Details for: PDK1

Gene ID: 5163

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: PDK1

Ensembl ID: ENSG00000152256

Description: pyruvate dehydrogenase kinase 1

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

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

  • OFF-bipolar cell CL0000750
    CSI 7.91
    rCSI 10.81%
    PRS 73.71
  • astrocyte of the cerebral cortex CL0002605
    CSI 6.48
    rCSI 14.53%
    PRS 50.7
  • retinal ganglion cell CL0000740
    CSI 6.23
    rCSI 13.76%
    PRS 54.69
  • colon epithelial cell CL0011108
    CSI 5.65
    rCSI 5.92%
    PRS 65.66
  • plasma cell CL0000786
    CSI 4.29
    rCSI 5.63%
    PRS 88.85
  • ON-bipolar cell CL0000749
    CSI 4.08
    rCSI 6.07%
    PRS 69.69
  • alpha-beta T cell CL0000789
    CSI 3.96
    rCSI 4.64%
    PRS 84.17
  • periportal region hepatocyte CL0019026
    CSI 3.94
    rCSI 15.32%
    PRS 71.37
  • choroid plexus epithelial cell CL0000706
    CSI 3.94
    rCSI 6.45%
    PRS 57.89
  • precursor B cell CL0000817
    CSI 3.86
    rCSI 3.39%
    PRS 77.67
  • rod bipolar cell CL0000751
    CSI 3.75
    rCSI 6.74%
    PRS 61.82
  • megakaryocyte CL0000556
    CSI 3.69
    rCSI 16.01%
    PRS 78.65
  • mucosal invariant T cell CL0000940
    CSI 3.55
    rCSI 2.87%
    PRS 78.96
  • megakaryocyte-erythroid progenitor cell CL0000050
    CSI 3.51
    rCSI 3.17%
    PRS 66.02
  • double negative thymocyte CL0002489
    CSI 3.34
    rCSI 2.32%
    PRS 80.21
  • naive T cell CL0000898
    CSI 3.34
    rCSI 2.32%
    PRS 83.71
  • naive thymus-derived CD8-positive, alpha-beta T cell CL0000900
    CSI 3.18
    rCSI 2.24%
    PRS 85.58
  • interneuron CL0000099
    CSI 3.17
    rCSI 6.37%
    PRS 58.02
  • central memory CD4-positive, alpha-beta T cell CL0000904
    CSI 3.15
    rCSI 1.86%
    PRS 85.36
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 3.11
    rCSI 3.87%
    PRS 48.09
  • stem cell CL0000034
    CSI 3
    rCSI 2.89%
    PRS 60.32
  • regular ventricular cardiac myocyte CL0002131
    CSI 2.97
    rCSI 18.57%
    PRS 60.33
  • radial glial cell CL0000681
    CSI 2.97
    rCSI 4.13%
    PRS 67.33
  • CD4-positive, alpha-beta memory T cell CL0000897
    CSI 2.89
    rCSI 2.08%
    PRS 82.47
  • cerebral cortex endothelial cell CL1001602
    CSI 2.89
    rCSI 5%
    PRS 59.19
  • chandelier pvalb GABAergic cortical interneuron CL4023036
    CSI 2.85
    rCSI 8.91%
    PRS 54.24
  • regular atrial cardiac myocyte CL0002129
    CSI 2.72
    rCSI 8.77%
    PRS 66.38
  • pancreatic D cell CL0000173
    CSI 2.68
    rCSI 2.64%
    PRS 71.36
  • keratinocyte CL0000312
    CSI 2.68
    rCSI 2.25%
    PRS 72.35
  • hepatic stellate cell CL0000632
    CSI 2.65
    rCSI 9.94%
    PRS 60.74
  • retinal rod cell CL0000604
    CSI 2.64
    rCSI 4.65%
    PRS 65.16
  • fallopian tube secretory epithelial cell CL4030006
    CSI 2.63
    rCSI 2.53%
    PRS 68.56
  • pancreatic A cell CL0000171
    CSI 2.61
    rCSI 2.73%
    PRS 72.35
  • IgA plasma cell CL0000987
    CSI 2.61
    rCSI 2.67%
    PRS 80.66
  • S cone cell CL0003050
    CSI 2.55
    rCSI 11.2%
    PRS 64.81
  • fibroblast of lung CL0002553
    CSI 2.46
    rCSI 2.29%
    PRS 69.52
  • plasmablast CL0000980
    CSI 2.41
    rCSI 1.89%
    PRS 75.27
  • pro-B cell CL0000826
    CSI 2.34
    rCSI 1.94%
    PRS 71.29
  • elicited macrophage CL0000861
    CSI 2.33
    rCSI 2.14%
    PRS 77.92
  • promyelocyte CL0000836
    CSI 2.31
    rCSI 3.34%
    PRS 76.87
  • cardiac muscle cell CL0000746
    CSI 2.3
    rCSI 3.3%
    PRS 58.31
  • Mueller cell CL0000636
    CSI 2.16
    rCSI 4.93%
    PRS 60.3
  • sst GABAergic cortical interneuron CL4023017
    CSI 2
    rCSI 2.57%
    PRS 51.37
  • IgG plasma cell CL0000985
    CSI 1.99
    rCSI 2.39%
    PRS 83.33
  • neuroblast (sensu Nematoda and Protostomia) CL0000338
    CSI 1.98
    rCSI 2.28%
    PRS 61.44
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 1.97
    rCSI 4.78%
    PRS 48.42
  • retinal cone cell CL0000573
    CSI 1.94
    rCSI 3.12%
    PRS 58.2
  • glycinergic amacrine cell CL4030028
    CSI 1.93
    rCSI 5.03%
    PRS 65.38
  • platelet CL0000233
    CSI 1.91
    rCSI 7.93%
    PRS 69.8
  • BEST4+ enteroycte CL4030026
    CSI 1.85
    rCSI 2.3%
    PRS 70.55
  • ON parasol ganglion cell CL4033052
    CSI 1.81
    rCSI 25.64%
    PRS 59.76
  • ON midget ganglion cell CL4033046
    CSI 1.81
    rCSI 36.78%
    PRS 59.12
  • VIP GABAergic cortical interneuron CL4023016
    CSI 1.79
    rCSI 2.14%
    PRS 49.79
  • retinal bipolar neuron CL0000748
    CSI 1.78
    rCSI 3.34%
    PRS 56.66
  • extravillous trophoblast CL0008036
    CSI 1.78
    rCSI 2.2%
    PRS 65.69
  • lymphoid lineage restricted progenitor cell CL0000838
    CSI 1.68
    rCSI 6.54%
    PRS 87.15
  • H2 horizontal cell CL0004218
    CSI 1.61
    rCSI 8%
    PRS 65.04
  • ventricular cardiac muscle cell CL2000046
    CSI 1.59
    rCSI 5.46%
    PRS 85.3
  • peripheral nervous system neuron CL2000032
    CSI 1.57
    rCSI 2.13%
    PRS 60.24
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 1.54
    rCSI 2.72%
    PRS 49.12
  • OFF midget ganglion cell CL4033047
    CSI 1.49
    rCSI 30.25%
    PRS 60.62
  • enteroendocrine cell CL0000164
    CSI 1.48
    rCSI 2.03%
    PRS 69.76
  • near-projecting glutamatergic cortical neuron CL4023012
    CSI 1.48
    rCSI 5.59%
    PRS 50.58
  • epicardial adipocyte CL1000309
    CSI 1.46
    rCSI 4.76%
    PRS 67.98
  • glioblast CL0000030
    CSI 1.46
    rCSI 2.33%
    PRS 60.64
  • retina horizontal cell CL0000745
    CSI 1.43
    rCSI 2.17%
    PRS 65.09
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 1.4
    rCSI 2.35%
    PRS 50.01
  • enteric smooth muscle cell CL0002504
    CSI 1.4
    rCSI 1.99%
    PRS 70.7
  • pancreatic acinar cell CL0002064
    CSI 1.39
    rCSI 1.84%
    PRS 75.07
  • amacrine cell CL0000561
    CSI 1.32
    rCSI 3.83%
    PRS 58.14
  • vascular associated smooth muscle cell CL0000359
    CSI 1.27
    rCSI 4.11%
    PRS 68.14
  • basal cell of epidermis CL0002187
    CSI 1.14
    rCSI 2.02%
    PRS 40.6
  • cerebral cortex pyramidal neuron CL4023111
    CSI 1.12
    rCSI 6.91%
    PRS 79.96
  • mature alpha-beta T cell CL0000791
    CSI 1.08
    rCSI 3.89%
    PRS 86.62
  • neural progenitor cell CL0011020
    CSI 1.07
    rCSI 4.7%
    PRS 58.12
  • sncg GABAergic cortical interneuron CL4023015
    CSI 1.06
    rCSI 1.71%
    PRS 51.95
  • glial cell CL0000125
    CSI 0.96
    rCSI 3.64%
    PRS 59.21
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 0.9
    rCSI 3.25%
    PRS 48.2
  • H1 horizontal cell CL0004217
    CSI 0.88
    rCSI 3.49%
    PRS 66.85
  • Hofbauer cell CL3000001
    CSI 0.88
    rCSI 1.66%
    PRS 78.8
  • GABAergic amacrine cell CL4030027
    CSI 0.82
    rCSI 2.81%
    PRS 56.85
  • promonocyte CL0000559
    CSI 0.6
    rCSI 1.02%
    PRS 76.86
  • L6b glutamatergic cortical neuron CL4023038
    CSI 0.51
    rCSI 1.59%
    PRS 51.73
  • corticothalamic-projecting glutamatergic cortical neuron CL4023013
    CSI 0.41
    rCSI 2.39%
    PRS 51.14

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 Analyzed for its expression specificity (CSI Z-SCORE), Pyruvate Dehydrogenase Kinase 1 ([PDK1](/details-gene/5163)) is identified as a ubiquitously expressed gene lacking cell-type specificity. The data suggest its role is not to define a particular cellular identity but rather to perform a core, "housekeeping" function in mitochondrial metabolism. This is consistent with its established role as a key regulator of the pyruvate dehydrogenase complex, a central hub in cellular energy production essential for a wide variety of cell types. ## Cellular Roles and Expression Landscape The expression profile of [PDK1](/details-gene/5163), when evaluated for specificity, highlights its broad and non-distinguishing nature. Across the **Overall** context, [PDK1](/details-gene/5163) consistently presents a CSI (Z-SCORE) of 0.00 with non-significant p-values (p > 0.4) in all top-ranked cell types. This lack of statistical specificity indicates that while the gene is expressed, its transcript levels are not significantly enriched in any single cell type compared to others. This pattern holds true across functionally diverse cells, including neurons like [retinal ganglion cells](/details-cell/CL0000740), glial cells such as [astrocytes of the cerebral cortex](/details-cell/CL0002605), metabolic cells like [periportal region hepatocytes](/details-cell/CL0019026), and various immune lineages including [plasma cells](/details-cell/CL0000786) and [alpha-beta T cells](/details-cell/CL0000789). The Percentile Rank Scores (PRS) are moderate to high (ranging from 50% to 88%), confirming that [PDK1](/details-gene/5163) is a relevantly expressed gene within these cellular contexts. However, the specificity analysis conclusively shows that it does not serve as a unique marker. Instead, this ubiquitous expression pattern strongly supports its role in a fundamental biological process required by nearly all cells. ## Pathways and Molecular Function The functional annotations for [PDK1](/details-gene/5163) align perfectly with its observed lack of cell-type specificity. As a mitochondrial matrix protein ([GO:0005759](https://www.ebi.ac.uk/QuickGO/term/GO:0005759)), its primary molecular function is [pyruvate dehydrogenase (acetyl-transferring) kinase activity](/details-cell/GO0004740). This activity is central to the [regulation of the pyruvate dehydrogenase (PDH) complex](/details-cell/R-HSA-204174), a critical metabolic checkpoint that governs the entry of pyruvate into the tricarboxylic acid (TCA) cycle. By phosphorylating and inactivating the PDH complex, [PDK1](/details-gene/5163) effectively shifts cellular metabolism away from mitochondrial aerobic respiration and towards glycolysis. This role places [PDK1](/details-gene/5163) at the heart of the [glucose metabolic process](/details-cell/GO0006006) and [pyruvate metabolism](/details-cell/R-HSA-70268). These are foundational pathways for cellular energy production, proliferation ([GO:0008283](https://www.ebi.ac.uk/QuickGO/term/GO:0008283)), and survival, explaining its broad necessity. Furthermore, its involvement in the [hypoxia-inducible factor-1alpha signaling pathway](/details-cell/GO0097411) underscores its importance in cellular adaptation to low-oxygen environments, a condition relevant to many tissues. The association with pyruvate metabolism has significant clinical implications, particularly in cancer, where metabolic reprogramming is a key hallmark (PubMed: [18541534](https://pubmed.ncbi.nlm.nih.gov/18541534), [22195962](https://pubmed.ncbi.nlm.nih.gov/22195962)). Its clinical association with lactic acidosis ([153245](https://omim.org/entry/602524)) further highlights its critical role in systemic metabolic homeostasis. ## Research Directions The ubiquitous expression of [PDK1](/details-gene/5163) suggests that its biological impact is likely controlled through post-transcriptional regulation, differential activity, or context-dependent expression changes rather than baseline transcript specificity. ### Proposed Testable Hypotheses 1. **Hypothesis:** The ubiquitous transcription of [PDK1](/details-gene/5163) masks cell-type-specific regulation at the level of protein activity. In highly proliferative cells, such as [precursor B cells](/details-cell/CL0000817), [PDK1](/details-gene/5163) kinase activity is significantly higher to promote Warburg-like aerobic glycolysis, despite comparable transcript levels to more quiescent cells like [astrocytes](/details-cell/CL0002605). * **Experimental Approach:** Use flow cytometry to isolate distinct cell populations from primary tissues. Perform targeted kinase activity assays on cell lysates using a specific [PDK1](/details-gene/5163) substrate. Complement this with phosphoproteomic analysis to quantify phosphorylation of the PDH complex, the direct downstream target of [PDK1](/details-gene/5163), in these different cell types. 2. **Hypothesis:** While its expression is not specific under homeostatic conditions, [PDK1](/details-gene/5163) becomes a specificity marker for metabolically stressed or pathological cells. For instance, within a tumor microenvironment, malignant [colon epithelial cells](/details-cell/CL0011108) will exhibit a significantly higher CSI (Z-SCORE) for [PDK1](/details-gene/5163) compared to adjacent healthy epithelial cells as a specific adaptation to hypoxia and nutrient stress. * **Experimental Approach:** Perform single-cell RNA sequencing on patient-derived colon cancer tissue. Computationally segregate malignant cells from healthy epithelial and stromal cells. Recalculate the CSI (Z-SCORE) for [PDK1](/details-gene/5163) within the tumor context to determine if its expression becomes a specific marker of the malignant phenotype, consistent with published findings (PubMed: [21763680](https://pubmed.ncbi.nlm.nih.gov/21763680)). 3. **Hypothesis:** The functional role of [PDK1](/details-gene/5163) is diversified across cell types through the expression of distinct protein isoforms that possess different regulatory properties or substrate affinities. The aggregate gene expression measurements in this dataset may obscure the cell-specific expression of these functionally distinct isoforms. * **Experimental Approach:** Conduct long-read RNA sequencing (e.g., PacBio or Oxford Nanopore) on a panel of diverse, isolated cell types (e.g., [megakaryocytes](/details-cell/CL0000556), [hepatocytes](/details-cell/CL0019026), and [T cells](/details-cell/CL0000789)). Analyze the data to identify and quantify full-length [PDK1](/details-gene/5163) transcript variants. Subsequently, clone and overexpress the identified dominant isoforms in a model cell line to assess their differential effects on PDH phosphorylation and metabolic flux. ### Therapeutic Potential [PDK1](/details-gene/5163) represents a promising therapeutic target, particularly in oncology. Its role in promoting glycolysis is critical for the survival and proliferation of many cancer cells (PubMed: [27505672](https://pubmed.ncbi.nlm.nih.gov/27505672)). Pharmacological inhibition of [PDK1](/details-gene/5163) could force cancer cells to rely on oxidative phosphorylation, increasing oxidative stress and potentially sensitizing them to other therapies. However, its ubiquitous expression in healthy tissues poses a significant challenge for systemic inhibition, which could lead to on-target toxicity. The development of next-generation inhibitors, such as those that selectively target cancer-specific isoforms or utilize tumor-targeted delivery systems, will be crucial for translating the therapeutic potential of [PDK1](/details-gene/5163) inhibition into clinical success.

Genular Protein ID: 2904860212

Symbol: PDK1_HUMAN

Name: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 7499431

Title: Diversity of the pyruvate dehydrogenase kinase gene family in humans.

PubMed ID: 7499431

DOI: 10.1074/jbc.270.48.28989

PubMed ID: 14702039

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

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 15815621

Title: Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

PubMed ID: 15815621

DOI: 10.1038/nature03466

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: 18541534

Title: Pyruvate dehydrogenase complex activity controls metabolic and malignant phenotype in cancer cells.

PubMed ID: 18541534

DOI: 10.1074/jbc.m801765200

PubMed ID: 21763680

Title: Overexpression of pyruvate dehydrogenase kinase 3 increases drug resistance and early recurrence in colon cancer.

PubMed ID: 21763680

DOI: 10.1016/j.ajpath.2011.05.050

PubMed ID: 21269460

Title: Initial characterization of the human central proteome.

PubMed ID: 21269460

DOI: 10.1186/1752-0509-5-17

PubMed ID: 22195962

Title: Tyrosine phosphorylation of mitochondrial pyruvate dehydrogenase kinase 1 is important for cancer metabolism.

PubMed ID: 22195962

DOI: 10.1016/j.molcel.2011.10.015

PubMed ID: 25944712

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

PubMed ID: 25944712

DOI: 10.1002/pmic.201400617

PubMed ID: 27505672

Title: Mitochondrial Akt regulation of hypoxic tumor reprogramming.

PubMed ID: 27505672

DOI: 10.1016/j.ccell.2016.07.004

PubMed ID: 17683942

Title: Distinct structural mechanisms for inhibition of pyruvate dehydrogenase kinase isoforms by AZD7545, dichloroacetate, and radicicol.

PubMed ID: 17683942

DOI: 10.1016/j.str.2007.07.001

PubMed ID: 17344846

Title: Patterns of somatic mutation in human cancer genomes.

PubMed ID: 17344846

DOI: 10.1038/nature05610

Sequence Information:

  • Length: 436
  • Mass: 49244
  • Checksum: D14CD594E0EA45A2
  • Sequence:
  • MRLARLLRGA ALAGPGPGLR AAGFSRSFSS DSGSSPASER GVPGQVDFYA RFSPSPLSMK 
    QFLDFGSVNA CEKTSFMFLR QELPVRLANI MKEISLLPDN LLRTPSVQLV QSWYIQSLQE 
    LLDFKDKSAE DAKAIYDFTD TVIRIRNRHN DVIPTMAQGV IEYKESFGVD PVTSQNVQYF 
    LDRFYMSRIS IRMLLNQHSL LFGGKGKGSP SHRKHIGSIN PNCNVLEVIK DGYENARRLC 
    DLYYINSPEL ELEELNAKSP GQPIQVVYVP SHLYHMVFEL FKNAMRATME HHANRGVYPP 
    IQVHVTLGNE DLTVKMSDRG GGVPLRKIDR LFNYMYSTAP RPRVETSRAV PLAGFGYGLP 
    ISRLYAQYFQ GDLKLYSLEG YGTDAVIYIK ALSTDSIERL PVYNKAAWKH YNTNHEADDW 
    CVPSREPKDM TTFRSA

Genular Protein ID: 4114871463

Symbol: B7Z7N6_HUMAN

Name: N/A

UniProtKB Accession Codes:

Database IDs:

Sequence Information:

  • Length: 360
  • Mass: 41303
  • Checksum: 4B86ADECF096D0F5
  • Sequence:
  • MFLRQELPVR LANIMKEISL LPDNLLRTPS VQLVQSWYIQ SLQELLDFKD KSAEDAKAIY 
    DFTDTVIRIR NRHNDVIPTM AQGVIEYKES FGVDPVTSQN VQYFLDRFYM SRISIRMLLN 
    QHSLLFGGKG KGSPSHRKHI GSINPNCNVL EVIKDGYENA RRLCDLYYIN SPELELEELN 
    AKSPGQPIQV VYVPSHLYHM VFELFKNAMR ATMEHHANRG VYPPIQVHVT LGNEDLTVKM 
    SDRGGGVPLR KIDRLFNYMY STAPRPRVET SRAVPLAGFG YGLPISRLYA QYFQGDLKLY 
    SLEGYGTDAV IYIKALSTDS IERLPVYNKA AWKHYNTNHE ADDWCVPSRE PKDMTTFRSA