Details for: ZBED3

Gene ID: 84327

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: ZBED3

Ensembl ID: ENSG00000132846

Description: zinc finger BED-type containing 3

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

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

  • neural crest cell CL0011012
    CSI 3.94
    rCSI 3.12%
    PRS 93.7
  • bronchus fibroblast of lung CL2000093
    CSI 3.63
    rCSI 2.95%
    PRS 96.72
  • epithelial cell CL0000066
    CSI 3.02
    rCSI 4.65%
    PRS 88.06
  • hematopoietic precursor cell CL0008001
    CSI 3
    rCSI 3.08%
    PRS 98.3
  • common myeloid progenitor CL0000049
    CSI 2.92
    rCSI 2.36%
    PRS 97.47
  • mesodermal cell CL0000222
    CSI 2.91
    rCSI 3.5%
    PRS 96.79
  • stem cell CL0000034
    CSI 2.82
    rCSI 2.72%
    PRS 94.95
  • granulocyte monocyte progenitor cell CL0000557
    CSI 2.8
    rCSI 2.42%
    PRS 97.45
  • megakaryocyte-erythroid progenitor cell CL0000050
    CSI 2.67
    rCSI 2.41%
    PRS 96.23
  • hematopoietic stem cell CL0000037
    CSI 2.65
    rCSI 1.76%
    PRS 97.4
  • cerebral cortex endothelial cell CL1001602
    CSI 2.59
    rCSI 4.47%
    PRS 94.03
  • glioblast CL0000030
    CSI 2.41
    rCSI 3.84%
    PRS 92.1
  • VIP GABAergic cortical interneuron CL4023016
    CSI 2.38
    rCSI 2.85%
    PRS 90.15
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 2.33
    rCSI 2.9%
    PRS 88.56
  • hematopoietic multipotent progenitor cell CL0000837
    CSI 1.96
    rCSI 4.71%
    PRS 98.79
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 1.8
    rCSI 3.02%
    PRS 90.24
  • endothelial cell of vascular tree CL0002139
    CSI 1.79
    rCSI 9.8%
    PRS 93.71
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 1.75
    rCSI 3.1%
    PRS 89.87
  • astrocyte of the cerebral cortex CL0002605
    CSI 1.73
    rCSI 3.88%
    PRS 90.44
  • pancreatic ductal cell CL0002079
    CSI 1.27
    rCSI 2.46%
    PRS 96.65
  • podocyte CL0000653
    CSI 0.99
    rCSI 4.42%
    PRS 96.4

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)

Loading network (please wait)...

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 [ZBED3](/details-gene/84327) (zinc finger BED-type containing 3) is a protein-coding gene located on chromosome 5q13.3. It encodes a zinc finger BED domain-containing protein that functions as a DNA-binding transcription factor. Functional annotations suggest its involvement in a diverse range of cellular processes, including the [positive regulation of canonical wnt signaling pathway](/details-go/GO:0090263), [actin filament organization](/details-go/GO:0007015), and the [response to insulin](/details-go/GO:0032868). Expression data indicates that **Overall**, [ZBED3](/details-gene/84327) is a significant gene in various progenitor and developmental cell types, such as [neural crest cell](/details-cell/CL0011012), [hematopoietic precursor cell](/details-cell/CL0008001), and [stem cell](/details-cell/CL0000034), as well as in structural cells like [bronchus fibroblast of lung](/details-cell/CL2000093), highlighting its potential roles in development, differentiation, and tissue homeostasis. ## Cellular Roles and Expression Landscape The expression profile of [ZBED3](/details-gene/84327) suggests a broad but significant role in undifferentiated and developing cell populations. **Overall**, it shows the highest significance in [neural crest cell](/details-cell/CL0011012) (CSI: 3.94), a multipotent embryonic cell population, which is consistent with its annotated role in [positive regulation of embryonic development](/details-go/GO:0040019). The gene is also highly significant across the hematopoietic lineage, from primitive progenitors like [hematopoietic precursor cell](/details-cell/CL0008001) (CSI: 3.00) and [hematopoietic stem cell](/details-cell/CL0000037) (CSI: 2.65) to more committed progenitors such as [common myeloid progenitor](/details-cell/CL0000049) (CSI: 2.92) and [granulocyte monocyte progenitor cell](/details-cell/CL0000557) (CSI: 2.80). This pattern suggests [ZBED3](/details-gene/84327) may be involved in maintaining pluripotency or guiding lineage commitment within the hematopoietic system. Beyond progenitor cells, [ZBED3](/details-gene/84327) demonstrates notable significance in structural and stromal cells, including [bronchus fibroblast of lung](/details-cell/CL2000093) (CSI: 3.63) and [epithelial cell](/details-cell/CL0000066) (CSI: 3.02). Its expression is also observed in various central nervous system cells, such as [cerebral cortex endothelial cell](/details-cell/CL1001602) (CSI: 2.59), [glioblast](/details-cell/CL0000030) (CSI: 2.41), and specific interneuron populations like [VIP GABAergic cortical interneuron](/details-cell/CL4023016) (CSI: 2.38). This widespread, yet specific, expression pattern points towards fundamental roles in cell regulation across multiple tissues. ## Pathways and Molecular Function [ZBED3](/details-gene/84327) is annotated as a [dna-binding transcription factor activity, rna polymerase ii-specific](/details-go/GO:0000981), indicating a primary role in gene expression regulation. This function is central to its involvement in the [wnt signaling pathway](/details-go/GO:0016055), where it is known to positively regulate the canonical branch ([GO:0090263](https://www.ebi.ac.uk/QuickGO/term/GO:0090263)). This pathway is critical for embryonic development and tissue homeostasis, which aligns with the gene's high expression in progenitor and stem cell populations. The protein is also associated with metabolic processes, specifically the [response to glucose](/details-go/GO:0009749) and [response to insulin](/details-go/GO:0032868). This is strongly supported by research identifying [ZBED3](/details-gene/84327) as a novel secreted protein associated with insulin resistance in humans ([Link](https://doi.org/10.1111/joim.12170)). Its GO annotation to the [extracellular space](/details-go/GO:0005615), in addition to the [cytoplasm](/details-go/GO:0005737) and [chromatin](/details-go/GO:0000785), is consistent with a dual function as both an intracellular transcription factor and a secreted signaling molecule. Additionally, [ZBED3](/details-gene/84327) participates in structural and organizational processes within the cell, including [actin filament organization](/details-go/GO:0007015) and the [establishment of spindle localization](/details-go/GO:0051293), suggesting it may influence cell morphology, division, and integrity. ## Research Directions The dual localization and function of [ZBED3](/details-gene/84327) as both an intracellular transcription factor linked to Wnt signaling and a secreted protein implicated in metabolic disease present compelling avenues for future research. **Proposed Hypotheses:** 1. Given its high significance in hematopoietic progenitors and its role in Wnt signaling, [ZBED3](/details-gene/84327) may act as a crucial regulator of hematopoietic stem cell self-renewal versus differentiation. Dysregulation of its expression could contribute to hematopoietic disorders by altering the balance of this cell fate decision. 2. Based on evidence that it is a secreted protein associated with insulin resistance ([Link](https://doi.org/10.1111/joim.12170)), secreted [ZBED3](/details-gene/84327) from stromal cells like [bronchus fibroblast of lung](/details-cell/CL2000093) may function as a paracrine factor that directly impairs insulin signaling in metabolically active tissues, such as liver, muscle, or adipose tissue. **Suggested Experimental Approach:** To test the second hypothesis regarding the paracrine effects of secreted [ZBED3](/details-gene/84327) on insulin resistance, a co-culture experiment could be designed. Fibroblasts engineered to overexpress and secrete [ZBED3](/details-gene/84327) would be co-cultured with a metabolically active cell line, such as HepG2 hepatocytes. The impact on insulin sensitivity in the hepatocytes would be assessed by measuring insulin-stimulated glucose uptake and the phosphorylation status of key insulin signaling pathway proteins, like AKT and GSK3B, via western blot. **Therapeutic Potential:** The role of secreted [ZBED3](/details-gene/84327) in promoting insulin resistance makes it a potential therapeutic target for type 2 diabetes and metabolic syndrome. A strategy focused on **inhibition** would be most appropriate. The development of a neutralizing monoclonal antibody that specifically targets the extracellular form of [ZBED3](/details-gene/84327) could block its systemic effects on insulin signaling. This approach offers the advantage of high specificity for the secreted, disease-associated protein while potentially sparing its intracellular functions in transcription and development.

Genular Protein ID: 3328789058

Symbol: ZBED3_HUMAN

Name: Zinc finger BED domain-containing protein 3

UniProtKB Accession Codes:

Q96IU2

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CTD 1 ChEBI 4 ChiTaRS 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 2 Ensembl 1 ExpressionAtlas 1 GO 21 GeneCards 1 GeneTree 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 3 KEGG 1 MANE-Select 1 MIM 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 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 Pumba 1 RNAct 1 RefSeq 2 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: 15372022

Title: The DNA sequence and comparative analysis of human chromosome 5.

PubMed ID: 15372022

DOI: 10.1038/nature02919

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 18691976

Title: Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.

PubMed ID: 18691976

DOI: 10.1016/j.molcel.2008.07.007

PubMed ID: 24283382

Title: Zinc-finger BED domain-containing 3 (Zbed3) is a novel secreted protein associated with insulin resistance in humans.

PubMed ID: 24283382

DOI: 10.1111/joim.12170

Sequence Information:

  • Length: 234
  • Mass: 25132
  • Checksum: 3E615F16B68EE3B2
  • Sequence:
    • MRSGEPACTM DQARGLDDAA ARGGQCPGLG PAPTPTPPGR LGAPYSEAWG YFHLAPGRPG 
HPSGHWATCR LCGEQVGRGP GFHAGTSALW RHLRSAHRRE LESSGAGSSP PAAPCPPPPG 
PAAAPEGDWA RLLEQMGALA VRGSRREREL ERRELAVEQG ERALERRRRA LQEEERAAAQ 
ARRELQAERE ALQARLRDVS RREGALGWAP AAPPPLKDDP EGDRDGCVIT KVLL