Details for: CL0011012

Cell ID: CL0011012

Cell Name: neural crest cell

Description: A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.

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 neural crest cell 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 neural crest cell. 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 neural crest cell. 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 neural crest cell. 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.
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Select a context for the target cell.
Target Cell for CSI:  neural crest cell (CL0011012)

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Nodes (Genes):
 Query Gene
Node size also reflects Target Cell CSI magnitude.
Node Color (Target Cell CSI in specific network):
 Very High
 High
 Medium
 Low
 Very Low
 N/A or Not Sig.
Edges (Interactions):
 STRING (Protein-Protein)
 ONTOLOGY (Shared Pathway)
 Colors vary by pathway category; default arrow applies.

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## Summary The [neural crest cell](/details-cell/CL0011012) is a multipotent, migratory cell population fundamental to vertebrate embryonic development. The gene significance profile underscores this role by revealing an exceptionally high and specific expression of genes involved in core cellular processes. Top markers are dominated by genes regulating chromatin architecture ([`HMGB1`](/details-gene/3146)), energy metabolism ([`GAPDH`](/details-gene/2597), [`COX1`](/details-gene/4512)), and ribosome biogenesis/RNA processing ([`NPM1`](/details-gene/4869), [`HNRNPA2B1`](/details-gene/3181)). This signature is consistent with a cell type that is highly metabolically active and transcriptionally plastic, primed for proliferation, long-range migration, and differentiation into a diverse array of cell lineages, including neurons, glia, and craniofacial cartilage. ## Key Characteristics and Function **Overall**, the gene expression profile of the [neural crest cell](/details-cell/CL0011012) is defined by a robust machinery for cellular maintenance, growth, and plasticity, rather than by a narrow set of lineage-specific markers. This reflects its identity as a transient, multipotent progenitor population. Key functional themes emerge from the top marker genes: * **High Metabolic Activity:** A prominent cluster of top markers is associated with energy production. This includes the glycolytic enzyme [`GAPDH`](/details-gene/2597) and numerous components of the mitochondrial electron transport chain, such as [`COX1`](/details-gene/4512), [`ND4`](/details-gene/4538), [`COX7C`](/details-gene/1350), [`ATP5MC2`](/details-gene/517), [`COX2`](/details-gene/4513), and [`NDUFA4`](/details-gene/4697). The high specificity (CSI Z-Score) of these genes suggests that an elevated metabolic state is a defining characteristic, likely fueling the high energetic demands of migration and proliferation during embryogenesis. * **Dynamic Transcriptional and Translational Regulation:** The cell exhibits a strong signature of genes involved in the biogenesis and processing of macromolecules. [`NPM1`](/details-gene/4869) is crucial for ribosome biogenesis, while heterogeneous nuclear ribonucleoproteins like [`HNRNPA2B1`](/details-gene/3181) and [`HNRNPDL`](/details-gene/9987) are key for mRNA splicing and metabolism. Furthermore, [`SRP14`](/details-gene/6727) is a component of the signal recognition particle, essential for protein targeting. This indicates a high capacity for protein synthesis, necessary for rapid cellular remodeling and differentiation. * **Chromatin Plasticity and Gene Regulation:** The top-ranked marker, [`HMGB1`](/details-gene/3146), is a non-histone chromatin protein that bends DNA and facilitates the assembly of transcription factor complexes, suggesting it plays a critical role in maintaining a plastic chromatin state permissive for broad transcriptional potential. This is further supported by the high significance of histone variant [`H3 3B`](/details-gene/3021) and the DNA/RNA-binding protein [`YBX1`](/details-gene/4904). * **Cytoskeletal Remodeling and Migration:** The high significance of genes like [`CFL1`](/details-gene/1072) (cofilin), an actin-depolymerizing factor, and [`MYL6`](/details-gene/4637) (myosin light chain) is consistent with the highly migratory nature of [neural crest cells](/details-cell/CL0011012). These proteins are essential for the dynamic regulation of the actin cytoskeleton required for cell movement. The list of least significant genes does not contain strong negative markers for specific alternative lineages, which is consistent with the multipotent and undifferentiated state of this cell type. ## Clinical Significance and Contextual Roles Given the singular **Overall** context, this analysis focuses on the general biological roles of the top markers and their implications for development and disease. The [neural crest cell](/details-cell/CL0011012) is the cell of origin for several pediatric cancers, most notably neuroblastoma, and defects in its development lead to a class of disorders known as neurocristopathies. The profile highlights genes implicated in cancer and cellular stress responses. [`HMGB1`](/details-gene/3146), the most specific marker, is known to be released from cells as a damage-associated molecular pattern (DAMP) that can promote inflammation and tumor progression ([Link](https://pubmed.ncbi.nlm.nih.gov/9036861/)). The high expression of housekeeping genes like [`GAPDH`](/details-gene/2597) is a common feature of rapidly proliferating cells, including many cancers. Similarly, [`NPM1`](/details-gene/4869) is frequently overexpressed in solid tumors and is involved in both ribosome biogenesis and the regulation of tumor suppressors like p53. The detoxification enzyme [`GSTP1`](/details-gene/2950) has a role in cellular response to oxidative stress, a critical factor during both normal development and pathological conditions. The pronounced metabolic signature, particularly the reliance on both glycolysis ([`GAPDH`](/details-gene/2597)) and oxidative phosphorylation (e.g., [`COX1`](/details-gene/4512)), points to a metabolic flexibility that is crucial for migrating through diverse embryonic microenvironments. Dysregulation of this metabolic plasticity could be a key factor in the pathogenesis of neurocristopathies or the malignant transformation into neuroblastoma. ## Potential Mechanisms and Research Directions 1. **Hypothesis: Metabolic state as a primary determinant of neural crest cell fate.** The data reveals that genes for energy metabolism are not merely 'housekeeping' but are among the most uniquely defining features of [neural crest cells](/details-cell/CL0011012). We hypothesize that the high and specific expression of both glycolytic and oxidative phosphorylation machinery reflects a state of metabolic plasticity that is actively regulated to control the switch between proliferation, migration, and differentiation. * **Surprising Findings:** The striking specificity (high CSI Z-Score) of fundamental metabolic genes like [`GAPDH`](/details-gene/2597) and [`COX1`](/details-gene/4512) is unexpected. It suggests that the quantitative level of metabolic flux, rather than just the presence of these pathways, is a key aspect of the [neural crest cell's](/details-cell/CL0011012) identity. * **Testable Questions:** How does targeted inhibition of glycolysis versus oxidative phosphorylation affect the migratory capacity and differentiation potential of [neural crest cells](/details-cell/CL0011012) into neuronal, glial, and mesenchymal lineages in vitro? Does the metabolic profile (e.g., lactate production vs. oxygen consumption) change dynamically as these cells commit to a specific fate? 2. **Hypothesis: Global chromatin accessibility maintained by HMGB1 is essential for multipotency.** The top marker is [`HMGB1`](/details-gene/3146), a general chromatin architectural protein, rather than a lineage-specific transcription factor. We hypothesize that [`HMGB1`](/details-gene/3146) is a cornerstone of the [neural crest cell](/details-cell/CL0011012) identity, maintaining a globally "open" and poised chromatin state. This permissive architecture, coupled with robust RNA processing machinery ([`HNRNPA2B1`](/details-gene/3181), [`NPM1`](/details-gene/4869)), allows for rapid transcriptional responses to diverse environmental cues encountered during migration, thereby underpinning their multipotency. * **Surprising Findings:** The prominence of a general chromatin regulator over canonical neural crest specifiers (e.g., SOX10, SNAIL) as the top defining marker suggests that maintaining developmental potential via chromatin landscape is a more unique feature of this cell state than the expression of any single master regulator. * **Testable Questions:** Does depletion of [`HMGB1`](/details-gene/3146) in embryonic stem cell-derived [neural crest cells](/details-cell/CL0011012) lead to a global reduction in chromatin accessibility (as measured by ATAC-seq) and a restricted differentiation potential? Can overexpression of [`HMGB1`](/details-gene/3146) enhance the reprogramming of other cell types towards a neural crest-like state?