surprising Findings:** While macrophages are the canonical immune cells associated with iron metabolism, the high specificity of ferritin genes in basophils suggests this function may be a more integral part of basophil biology than previously recognized. * **Testable Questions:** Do activated basophils exhibit increased iron uptake, and does their degranulation release iron-laden ferritin into the extracellular space? Furthermore, does modulating intracellular iron availability affect the basophil's capacity for activation and mediator release?