Podocyte Literature Mining

This document contains our literature mined results related to podocyte. The contents are generated using our ontology-based CAP-LM (Cell Annotation Pipeline - Literature Mining) tool.

Note: This page is an illustrative web page for our CAP-LM tool development for CellCards.

Podocyte-associated Genes and Proteins

Using the BioLitMine, we identified 2,297 human genes named in 668 publications indexed with the MESH term "podocyte". See more details in the specific BioLiteMine link here.

Podocyte-associated Gene-gene or Protein-protein Interactions

Using the Dignet dynamic gene interaction literature mining program, we have identified over 700 podocyte-associated gene-gene interactions.

Furthermore, we have developed a SciMinor and BioBERT-based literature mining program, and used it to identify more podocyte-associated gene interactions from the PubMed literature. More information will be provided soon.

Podocyte Biomarkers Mined from the literature

    As seen in the Podocyte Cell Card page, 4 podoctye biomarkers are identified, including:

• NPHS1 (nephrin): OGG_3000004868. PR_000011365. HGNC:7908. References: PMC6597610 , PMC7213795, PMC6597610
• NPHS2 (podocin): OGG_3000007827. PR_000011366. HGNC:13394. References: PMC6597610, PMC7213795.
• PODXL (podocalyxin): OGG_3000005420. PR_000012955. HGNC:9171. References: PMC6597610, PMC7213795, PMC6597610.
• PTPRQ (Protein Tyrosine Phosphatase Receptor Type Q): OGG_3000374462. PR_000013477. HGNC: 9679. GeneCards: PTPRQ.

    Literature mined sentences on the podocyte-related biomarkers:

• NPHS1 (nephrein)-related sentences (selected):
  
  
  • "Nephrin is a 180 KD trans-membrane protein expressed in glomerular podocytes". Ref: PMC4363192.
  • "Nephrin forms an integral part of podocytes, which-together with endothelial cells and the basement-form the glomerular filtration barrier". Ref: PMC4363192.
  • "The investigators concluded that nephrinuria is a reliable biomarker of preclinical diabetic nephropathy". Ref: PMC4363192.
  • "The urinary mRNA profiles of nephrin, podocalyxin, and podocin were found to increase with the progression of DN, which suggested that quantification of podocyte-associated molecules will be useful biomarkers of DN". PMID: 31425946.
  • "Mutations in nephrin (NPHS1), podocin (NPHS2), laminin beta2 (LAMB2), and alpha-actinin-4 (ACTN4) have been shown to induce ER stress in HEK293 cells and podocytes in hereditary nephrotic syndromes; various founder mutations in collagen IV alpha chains (COL4A) have been demonstrated to activate podocyte ER stress in collagen IV nephropathies; and mutations in uromodulin (UMOD) have been reported to trigger tubular ER stress in autosomal dominant tubulointerstitial kidney disease." PMID: 30099615.
  • "Urinary nephrin excretion was also significantly increased in albuminuric Akita mice at 16 and 20 weeks of age and correlated with the albumin excretion rate." PMID: 22496773.
  • Check over 460 more sentences by clicking the Google sheet: Here.
  
  
• NPHS2 (podocin)-related sentences (selected):
  
  
  • "In this context, quantification of podocin could be of great interest since it is a protein exclusively present in highly specialized glomerulus cells called podocytes". PMID: 24552645.
  • "RESULTS: Patients with ADPKD had higher podocin and podocalyxin levels compared to the control group". PMID: 31117091.
  • "The urine podocin/creatinine ratio as a novel biomarker of cardiorenal syndrome in dogs due to degenerative mitral valve disease. PMID: 31356184.
  • "NPHS1, PLCE1, NPHS2, and SMARCAL1 were the most common genes in which we detected a mutation". PMID: 29127259.
  • "The urinary excretion of nephrin and podocin, two podocyte-specific markers, and WAP-four-disulfide core domain protein 2 (WFDC-2), a marker of tubulointerstitial fibrosis, was determined by ELISA in comparison with healthy controls". PMID: 31798788.
  • Check over 270 more sentences by clicking the Google sheet: Here.

    More to add. Stay tuned ...

Podocyte Functions mined from the Literature

    More to come ...

Podocyte Cell Lineage related Literature Mining

    This section includes the following parts:

• Cell types from first single cell to podocyte ...
• Cell differentiator (or Activator): Genes/proteins that activate cell differentiation ...
• Biomarkers for the cell differentiation ...
• Identify cell types from other organisms analogous (or homologous) ...

    More to come ...

Note: This is a manually generated website. Lessons learned will be used for automatic cell card content generation. Feedback is welcome. Thanks!

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