The Kyoto Encyclopedia of Genes and Genomes—KEGG

Wixon, Jo; Kell, Douglas B.

doi:10.1002/(sici)1097-0061(200004)17:1<48::aid-yea2>3.0.co;2-h

Cited by 163 publications

(55 citation statements)

References 4 publications

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“…The databases were queried by providing the list of official names of genes of interest. The resulting KEGG Pathway ( 32 – 35 ) table was then imported into R for generating bar plots. ClueGO v2.5.7 ( 36 ) add-on of the Cytoscape Platform v3.72 ( 37 ) was used to generate Figures 1C, D .…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic and Network Analysis of Minor Salivary Glands of Patients With Primary Sjögren’s Syndrome

et al. 2021

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Primary Sjögren’s syndrome (pSS) is a systemic autoimmune disease characterized primarily by immune-mediated destruction of exocrine tissues, such as those of the salivary and lacrimal glands, resulting in the loss of saliva and tear production, respectively. This disease predominantly affects middle-aged women, often in an insidious manner with the accumulation of subtle changes in glandular function occurring over many years. Patients commonly suffer from pSS symptoms for years before receiving a diagnosis. Currently, there is no effective cure for pSS and treatment options and targeted therapy approaches are limited due to a lack of our overall understanding of the disease etiology and its underlying pathology. To better elucidate the underlying molecular nature of this disease, we have performed RNA-sequencing to generate a comprehensive global gene expression profile of minor salivary glands from an ethnically diverse cohort of patients with pSS. Gene expression analysis has identified a number of pathways and networks that are relevant in pSS pathogenesis. Moreover, our detailed integrative analysis has revealed a primary Sjögren’s syndrome molecular signature that may represent important players acting as potential drivers of this disease. Finally, we have established that the global transcriptomic changes in pSS are likely to be attributed not only to various immune cell types within the salivary gland but also epithelial cells which are likely playing a contributing role. Overall, our comprehensive studies provide a database-enriched framework and resource for the identification and examination of key pathways, mediators, and new biomarkers important in the pathogenesis of this disease with the long-term goals of facilitating earlier diagnosis of pSS and to mitigate or abrogate the progression of this debilitating disease.

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Section: Methodsmentioning

confidence: 99%

Transcriptomic and Network Analysis of Minor Salivary Glands of Patients With Primary Sjögren’s Syndrome

et al. 2021

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“…Along with Nr annotations, the “Database for Annotation, Visualization and Integrated Discovery” (DAVID; Dennis et al, 2003) was used to obtain GO annotations of unigenes. The KEGG pathway annotations of tsetse fly gene orthologs were performed using the BLASTX software against the KEGG database (Wixon and Kell, 2000). …”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics of Glossina palpalis gambiensis and G. morsitans morsitans to Reveal Gene Orthologs Involved in Infection by Trypanosoma brucei gambiense

et al. 2017

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Blood-feeding Glossina palpalis gambiense (Gpg) fly transmits the single-celled eukaryotic parasite Trypanosoma brucei gambiense (Tbg), the second Glossina fly African trypanosome pair being Glossina morsitans/T.brucei rhodesiense. Whatever the T. brucei subspecies, whereas the onset of their developmental program in the zoo-anthropophilic blood feeding flies does unfold in the fly midgut, its completion is taking place in the fly salivary gland where does emerge a low size metacyclic trypomastigote population displaying features that account for its establishment in mammals-human individuals included. Considering that the two Glossina—T. brucei pairs introduced above share similarity with respect to the developmental program of this African parasite, we were curious to map on the Glossina morsitans morsitans (Gmm), the Differentially Expressed Genes (DEGs) we listed in a previous study. Briefly, using the gut samples collected at days 3, 10, and 20 from Gpg that were fed or not at day 0 on Tbg—hosting mice, these DGE lists were obtained from RNA seq—based approaches. Here, post the mapping on the quality controlled DEGs on the Gmm genome, the identified ortholog genes were further annotated, the resulting datasets being compared. Around 50% of the Gpg DEGs were shown to have orthologs in the Gmm genome. Under one of the three Glossina midgut sampling conditions, the number of DEGs was even higher when mapping on the Gmm genome than initially recorded. Many Gmm genes annotated as “Hypothetical” were mapped and annotated on many distinct databases allowing some of them to be properly identified. We identify Glossina fly candidate genes encoding (a) a broad panel of proteases as well as (b) chitin—binding proteins, (c) antimicrobial peptide production—Pro3 protein, transferrin, mucin, atttacin, cecropin, etc—to further select in functional studies, the objectives being to probe and validated fly genome manipulation that prevents the onset of the developmental program of one or the other T. brucei spp. stumpy form sampled by one of the other bloodfeeding Glossina subspecies.

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“…However, as mentioned above, when potential PPARs target genes are evaluated, the RXR target genes must also be considered. Several genes have been linked to the different PPARs, including some Apo-family of lipid transporters; other nuclear receptors, such as LXR; the UCP-3 (energy metabolism); among others (Kanehisa and Goto, 2000; Heinäniemi et al, 2007; Kanehisa et al, 2014). Interestingly, some authors have demonstrated that among the PPAR target genes might also be present some key components of relevant cellular signaling pathways, such as Wnt (Toledo and Inestrosa, 2010) and mTOR (Hagland et al, 2013), among others.…”

Section: Nuclear Receptors (Nrs): Ppars and Their Potential Role In Amentioning

confidence: 99%

Alzheimerâ€™s disease: relevant molecular and physiopathological events affecting amyloid-Î² brain balance and the putative role of PPARs

Zolezzi

Bastías-Candia

Santos

et al. 2014

Front. Aging Neurosci.

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Alzheimer’s disease (AD) is the most common form of age-related dementia. With the expected aging of the human population, the estimated morbidity of AD suggests a critical upcoming health problem. Several lines of research are focused on understanding AD pathophysiology, and although the etiology of the disease remains a matter of intense debate, increased brain levels of amyloid-β (Aβ) appear to be a critical event in triggering a wide range of molecular alterations leading to AD. It has become evident in recent years that an altered balance between production and clearance is responsible for the accumulation of brain Aβ. Moreover, Aβ clearance is a complex event that involves more than neurons and microglia. The status of the blood-brain barrier (BBB) and choroid plexus, along with hepatic functionality, should be considered when Aβ balance is addressed. Furthermore, it has been proposed that exposure to sub-toxic concentrations of metals, such as copper, could both directly affect these secondary structures and act as a seeding or nucleation core that facilitates Aβ aggregation. Recently, we have addressed peroxisomal proliferator-activated receptors (PPARs)-related mechanisms, including the direct modulation of mitochondrial dynamics through the PPARγ-coactivator-1α (PGC-1α) axis and the crosstalk with critical aging- and neurodegenerative-related cellular pathways. In the present review, we revise the current knowledge regarding the molecular aspects of Aβ production and clearance and provide a physiological context that gives a more complete view of this issue. Additionally, we consider the different structures involved in AD-altered Aβ brain balance, which could be directly or indirectly affected by a nuclear receptor (NR)/PPAR-related mechanism.

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The Kyoto Encyclopedia of Genes and Genomes—KEGG

Cited by 163 publications

References 4 publications

Transcriptomic and Network Analysis of Minor Salivary Glands of Patients With Primary Sjögren’s Syndrome

Transcriptomic and Network Analysis of Minor Salivary Glands of Patients With Primary Sjögren’s Syndrome

Comparative Genomics of Glossina palpalis gambiensis and G. morsitans morsitans to Reveal Gene Orthologs Involved in Infection by Trypanosoma brucei gambiense

Alzheimerâ€™s disease: relevant molecular and physiopathological events affecting amyloid-Î² brain balance and the putative role of PPARs

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