Details for: SOX1

Gene ID: 6656

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: SOX1

Ensembl ID: ENSG00000182968

Description: SRY-box transcription factor 1

Cell Significance Landscape

Associated with

Significant Cells

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

  • glial cell CL0000125
    CSI 7.68
    rCSI 29.24%
    PRS 99.55
  • neural progenitor cell CL0011020
    CSI 7.5
    rCSI 33.01%
    PRS 98.06
  • cerebral cortex GABAergic interneuron CL0010011
    CSI 5.86
    rCSI 17.31%
    PRS 100
  • VIP GABAergic cortical interneuron CL4023016
    CSI 5.71
    rCSI 6.82%
    PRS 99.74
  • GABAergic neuron CL0000617
    CSI 4.39
    rCSI 14.72%
    PRS 98.87
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 2.61
    rCSI 4.37%
    PRS 99.76
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 2.25
    rCSI 3.97%
    PRS 99.7

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 [SOX1](/details-gene/6656) is a protein-coding gene located on chromosome 13q34 that encodes SRY-box transcription factor 1, a member of the SOX (SRY-related HMG-box) family of DNA-binding proteins. Functionally, [SOX1](/details-gene/6656) is a critical regulator of embryonic development, particularly in neurogenesis. Its involvement in processes such as `[brain development](/details-cell/GO:0007420)` and `[neuron differentiation](/details-cell/GO:0030182)` is substantiated by its high expression significance in neural cell types. **Overall**, it is a defining marker for `[glial cell](/details-cell/CL0000125)` and `[neural progenitor cell](/details-cell/CL0011020)`, underscoring its role in both the establishment and maintenance of the central nervous system. Its clinical relevance is noted in OMIM ([602148](https://omim.org/entry/602148)). ## Cellular Roles and Expression Landscape The expression profile of [SOX1](/details-gene/6656) reveals a highly specific role within the nervous system. **Overall**, the gene shows the highest significance in cell types integral to neural development and function. It is a top marker in `[neural progenitor cell](/details-cell/CL0011020)` (CSI: 7.50) and `[glial cell](/details-cell/CL0000125)` (CSI: 7.68), indicating a fundamental role in the generation and support of neural tissues. Beyond progenitor and glial populations, [SOX1](/details-gene/6656) demonstrates significant expression in mature, specialized neuronal subtypes, particularly inhibitory interneurons. It is highly significant in `[cerebral cortex GABAergic interneuron](/details-cell/CL0010011)` (CSI: 5.86), `[VIP GABAergic cortical interneuron](/details-cell/CL4023016)` (CSI: 5.71), and `[GABAergic neuron](/details-cell/CL0000617)` more broadly (CSI: 4.39). This expression pattern suggests that in addition to its developmental functions, [SOX1](/details-gene/6656) may be involved in maintaining the identity and function of these specific interneuron circuits in the brain. The consistent and high significance across these related cell types points to [SOX1](/details-gene/6656) as a core transcriptional regulator in the neural lineage, as initially described in early cloning studies ([Link](https://pubmed.ncbi.nlm.nih.gov/9337405/)). ## Pathways and Molecular Function [SOX1](/details-gene/6656) functions as a transcription factor located in the `[nucleus](/details-cell/GO:0005634)`, where it engages in `[dna-binding transcription factor activity, rna polymerase ii-specific](/details-cell/GO:0000981)`. Its primary role is to modulate gene expression programs that drive cell fate decisions during embryogenesis. This is supported by its association with fundamental developmental pathways in Reactome, including `[Developmental biology](/details-pathway/R-HSA-1266738)` and `[Gastrulation](/details-pathway/R-HSA-9758941)`. The gene's specific involvement in the nervous system is highlighted by its role in processes such as `[forebrain neuron development](/details-cell/GO:0021884)` and `[regulation of oligodendrocyte differentiation](/details-cell/GO:0048713)`. These annotated functions are highly consistent with its observed cellular expression pattern in neural progenitors and glia. Furthermore, its participation in Reactome pathways like `[Formation of the anterior neural plate](/details-pathway/R-HSA-9823739)` places it at the earliest stages of central nervous system specification, solidifying its status as a master regulator of neurogenesis. ## Research Directions Given that [SOX1](/details-gene/6656) is a key developmental transcription factor, research should focus on elucidating its precise regulatory mechanisms and its potential for therapeutic applications in regenerative medicine. ### Proposed Hypotheses: 1. The high significance of [SOX1](/details-gene/6656) in both `[neural progenitor cell](/details-cell/CL0011020)` and multiple mature `[GABAergic neuron](/details-cell/CL0000617)` subtypes suggests it performs a dual role: initiating a neurogenic program in progenitors and later contributing to the maintenance of the specific transcriptional identity of inhibitory interneurons in the adult brain. 2. Based on its role in `[regulation of oligodendrocyte differentiation](/details-cell/GO:0048713)` and its high expression in `[glial cell](/details-cell/CL0000125)`, [SOX1](/details-gene/6656) may act as a critical switch point that governs the balance between neurogenesis and gliogenesis from a common progenitor pool. Dysregulation of [SOX1](/details-gene/6656) could therefore contribute to diseases characterized by either abnormal neuronal development or defects in myelination. ### Key Experiment: To test the second hypothesis regarding its role as a fate switch, one could utilize an *in vitro* differentiation model of human pluripotent stem cells (hPSCs). By engineering an hPSC line with a doxycycline-inducible CRISPR interference (CRISPRi) system targeting [SOX1](/details-gene/6656), its expression can be suppressed at specific stages of neural differentiation. Following knockdown, cell populations could be analyzed via single-cell RNA sequencing (scRNA-seq) to quantitatively assess whether the loss of [SOX1](/details-gene/6656) function skews progenitor differentiation away from neuronal fates and towards oligodendrocyte or astrocyte lineages, as identified by key marker gene expression (e.g., OLIG2, GFAP). ### Therapeutic Potential: As an intracellular transcription factor, [SOX1](/details-gene/6656) is not a conventional drug target for small molecule inhibition. However, its potent ability to drive neurogenesis makes it a highly valuable tool in the field of regenerative medicine. The controlled expression or activation of [SOX1](/details-gene/6656), potentially in combination with other transcription factors, could be a key strategy to improve protocols for the directed differentiation of stem cells into specific, clinically relevant neuronal subtypes. This approach could facilitate the development of cell replacement therapies for neurodegenerative disorders such as Parkinson's disease or spinal cord injury.

Genular Protein ID: 180154708

Symbol: SOX1_HUMAN

Name: Transcription factor SOX-1

UniProtKB Accession Codes:

O00570 Q5W0Q1

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CDD 1 CTD 1 DNASU 1 DisGeNET 1 EMBL 3 Ensembl 1 GO 19 Gene3D 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 4 KEGG 1 MANE-Select 1 MIM 1 MINT 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRO 1 PROSITE 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 2 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 RNAct 1 Reactome 2 RefSeq 1 SMART 1 SMR 1 STRING 1 SUPFAM 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 9337405

Title: Cloning and mapping of the human SOX1: a highly conserved gene expressed in the developing brain.

PubMed ID: 9337405

DOI: 10.1007/s003359900597

PubMed ID: 15057823

Title: The DNA sequence and analysis of human chromosome 13.

PubMed ID: 15057823

DOI: 10.1038/nature02379

Sequence Information:

  • Length: 391
  • Mass: 39023
  • Checksum: DD519BA97CF5E052
  • Sequence:
    • MYSMMMETDL HSPGGAQAPT NLSGPAGAGG GGGGGGGGGG GGGAKANQDR VKRPMNAFMV 
WSRGQRRKMA QENPKMHNSE ISKRLGAEWK VMSEAEKRPF IDEAKRLRAL HMKEHPDYKY 
RPRRKTKTLL KKDKYSLAGG LLAAGAGGGG AAVAMGVGVG VGAAAVGQRL ESPGGAAGGG 
YAHVNGWANG AYPGSVAAAA AAAAMMQEAQ LAYGQHPGAG GAHPHAHPAH PHPHHPHAHP 
HNPQPMHRYD MGALQYSPIS NSQGYMSASP SGYGGLPYGA AAAAAAAAGG AHQNSAVAAA 
AAAAAASSGA LGALGSLVKS EPSGSPPAPA HSRAPCPGDL REMISMYLPA GEGGDPAAAA 
AAAAQSRLHS LPQHYQGAGA GVNGTVPLTH I