PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

Thomas, Paul D.; Muruganujan, Anushya; Ebert, Dustin; Huang, Xiaosong; Thomas, Paul D.

doi:10.1093/nar/gky1038

Cited by 2,501 publications

(2,223 citation statements)

References 22 publications

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“…To inquire in an unbiased way about the differences in signaling pathways and cellular processes affected by IOP, GO analysis using PANTHER was performed (Mi, Muruganujan, Ebert, Huang, & Thomas, ). This approach revealed that processes of the immune system response, inflammation, and extracellular matrix composition and cell–matrix interaction were significantly changed in IOP samples (Table ).…”

Section: Resultsmentioning

confidence: 99%

“…Expectedly, GCV treatment prevented IOPinduced increase in p16Ink4a expression observed in non treated eyes ( Figure 3b). Importantly, this was accompanied by significant decrease in numbers of IOP-induced β-galactosidase-positive senescent cells in 3-day GCV treated retinas as compared to nontreated cells (Figure 3c To inquire in an unbiased way about the differences in signaling pathways and cellular processes affected by IOP, GO analysis using PANTHER was performed (Mi, Muruganujan, Ebert, Huang, & Thomas, 2019). This approach revealed that processes of the immune system response, inflammation, and extracellular matrix composition and cell-matrix interaction were significantly changed in IOP samples (Table 1).…”

Section: Re Sultsmentioning

confidence: 99%

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Early removal of senescent cells protects retinal ganglion cells loss in experimental ocular hypertension

et al. 2019

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Experimental ocular hypertension induces senescence of retinal ganglion cells (RGCs) that mimics events occurring in human glaucoma. Senescence‐related chromatin remodeling leads to profound transcriptional changes including the upregulation of a subset of genes that encode multiple proteins collectively referred to as the senescence‐associated secretory phenotype (SASP). Emerging evidence suggests that the presence of these proinflammatory and matrix‐degrading molecules has deleterious effects in a variety of tissues. In the current study, we demonstrated in a transgenic mouse model that early removal of senescent cells induced upon elevated intraocular pressure (IOP) protects unaffected RGCs from senescence and apoptosis. Visual evoked potential (VEP) analysis demonstrated that remaining RGCs are functional and that the treatment protected visual functions. Finally, removal of endogenous senescent retinal cells after IOP elevation by a treatment with senolytic drug dasatinib prevented loss of retinal functions and cellular structure. Senolytic drugs may have the potential to mitigate the deleterious impact of elevated IOP on RGC survival in glaucoma and other optic neuropathies.

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Section: Resultsmentioning

confidence: 99%

Section: Re Sultsmentioning

confidence: 99%

Early removal of senescent cells protects retinal ganglion cells loss in experimental ocular hypertension

et al. 2019

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“…After protein identification with Protein Pilot software, the data were analysed with the UniprotKB database (http://www.uniprot.org.br, Boutet et al, ) to obtain gene ontology (GO) annotations using the categories molecular function, biological process, protein class and cellular component. Figures from the GO data were prepared with the free software Panther (Panther Classification System, http://www.pantherdb.org, Mi, Muruganujan, Ebert, Huang, & Thomas, ).…”

Section: Methodsmentioning

confidence: 99%

“…Gene ontology analysis of the proteins according to the categories molecular function, biological process and cellular component was performed with the UniprotKB program (http://www.uniprot.org, Boutet et al, ). Images were produced online via http://www.pantherdb.org, Panther version 10 (Mi et al, ).…”

Section: Methodsmentioning

confidence: 99%

Proteomic analysis of amniotic and allantoic fluid from buffaloes during foetal development

Boy

Codognoto

Faleiros‐Lima

et al. 2019

Reprod Domestic Animals

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The objective of this study was to describe the dynamic changes in protein composition and protein abundance in amniotic and allantoic fluids from buffaloes during gestation. Amniotic and allantoic fluids were collected during the first, second and third trimesters of gestation. The foetuses were measured and weighed. Fluid samples were centrifuged at 800 g for 10 min and then at 10,000 g for 60 min at 4°C. The supernatant was collected to determine the total protein concentration. Based on total protein concentration, an aliquot (50 μg) was used for in‐solution tryptic digestion, and mass spectrometry analysis (nano‐LC‐MS/MS) was performed. A multivariate statistical analysis of the proteomic data was conducted. Across the different stages of buffalo gestation, fifty‐one proteins were found in the amniotic fluid, and twenty‐one were found in the allantoic fluid. A total of twelve proteins were common among the stages, and four presented significant differences (VIP score α > 1). Fibronectin and alpha‐1‐antiproteinase were more abundant in the amniotic fluid than in the allantoic fluid. Alpha‐2‐macroglobulin and alpha‐2‐HS‐glycoprotein were more abundant in the allantoic fluid than in the amniotic fluid. Alpha‐2‐macroglobulin participates in remodelling and growth of the uterus at beginning of the gestation (first trimester), and these findings indicate that can serve as a potential tool for the early diagnosis of pregnancy in buffaloes.

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“…Lists were generated by taking all proteins with a log 2 fold change greater than 0.2 comparing WT MHV68 to R443I and looking at the molecular function enrichment in Panther DB [66]. Graphs display the mean with standard deviation of 9 biological replicates including mock, MHV68 and R443I infection conditions.…”

Section: S2 Fig Tmt-ms Fractionation Validation and Panther Db Termsmentioning

confidence: 99%

RNA decay during gammaherpesvirus infection reduces RNA polymerase II occupancy of host promoters but spares viral promoters

et al. 2020

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In mammalian cells, widespread acceleration of cytoplasmic mRNA degradation is linked to impaired RNA polymerase II (Pol II) transcription. This mRNA decay-induced transcriptional repression occurs during infection with gammaherpesviruses including Kaposi's sarcomaassociated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68), which encode an mRNA endonuclease that initiates widespread RNA decay. Here, we show that MHV68induced mRNA decay leads to a genome-wide reduction of Pol II occupancy at mammalian promoters. This reduced Pol II occupancy is accompanied by down-regulation of multiple Pol II subunits and TFIIB in the nucleus of infected cells, as revealed by mass spectrometrybased global measurements of protein abundance. Viral genes, despite the fact that they require Pol II for transcription, escape transcriptional repression. Protection is not governed by viral promoter sequences; instead, location on the viral genome is both necessary and sufficient to escape the transcriptional repression effects of mRNA decay. We propose a model in which the ability to escape from transcriptional repression is linked to the localization of viral DNA within replication compartments, providing a means for these viruses to counteract decay-induced transcript loss. Author summaryWhile transcription and messenger RNA (mRNA) decay are often considered to be the unlinked beginning and end of gene expression, recent data indicate that alterations to either stage can impact the other. Here we study this connection in the context of lytic gammaherpesvirus infection, which accelerates mRNA degradation through the expression of the viral endonuclease muSOX. We show that RNA polymerase II promoter occupancy is broadly reduced across mammalian promoters in response to infection-induced mRNA PLOS Pathogens | https://doi.

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PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

Cited by 2,501 publications

References 22 publications

Early removal of senescent cells protects retinal ganglion cells loss in experimental ocular hypertension

Early removal of senescent cells protects retinal ganglion cells loss in experimental ocular hypertension

Proteomic analysis of amniotic and allantoic fluid from buffaloes during foetal development

RNA decay during gammaherpesvirus infection reduces RNA polymerase II occupancy of host promoters but spares viral promoters

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