g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

Raudvere, Uku; Kolberg, Liis; Kuzmin, Ivan; Arak, T. V.; Adler, Priit; Peterson, Hedi; Vilo, Jaak

doi:10.1093/nar/gkz369

Cited by 4,343 publications

(4,083 citation statements)

References 39 publications

Supporting

Mentioning

3,700

Contrasting

Unclassified

Order By: Relevance

“…The 37 downstream genes were enriched for sequence motifs from the ELF transcription factors, which have a strong sequence resemblance. Significant associations were observed for ELF3, ELF4 and ELF5 (p-adj: 3.3×10^-7, 6.8×10^-5 and 2.2×10^-6 respectively, g:Profiler 24 ), and 20 out of the 37 trans-eGenes were also known match the ELF2 sequence motif. A second hotspot, in cis linked to a CREB3L2 and in trans linked to 8 eGenes, was interesting as we observed an enrichment for the reactome pathway: "ER to Golgi Anterograde Transport" (p-adj<5.6×10^-5), CREB3L2 was previously linked to both the ER and Golgi complex 25 .…”

Section: Mapping Large-effect Rare Variants Impacting Gene Expressionmentioning

confidence: 99%

Systematic assessment of regulatory effects of human disease variants in pluripotent cells

Bonder

Smail

Gloudemans

et al. 2019

Preprint

View full text Add to dashboard Cite

Identifying regulatory genetic effects in pluripotent cells provides important insights into disease variants with potentially transient or developmental origins. Combining existing and newlygenerated data, we established a population-scale resource of 1,367 induced pluripotent stem cell lines derived from 948 unique donors, with matched RNA-sequencing (RNA-seq) and genetic information. The sample size of our study allowed us to significantly expand our knowledge of quantitative trait loci (QTL) in pluripotent human cells and their broad trait and disease relevance.We identified cis-QTL for conventional gene expression levels but also transcript-ratio, exon expression levels, alternative-splicing and alternative polyadenylation usage, cumulatively yielding cis regulatory effects for 18,556 genes. We assessed the effects of rare variants identified from whole-genome sequencing data, by relating these to gene expression outliers, observing an enrichment for rare, deleterious variants in iPSCs with outlying expression profiles, which exceeds previous observations in differentiated tissues. Finally, we assessed distal QTL on a genomewide scale, identifying 193 trans-eQTL, linked to 191 trans-eGenes (FDR <10%), 38% of which were replicated in independent samples.By linking our regulatory map of rare and common QTL to comprehensive GWAS data, we identified high-confidence colocalization events for 4,336 individual GWAS loci, which includes physical traits such as height and coronary artery disease. In addition, we identify rare variant associations for metabolic rate and trans-eQTL linked to both cancer and height. Collectively, our data greatly expand the regulatory landscape in human pluripotent cells, and catalogues traitassociated variants that have potential developmental or transient contexts.

show abstract

Section: Mapping Large-effect Rare Variants Impacting Gene Expressionmentioning

confidence: 99%

Systematic assessment of regulatory effects of human disease variants in pluripotent cells

Bonder

Smail

Gloudemans

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Gene Ontology (GO) enrichment analysis of differentially expressed miRNA genes were implemented by the iDEP.90 web-based analysis software, PANTHER GO Enrichment Analysis (http://geneontology.org/) (Ashburner et al, 2000;The Gene Ontology Consortium, 2019;Mi, Muruganujan & Thomas, 2012), g:Profiler/g:GOSt/g:Convert (https://biit.cs.ut.ee/gprofiler/gost) (Raudvere et al, 2019;Reimand et al, 2007), ClueGO and CluePedia Cytoscape plug-in (http://apps.cytoscape.org/apps/cluego) (Bindea et al, 2009) and GOseq R package, in which gene length bias was corrected. GO terms with corrected p-value less than 0.05 were considered significantly enriched by differential expressed genes (Young et al, 2010).…”

Section: Gene Ontology and Kegg Enrichment Analysis Of Differentiallymentioning

confidence: 99%

Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells

Chuammitri

Vannamahaxay

Sornpet

et al. 2020

PeerJ

View full text Add to dashboard Cite

Background: MicroRNAs (miRNAs) play an essential role in gene regulators in many biological and molecular phenomena. Unraveling the involvement of miRNA as a key cellular factor during in vitro canine parvovirus (CPV) infection may facilitate the discovery of potential intervention candidates. However, the examination of miRNA expression profiles in CPV in tissue culture systems has not been fully elucidated. Method: In the present study, we utilized high-throughput small RNA-seq (sRNAseq) technology to investigate the altered miRNA profiling in miRNA libraries from uninfected (Control) and CPV-2c infected Crandell Reese Feline Kidney cells. Results: We identified five of known miRNAs (miR-222-5p, miR-365-2-5p, miR-1247-3p, miR-322-5p and miR-361-3p) and three novel miRNAs (Novel 137, Novel 141 and Novel 102) by sRNA-seq with differentially expressed genes in the miRNA repertoire of CPV-infected cells over control. We further predicted the potential target genes of the aforementioned miRNAs using sequence homology algorithms. Notably, the targets of miR-1247-3p exhibited a potential function associated with cellular defense and humoral response to CPV. To extend the probing scheme for gene targets of miR-1247-3p, we explored and performed Gene Ontology (GO) enrichment analysis of its target genes. We discovered 229 putative targets from a total of 38 enriched GO terms. The top over-represented GO enrichment in biological process were lymphocyte activation and differentiation, marginal zone B cell differentiation, negative regulation of cytokine production, negative regulation of programed cell death, and negative regulation of signaling. We next constructed a GO biological process network composed of 28 target genes of miR-1247-3p, of How to cite this article Chuammitri P, Vannamahaxay S, Sornpet B, Pringproa K, Patchanee P. 2020. Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells. PeerJ 8:e8522

show abstract

“…For Kuiper's test, the distribution of GO terms was compared with an empirically-determined background distribution. Gene identifiers were submitted to g:Profiler (Raudvere et al , 2019) for KEGG and Wiki pathway enrichment analysis.…”

Section: Pathway Enrichment Analysismentioning

confidence: 99%

Changes in ambient temperature are the prevailing cue in determiningBrachypodium distachyondiurnal gene regulation

MacKinnon

Cole

et al. 2019

Preprint

View full text Add to dashboard Cite

1 SUMMARY• Plants are continuously exposed diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24-hour period, enabling the anticipation of these events. • We used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions. • Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion reported in other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 h to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon , we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore we identified sequence motifs enriched in the promoters of similarly-phased genes, some potentially associated with transcription factors. • When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species. REFERENCESAdams S, Grundy J, Veflingstad SR, Dyer NP, Hannah MA, Ott S, Carré IA . 2018 . Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome-wide analysis of LHY binding targets. New Phytologist 220 : 893-907. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ . 1990 . Basic local alignment search tool. Journal of Molecular Biology 215 : 403-410. Arsovski AA, Pradinuk J, Guo XQ, Wang S, Adams KL . 2015 . Evolution of cis-regulatory elements and regulatory networks in duplicated genes of Arabidopsis. Plant Physiology 169 : 2982. AAR, et al. 2015 . ELF3 controls thermoresponsive growth in Arabidopsis. Current Biology: CB 25 : 194-199. Calixto CPG, Waugh R, Brown JWS . 2015 . Evolutionary relationships among barley and Arabidopsis core circadian clock and clock-associated genes. Journal of Molecular Evolution 80 : 108-119. Campoli C, Shtaya M, Davis S, von Korff M . 2012 . Expression conservation within the circadian clock of a monocot: natural variation at barley Ppd-H1 affects circadian expression of flowering time genes, but 17 not clock orthologs. BMC Plant Biology 12 : 97. Casal JJ, Qüesta JI . 2018 . Light and temperature cues: multitasking receptors and transcriptional integrators. The New Phytologist Dowson-Day MJ, Millar AJ . 1999 . Circadian dysfunction causes aberrant hypocotyl elongation patterns in Arabidopsis. The Plant Journal: for cell and molecular biology 17 : 63-71. Edwards KD, Anderson PE, Hall A, Salathia NS, Locke JC, Lynn JR, Straume M, Smith JQ, Millar AJ . 2006 . FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis c...

show abstract

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

Cited by 4,343 publications

References 39 publications

Systematic assessment of regulatory effects of human disease variants in pluripotent cells

Systematic assessment of regulatory effects of human disease variants in pluripotent cells

Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells

Changes in ambient temperature are the prevailing cue in determiningBrachypodium distachyondiurnal gene regulation

Contact Info

Product

Resources

About