Details for: TBRG4

Gene ID: 9238

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: TBRG4

Ensembl ID: ENSG00000136270

Description: transforming growth factor beta regulator 4

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

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

  • CD14-low, CD16-positive monocyte CL0002396
    CSI 5.79
    rCSI 4.46%
    PRS 92.32
  • transit amplifying cell of colon CL0009011
    CSI 4.96
    rCSI 5.83%
    PRS 89.49
  • perivascular cell CL4033054
    CSI 4.88
    rCSI 6.68%
    PRS 92.4
  • BEST4+ enteroycte CL4030026
    CSI 4.06
    rCSI 5.04%
    PRS 89.1
  • unswitched memory B cell CL0000970
    CSI 3.94
    rCSI 3.31%
    PRS 96.71
  • naive T cell CL0000898
    CSI 3.22
    rCSI 2.24%
    PRS 97.32
  • rod bipolar cell CL0000751
    CSI 3.08
    rCSI 5.53%
    PRS 83.98
  • epithelial cell of lower respiratory tract CL0002632
    CSI 3
    rCSI 2.33%
    PRS 91.96
  • plasmacytoid dendritic cell, human CL0001058
    CSI 2.95
    rCSI 2.06%
    PRS 92.35
  • fibroblast of lung CL0002553
    CSI 2.89
    rCSI 2.69%
    PRS 90.42
  • neural crest cell CL0011012
    CSI 2.8
    rCSI 2.21%
    PRS 81.62
  • megakaryocyte-erythroid progenitor cell CL0000050
    CSI 2.53
    rCSI 2.28%
    PRS 88.15
  • pro-B cell CL0000826
    CSI 2.48
    rCSI 2.05%
    PRS 90.88
  • mature alpha-beta T cell CL0000791
    CSI 2.47
    rCSI 8.94%
    PRS 97.93
  • ionocyte CL0005006
    CSI 2.46
    rCSI 2.64%
    PRS 90.73
  • intestine goblet cell CL0019031
    CSI 2.33
    rCSI 2.07%
    PRS 86.7
  • hematopoietic stem cell CL0000037
    CSI 2.31
    rCSI 1.54%
    PRS 90.94
  • periportal region hepatocyte CL0019026
    CSI 2.24
    rCSI 8.7%
    PRS 86.56
  • common myeloid progenitor CL0000049
    CSI 2.22
    rCSI 1.8%
    PRS 90.77
  • intermediate monocyte CL0002393
    CSI 2.21
    rCSI 3.34%
    PRS 93.22
  • keratinocyte CL0000312
    CSI 2.17
    rCSI 1.82%
    PRS 89.92
  • mesodermal cell CL0000222
    CSI 2.17
    rCSI 2.6%
    PRS 87.96
  • promyelocyte CL0000836
    CSI 2.14
    rCSI 3.09%
    PRS 91.89
  • retina horizontal cell CL0000745
    CSI 2.12
    rCSI 3.24%
    PRS 86.11
  • granulocyte monocyte progenitor cell CL0000557
    CSI 2.04
    rCSI 1.77%
    PRS 91.52
  • placental villous trophoblast CL2000060
    CSI 2.01
    rCSI 3.11%
    PRS 87.54
  • myeloid leukocyte CL0000766
    CSI 2
    rCSI 1.84%
    PRS 90.31
  • stem cell CL0000034
    CSI 1.97
    rCSI 1.9%
    PRS 84.85
  • transit amplifying cell CL0009010
    CSI 1.94
    rCSI 2.97%
    PRS 92.86
  • group 3 innate lymphoid cell CL0001071
    CSI 1.88
    rCSI 1.41%
    PRS 92.66
  • intestinal epithelial cell CL0002563
    CSI 1.88
    rCSI 1.97%
    PRS 86.87
  • extravillous trophoblast CL0008036
    CSI 1.87
    rCSI 2.32%
    PRS 87.65
  • fallopian tube secretory epithelial cell CL4030006
    CSI 1.87
    rCSI 1.8%
    PRS 87.89
  • ciliated epithelial cell CL0000067
    CSI 1.83
    rCSI 1.61%
    PRS 80.39
  • colon epithelial cell CL0011108
    CSI 1.77
    rCSI 1.86%
    PRS 86.8
  • radial glial cell CL0000681
    CSI 1.74
    rCSI 2.42%
    PRS 87.77
  • peripheral nervous system neuron CL2000032
    CSI 1.73
    rCSI 2.35%
    PRS 82.61
  • neuroblast (sensu Vertebrata) CL0000031
    CSI 1.55
    rCSI 1.99%
    PRS 85.81
  • lung ciliated cell CL1000271
    CSI 1.54
    rCSI 1.78%
    PRS 83.47
  • mesenchymal cell CL0008019
    CSI 1.51
    rCSI 3.83%
    PRS 84.02
  • club cell CL0000158
    CSI 1.48
    rCSI 2.17%
    PRS 84.54
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 1.43
    rCSI 2.52%
    PRS 74.85
  • basal cell CL0000646
    CSI 1.34
    rCSI 1.8%
    PRS 86.63
  • type B pancreatic cell CL0000169
    CSI 1.34
    rCSI 2.96%
    PRS 89.16
  • erythroid progenitor cell CL0000038
    CSI 0.56
    rCSI 3.22%
    PRS 91.66
  • primitive red blood cell CL0002355
    CSI 0.55
    rCSI 2.99%
    PRS 91.7

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.

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)

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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 Transforming growth factor beta regulator 4 ([TBRG4](/details-gene/9238)) is a protein-coding gene located on chromosome 7p13. Functionally, it is primarily associated with the regulation of mitochondrial RNA (mRNA) processing and stability, as indicated by its inclusion in the FASTK (Fas-activated serine/threonine kinase) family of proteins involved in mitochondrial RNA metabolism ([R-HSA-9837092](https://reactome.org/content/detail/R-HSA-9837092)). It is also annotated with roles in the regulation of the cell cycle and cell proliferation ([GO:0051726](https://www.ebi.ac.uk/QuickGO/term/GO:0051726)). **Overall**, [TBRG4](/details-gene/9238) shows significant expression across a diverse range of cell types, with the highest significance observed in [CD14-low, CD16-positive monocytes](/details-cell/CL0002396), various progenitor cells like [transit amplifying cell of colon](/details-cell/CL0009011), and specialized cell types such as [perivascular cells](/details-cell/CL4033054). This broad expression pattern suggests a fundamental role in core cellular processes related to mitochondrial function and proliferation. ## Cellular Roles and Expression Landscape The expression profile of [TBRG4](/details-gene/9238) highlights its importance in cells characterized by high metabolic activity, rapid proliferation, or specialized functions. **Overall**, its most significant expression is in [CD14-low, CD16-positive monocytes](/details-cell/CL0002396), a subset of monocytes associated with patrolling and inflammatory responses. This suggests a potential role for [TBRG4](/details-gene/9238) in supporting the energetic demands of these immune effector cells. The gene also demonstrates high significance in several progenitor and rapidly dividing cell populations, including [transit amplifying cells of the colon](/details-cell/CL0009011) and [megakaryocyte-erythroid progenitor cells](/details-cell/CL0000050). This pattern is consistent with its annotated function in regulating cell proliferation ([GO:0008284](https://www.ebi.ac.uk/QuickGO/term/GO:0008284)) and suggests it may be crucial for coordinating mitochondrial activity with the cell cycle during tissue renewal and hematopoiesis. Furthermore, [TBRG4](/details-gene/9238) is significantly expressed in a variety of other cell types, including adaptive immune cells like [unswitched memory B cells](/details-cell/CL0000970) and [naive T cells](/details-cell/CL0000898), as well as specialized structural and epithelial cells like [perivascular cells](/details-cell/CL4033054) and [BEST4+ enteroycytes](/details-cell/CL4030026). The widespread, yet specific, expression across such functionally distinct lineages underscores a role in a fundamental biological process, likely related to mitochondrial health and energy production, that is essential for a wide array of cell types. ## Pathways and Molecular Function The functional annotations for [TBRG4](/details-gene/9238) converge on its role within the mitochondrion, specifically in post-transcriptional gene regulation. It is a key component of mitochondrial RNA processing pathways, as detailed by its involvement in [mitochondrial mRNA processing](/details-go/GO0090615) and the [regulation of mitochondrial mRNA stability](/details-go/GO0044528). The Reactome database places it within the [FASTK family proteins that regulate processing and stability of mitochondrial RNAs](/details-go/R-HSA-9837092) pathway, a group of proteins critical for the maturation of mitochondrially encoded transcripts essential for oxidative phosphorylation. This is consistent with its localization to the [mitochondrial matrix](/details-go/GO0005759) and its molecular function as an [RNA binding](/details-go/GO0003723) protein. In addition to its primary mitochondrial role, [TBRG4](/details-gene/9238) is also implicated in the broader [regulation of the cell cycle](/details-go/GO0051726). This dual function suggests that [TBRG4](/details-gene/9238) may act as a molecular link, coordinating mitochondrial gene expression and energy output with the demands of cell division and proliferation. This connection is supported by early research identifying it as a cell cycle progression restoration (CPR) gene ([Link](https://pubmed.ncbi.nlm.nih.gov/9383053/)). ## Research Directions The widespread importance of [TBRG4](/details-gene/9238) in both immune and progenitor cells, coupled with its core function in mitochondrial RNA metabolism, opens several avenues for future investigation. **Proposed Hypotheses:** 1. Given its top expression in [CD14-low, CD16-positive monocytes](/details-cell/CL0002396) and its role in mitochondrial function, **[TBRG4](/details-gene/9238) is essential for the metabolic reprogramming that underpins the activation, differentiation, and pro-inflammatory functions of monocytes.** Its dysregulation may impair the innate immune response to pathogens or tissue damage. 2. Based on its high significance in [transit amplifying cells](/details-cell/CL0009011) and its link to cell cycle regulation, **[TBRG4](/details-gene/9238) functions as a critical checkpoint protein that couples mitochondrial biogenesis and respiratory capacity to the G1/S transition in rapidly dividing progenitor cells.** Its loss could lead to stalled proliferation, stem cell exhaustion, or impaired tissue regeneration, particularly in high-turnover tissues like the colonic epithelium. **Key Experimental Approach:** To test the first hypothesis regarding the role of [TBRG4](/details-gene/9238) in monocyte function, one could utilize a human monocyte cell line (e.g., THP-1) or primary CD14+ monocytes. Using CRISPR-Cas9 to generate a stable [TBRG4](/details-gene/9238) knockout line, researchers could then perform a series of functional assays. After stimulating control and knockout cells with an inflammatory agent like lipopolysaccharide (LPS), key experiments would include: (i) assessing changes in mitochondrial respiration and glycolysis using a Seahorse XF Analyzer to quantify metabolic reprogramming; (ii) measuring the production of key inflammatory cytokines (e.g., TNF-alpha, IL-6, IL-1beta) via ELISA or qPCR; and (iii) performing RNA-sequencing to determine the impact on mitochondrial transcript stability and the broader inflammatory gene expression signature. **Therapeutic Potential:** As an intracellular protein localized to the mitochondria, [TBRG4](/details-gene/9238) is not an ideal target for conventional antibody-based therapies. Its broad expression across many healthy, essential cell types suggests that systemic **inhibition** could lead to significant on-target toxicity. Therefore, it is likely a poor direct therapeutic target for systemic diseases. However, in pathologies characterized by uncontrolled proliferation and metabolic dysregulation, such as certain cancers, [TBRG4](/details-gene/9238) could be a node of vulnerability. Therapeutic strategies would likely require advanced delivery systems, such as lipid nanoparticles carrying siRNA or ASOs, to achieve cell-type specific targeting and minimize systemic side effects.

Genular Protein ID: 1317577111

Symbol: FAKD4_HUMAN

Name: Cell cycle progression restoration protein 2

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 10231032

Title: Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.

PubMed ID: 10231032

DOI: 10.1093/dnares/6.1.63

PubMed ID: 17974005

Title: The full-ORF clone resource of the German cDNA consortium.

PubMed ID: 17974005

DOI: 10.1186/1471-2164-8-399

PubMed ID: 12690205

Title: Human chromosome 7: DNA sequence and biology.

PubMed ID: 12690205

DOI: 10.1126/science.1083423

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: 9383053

Title: Human CPR (cell cycle progression restoration) genes impart a Far-phenotype on yeast cells.

PubMed ID: 9383053

DOI: 10.1093/genetics/147.3.1063

PubMed ID: 12759187

Title: Pig whey acidic protein gene is surrounded by two ubiquitously expressed genes.

PubMed ID: 12759187

DOI: 10.1016/s0167-4781(03)00051-4

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: 19608861

Title: Lysine acetylation targets protein complexes and co-regulates major cellular functions.

PubMed ID: 19608861

DOI: 10.1126/science.1175371

PubMed ID: 20869947

Title: Fast kinase domain-containing protein 3 is a mitochondrial protein essential for cellular respiration.

PubMed ID: 20869947

DOI: 10.1016/j.bbrc.2010.09.075

PubMed ID: 21269460

Title: Initial characterization of the human central proteome.

PubMed ID: 21269460

DOI: 10.1186/1752-0509-5-17

PubMed ID: 22814378

Title: N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB.

PubMed ID: 22814378

DOI: 10.1073/pnas.1210303109

PubMed ID: 23186163

Title: Toward a comprehensive characterization of a human cancer cell phosphoproteome.

PubMed ID: 23186163

DOI: 10.1021/pr300630k

PubMed ID: 25944712

Title: N-terminome analysis of the human mitochondrial proteome.

PubMed ID: 25944712

DOI: 10.1002/pmic.201400617

PubMed ID: 28335001

Title: FASTKD1 and FASTKD4 have opposite effects on expression of specific mitochondrial RNAs, depending upon their endonuclease-like RAP domain.

PubMed ID: 28335001

DOI: 10.1093/nar/gkx164

Sequence Information:

  • Length: 631
  • Mass: 70738
  • Checksum: 4EFC3AF5D5BBABD3
  • Sequence:
  • MAAHLVKRCT CLLREAARQA PAMAPVGRLR LAWVAHKTLT SSATSPISHL PGSLMEPVEK 
    ERASTPYIEK QVDHLIKKAT RPEELLELLG GSHDLDSNQA AMVLIRLSHL LSEKPEDKGL 
    LIQDAHFHQL LCLLNSQIAS VWHGTLSKLL GSLYALGIPK ASKELQSVEQ EVRWRMRKLK 
    YKHLAFLAES CATLSQEQHS QELLAELLTH LERRWTEIED SHTLVTVMMK VGHLSEPLMN 
    RLEDKCLELV EHFGPNELRK VLVMLAAQSR RSVPLLRAIS YHLVQKPFSL TKDVLLDVAY 
    AYGKLSFHQT QVSQRLATDL LSLMPSLTSG EVAHCAKSFA LLKWLSLPLF EAFAQHVLNR 
    AQDITLPHLC SVLLAFARLN FHPDQEDQFF SLVHEKLGSE LPGLEPALQV DLVWALCVLQ 
    QAREAELQAV LHPEFHIQFL GGKSQKDQNT FQKLLHINAT ALLEYPEYSG PLLPASAVAP 
    GPSALDRKVT PLQKELQETL KGLLGSADKG SLEVATQYGW VLDAEVLLDS DGEFLPVRDF 
    VAPHLAQPTG SQSPPPGSKR LAFLRWEFPN FNSRSKDLLG RFVLARRHIV AAGFLIVDVP 
    FYEWLELKSE WQKGAYLKDK MRKAVAEELA K

Genular Protein ID: 3061943076

Symbol: B3KM73_HUMAN

Name: N/A

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

Sequence Information:

  • Length: 493
  • Mass: 55111
  • Checksum: CEDDCDF1986358D9
  • Sequence:
  • MAAHLVKRCT CLLREAARQA PAMAPVGRLR LAWVAHKTLT SSATSPISHL PGSLMEPVEK 
    ERASTPYIEK QVDHLIKKAT RPEELLELLG GSHDLDSNQA AMVLIRLSHL LSEKPEDKGL 
    LIQDAHFHQL LCLLNSQIAS VWHGTLSKLL GSLYALGIPK ASKELQSVEQ EVRWRMRKLK 
    YKHLAFLAES CATLSQEQHS QELLAELLTH LERRWTEIED SHTLVTVMMK VGHLSEPLMN 
    RLEDKHVLNR AQDITLPHLC SVLLAFARLN FHPDQEDQFF SLVHEKLGSE LPGLEPALQV 
    DLVWALCVLQ QAREAELQAV LHPEFHIQFL GGKSQKDQNT FQKLLHINAT ALLEYPEYSG 
    PLLPASAVAP GPSALDRKVT PLQKELQETL KGLLGSADKG SLEVATQYGW VLDAEVLLDS 
    DGEFLPVRDF VAPHLAQPTG SQSPPPGSKR LAFLRWEFPN FNSRSKDLLG RFVLARRHIV 
    AAGFLIVDVP FYE

Genular Protein ID: 2507516224

Symbol: B3KRS4_HUMAN

Name: N/A

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

Sequence Information:

  • Length: 456
  • Mass: 51368
  • Checksum: 19D4B1AC5A47BA75
  • Sequence:
  • MRKLKYKHLA FLAESCATLS QEQHSQELLA ELLTHLERRW TEIEDSHTLV TVMMKVGHLS 
    EPLMNRLEDK CLELVEHFGP NELRKVLVML AAQSRRSVPL LRAISYHLVQ KPFSLTKDVL 
    LDVAYAYGKL SFHQTQVSQR LATDLLSLMP SLTSGEVAHC AKSFALLKWL SLPLFEAFAQ 
    HVLNRAQDIT LPHLCSVLLA FARLNFHPDQ EDQFFSLVHE KLGSELPGLE PALQVDLVWA 
    LCVLQQAREA ELQAVLHPEF HIQFLGGKSQ KDQNTFQKLL HINATALLEY PEYSGPLLPA 
    SAVAPGPSAL DRKVTPLQKE LQETLKGLLG SADKGSLEVA TQYGWVLDAE VLLDSDGEFL 
    PVRDFVAPHL AQPTGSQSPP PGSKRLAFLR WEFPNFNSRS KDLLGRFVLA RRHIVAAGFL 
    IVDVPFYEWL ELKSEWQKGA YLKDKMRKAV AEELAK

Genular Protein ID: 241452161

Symbol: B4DU42_HUMAN

Name: N/A

UniProtKB Accession Codes:

Database IDs:

Sequence Information:

  • Length: 642
  • Mass: 71857
  • Checksum: 45827D7868344AF0
  • Sequence:
  • MEVSGGARCD IMAAHLVKRC TCLLREAARQ APAMAPVGRL RLAWVAHKTL TSSATSPISH 
    LPGSLMEPVE KERASTPYIE KQVDHLIKKA TRPEELLELL GGSHDLDSNQ AAMVLIRLSH 
    LLSEKPEDKG LLIQDAHFHQ LLCLLNSQIA SVWHGTLSKL LGSLYALGIP KASKELQSVE 
    QEVRWRMRKL KYKHLAFLAE SCATLSQEQH SQELLAELLT HLERRWTEIE DSHTLVTVMM 
    KVGHLSEPLM NRLEDKCLEL VEHFGPNELR KVLVMLAAQS RRSVPLLRAI SYHLVQKPFS 
    LTKDVLLDVA YAYGKLSFHQ TQVSQRLATD LLSLMPSLTS GEVAHCAKSF ALLKWLSLPL 
    FEAFAQHVLN RAQDITLPHL CSVLLAFARL NFHPDQEDQF FSLVHEKLGS ELPGLEPALQ 
    VDLVWALCVL QQAREAELQA VLHPEFHIQF LGGKSQKDQN TFQKLLHINA TALLEYPEYS 
    GPLLPASAVA PGPSALDRKV TPLQKELQET LKGLLGSADK GSLEVATQYG WVLDAEVLLD 
    SDGEFLPVRD FVAPHLAQPT GSQSPPPGSK RLAFLRWEFP NFNSRSKDLL GRFVLARRHI 
    VAAGFLIVDV PFYEWLELKS EWQKGAYLKD KMRKAVAEEL AK