Details for: CL0002319

Cell ID: CL0002319

Cell Name: neural cell

Description: A cell that is part of the nervous system.

Selected Context(s): Overall

Gene Significance Landscape

Display Options
Score:
Display
Genes

Contexts:

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 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 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 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 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.
Select a context for the baseline cell.
Select a context for the target cell.
Target Cell for CSI:  neural cell (CL0002319)

 Legend
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 A [neural cell](/details-cell/CL0002319) is a fundamental component of the nervous system, responsible for information processing and transmission. The gene significance profile underscores this role, revealing a molecular identity dominated by proteins essential for synaptic communication, electrical excitability, and the structural integrity of neural circuits. The high specificity score (`csi_z`) for the transcription factor [MYT1L](/details-gene/23040) (CSI: 28.24) suggests it is a master regulator in establishing this specialized phenotype. **Overall**, the transcriptomic signature is that of a highly specialized cell type defined by its unique machinery for cell-cell signaling and network formation rather than by ubiquitous metabolic or housekeeping functions. ## Key Characteristics and Function The defining features of a [neural cell](/details-cell/CL0002319) revolve around its capacity for electrochemical signaling and intricate connectivity. The top marker genes, identified by their highly specific expression, can be grouped into several core functional clusters. * **Synaptic Transmission and Plasticity:** A prominent group of markers is involved in neurotransmission. This includes receptors for the principal excitatory and inhibitory neurotransmitters, such as metabotropic glutamate receptors ([GRM5](/details-gene/2915), [GRID1](/details-gene/2894)), an AMPA glutamate receptor ([GRIA4](/details-gene/2893)), and GABA-A receptors ([GABRB1](/details-gene/2560), [GABRG3](/details-gene/2567)). Intracellular signaling is highlighted by [RIT2](/details-gene/6014), a neuron-specific small G-protein that regulates the MAPK cascade, suggesting a role in synaptic plasticity and survival signaling ([Link](https://doi.org/10.1523/jneurosci.16-21-06784.1996)). Furthermore, [ERC2](/details-gene/26059) is implicated in synaptic vesicle priming, a critical step in neurotransmitter release. * **Ion Channels and Membrane Excitability:** The cell's electrical properties are defined by a suite of specific ion channels. These include a voltage-gated N-type calcium channel ([CACNA1B](/details-gene/774)), a voltage-gated sodium channel ([SCN2A](/details-gene/6326)), and the hyperpolarization-activated "pacemaker" channel [HCN1](/details-gene/348980). The sodium/calcium/potassium exchanger [SLC24A2](/details-gene/25769) further underscores the critical importance of maintaining precise ionic gradients for neuronal function. * **Cell Adhesion and Synapse Organization:** A large number of top markers are cell adhesion molecules, crucial for establishing and maintaining the complex architecture of neural circuits. This includes members of the CSMD family ([CSMD3](/details-gene/114788), [CSMD2](/details-gene/114784)), the LRRTM family ([LRRTM4](/details-gene/80059), [LRRTM3](/details-gene/347731)), contactins ([CNTNAP5](/details-gene/129684), [CNTN1](/details-gene/1272)), and other adhesion proteins like [KIRREL3](/details-gene/84623), [CDH9](/details-gene/1007), and [OPCML](/details-gene/4978). This extensive and diverse repertoire of adhesion molecules suggests a sophisticated molecular code for synaptic targeting and network stability. * **Neural Development and Regulation:** The top marker, [MYT1L](/details-gene/23040), is a DNA-binding transcription factor involved in neurogenesis. Its exceptionally high specificity highlights its role as a key determinant of neuronal identity. The neuregulin [NRG3](/details-gene/10718), a ligand for the ErbB4 receptor, is also highly specific and known to be involved in nervous system development and oligodendrocyte survival ([Link](https://doi.org/10.1242/jcs.02799)). Conversely, the anti-markers for this cell type are dominated by genes involved in ubiquitous cellular processes. The strong negative CSI values for multiple mitochondrial genes involved in the electron transport chain (e.g., [ND1](/details-gene/4535), [CYTB](/details-gene/4519), [COX2](/details-gene/4513), [ATP6](/details-gene/4508)) do not imply a lack of mitochondria, but rather indicate that the expression of these core metabolic genes is not a unique or specific feature compared to other cell types. Similarly, genes involved in general translation ([EEF1B2](/details-gene/1933)), RNA processing ([HNRNPA2B1](/details-gene/3181), [DDX5](/details-gene/1655)), and antiproliferation ([BTG1](/details-gene/694)) are negatively associated, further reinforcing that the identity of a [neural cell](/details-cell/CL0002319) is defined by its specialized synaptic and electrical functions, not these fundamental housekeeping roles. ## Clinical Significance and Contextual Roles The gene expression profile of [neural cells](/details-cell/CL0002319) directly implicates them in a range of neurological and developmental disorders. The high specificity of genes whose dysfunction is linked to disease highlights the cell's vulnerability. **Overall**, the enrichment for genes involved in synaptic function and excitability provides a molecular basis for disorders like epilepsy, neurodevelopmental conditions, and neurodegeneration. For instance, [CSMD3](/details-gene/114788) has been identified as a candidate gene for benign adult familial myoclonic epilepsy ([Link](https://doi.org/10.1016/s0006-291x(03)01555-9)). Genes encoding voltage-gated ion channels, such as [SCN2A](/details-gene/6326) and [CACNA1B](/details-gene/774), are well-established members of gene families linked to various channelopathies, including epilepsies and developmental encephalopathies. The specific expression of these channels in [neural cells](/details-cell/CL0002319) makes these cells the primary site of pathology when mutations occur. The prevalence of cell adhesion molecules ([LRRTM4](/details-gene/80059), [CNTNAP5](/details-gene/129684), [KIRREL3](/details-gene/84623)) as defining markers is significant, as disruptions in these molecules are increasingly associated with autism spectrum disorders and schizophrenia. These genes are essential for building and maintaining correct synaptic connections, and their specific expression in [neural cells](/details-cell/CL0002319) suggests that aberrant expression could lead to mis-wiring of neural circuits, a proposed etiology for several neuropsychiatric conditions. The significance of [NRG3](/details-gene/10718) is also notable, as the neuregulin signaling pathway has been genetically linked to schizophrenia. ## Potential Mechanisms and Research Directions 1. **Hypothesis:** The high expression specificity of the CUB and sushi domain-containing proteins [CSMD3](/details-gene/114788) and [CSMD2](/details-gene/114784) suggests they function as critical, non-redundant organizers of specific synaptic connections or microdomains within the [neural cell](/details-cell/CL0002319) membrane, and their dysfunction contributes directly to neurological disorders like epilepsy. * **Surprising Findings:** It is noteworthy that proteins from the CSMD family, first implicated as tumor suppressors in epithelial tissues ([Link](https://doi.org/10.1016/s0888-7543(03)00149-6)), are among the most specific markers for [neural cells](/details-cell/CL0002319). This dual context suggests a conserved role in regulating cell-cell interactions that is repurposed for synaptic organization in the nervous system. * **Testable Questions:** What are the specific binding partners of [CSMD2](/details-gene/114784) and [CSMD3](/details-gene/114788) at the synapse? Does the conditional knockout of these genes in mature neurons lead to altered synaptic protein composition, reduced synapse density, or electrophysiological defects consistent with the epileptic phenotype observed in human studies? 2. **Hypothesis:** The transcription factor [MYT1L](/details-gene/23040) and the neuron-specific G-protein [RIT2](/details-gene/6014) operate in a coordinated regulatory axis, where [MYT1L](/details-gene/23040) establishes a neuronal identity that includes high-level expression of [RIT2](/details-gene/6014), which in turn integrates extracellular signals via the MAPK pathway to maintain the mature, functional state of the [neural cell](/details-cell/CL0002319). * **Surprising Findings:** While the roles of [MYT1L](/details-gene/23040) in development and [RIT2](/details-gene/6014) in signaling are known, their co-emergence as top *specificity* markers is striking. It suggests that the [RIT2](/details-gene/6014)-mediated signaling pathway is not just an active "workhorse" pathway but is itself a core component of the cell's defined identity, on par with a master transcriptional regulator. * **Testable Questions:** Does chromatin immunoprecipitation sequencing (ChIP-seq) for [MYT1L](/details-gene/23040) in a neuronal model system reveal direct binding to the regulatory regions of the [RIT2](/details-gene/6014) gene? Conversely, does the inhibition of [RIT2](/details-gene/6014) activity lead to destabilization of the neuronal transcriptome, potentially through feedback mechanisms that alter [MYT1L](/details-gene/23040) expression or activity?