g:Profiler—a web server for functional interpretation of gene lists (2016 update)

Reimand, Jüri; Arak, T. V.; Adler, Priit; Kolberg, Liis; Reisberg, Sulev; Peterson, Hedi; Vilo, Jaak

doi:10.1093/nar/gkw199

Cited by 1,270 publications

(1,230 citation statements)

References 54 publications

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“…Cufflinks (v2.1.1) was used to estimate the relative abundance of transcripts based on how many reads supported each one, taking into account biases in library preparation protocols. Expression data was statistically analyzed in R. Functional annotation and pathway analysis was carried out using a combination of gProfiler (Reimand et al 2016) and Gene Ontology (Ashburner et al 2000), and KEGG pathways (Kanehisa and Goto 2000;Kanehisa et al 2015) implemented in ClueGO in Cytoscape v3.2 (Bindea et al 2009). A hypergeometric test with Benjamin and Hochberg false discovery rate (FDR) was performed using the default parameters implemented in ClueGO.…”

Section: Data Handling Proceduresmentioning

confidence: 99%

Characterization of genes and pathways that respond to heat stress in Holstein calves through transcriptome analysis

Srikanth

Kwon

Lee

2017

Cell Stress and Chaperones

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This study aimed to investigate the genes and pathways that respond to heat stress in Holstein bull calves exposed to severe ranges of temperature and humidity. A total of ten animals from 4 to 6 months of age were subjected to heat stress at 37°C and 90 % humidity for 12 h. Skin and rectal temperatures were measured before and after heat stress; while no correlation was found between them before heat stress, a moderate correlation was detected after heat stress, confirming rectal temperature to be a better barometer for monitoring heat stress. RNAseq analysis identified 8567 genes to be differentially regulated, out of which 465 genes were significantly upregulated (≥2-fold, P < 0.05) and 49 genes were significantly downregulated (≤2-fold, P < 0.05) in response to heat stress. Significant terms and pathways enriched in response to heat stress included chaperones, cochaperones, cellular response to heat stress, phosphorylation, kinase activation, immune response, apoptosis, Toll-like receptor signaling pathway, Pi3K/AKT activation, protein processing in endoplasmic reticulum, interferon signaling, pathways in cancer, estrogen signaling pathway, and MAPK signaling pathway. The differentially expressed genes were validated by quantitative realtime PCR analysis, which confirmed the tendency of the expression. The genes and pathways identified in this analysis extend our understanding of transcriptional response to heat stress and their likely functioning in adapting the animal to hyperthermic stress. The identified genes could be used as candidate genes for association studies to select and breed animals with improved heat tolerance.

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Section: Data Handling Proceduresmentioning

confidence: 99%

Characterization of genes and pathways that respond to heat stress in Holstein calves through transcriptome analysis

Srikanth

Kwon

Lee

2017

Cell Stress and Chaperones

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“…Analysis of gene sets and significance estimation is carried out using g: Profiler (http://biit.cs.ut.ee/gprofiler/index.cgi) [39]. This web server uses hyper geometric distribution for significance estimation.…”

Section: Functional Impact Of Alternative Splicingmentioning

confidence: 99%

Genome‐wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron‐based splicing and its possible function through network analysis

et al. 2015

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a b s t r a c tIn this study, using homology mapping of assembled expressed sequence tags against the genomic data, we identified alternative splicing events in barley. Results demonstrated that intron retention is frequently associated with specific abiotic stresses. Network analysis resulted in discovery of some specific sub-networks between miRNAs and transcription factors in genes with high number of alternative splicing, such as cross talk between SPL2, SPL10 and SPL11 regulated by miR156 and miR157 families. To confirm the alternative splicing events, elongation factor protein (MLOC_3412) was selected followed by experimental verification of the predicted splice variants by Semi quantitative Reverse Transcription PCR (qRT-PCR). Our novel integrative approach opens a new avenue for functional annotation of alternative splicing through regulatory-based network discovery.

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“…Functional analysis was undertaken using the functional enrichment analysis tool g:Profiler 40 . Genes identified as containing mammalian-classifying splicing events were compared to a background of multi-exon genes conserved within vertebrates.…”

Section: Functional Analysismentioning

confidence: 99%

Whippet: an efficient method for the detection and quantification of alternative splicing reveals extensive transcriptomic complexity

Sterne-Weiler

Weatheritt

Best

et al. 2017

Preprint

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Alternative splicing (AS) is a widespread process underlying the generation of transcriptomic and proteomic diversity in metazoans. Major challenges in comprehensively detecting and quantifying patterns of AS are that RNA-seq datasets are expanding near exponentially, while existing analysis tools are computationally inefficient and ineffective at handling complex splicing patterns. Here, we describe Whippet, a method that rapidly, and with minimal hardware requirements, models and quantifies splicing events of any complexity without significant loss of accuracy.Using an entropic measure of splicing complexity, Whippet reveals that approximately 33% of human protein coding genes contain complex AS events that result in substantial expression of multiple splice isoforms. These events frequently affect tandem arrays of folded protein domains. Remarkably, high-entropy AS events are more prevalent in tumour relative to matched normal tissues, and these differences correlate with increased expression of proto-oncogenic splicing factors. Whippet thus affords the rapid and accurate analysis of AS events of any complexity, and as such will facilitate biomedical research.

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g:Profiler—a web server for functional interpretation of gene lists (2016 update)

Cited by 1,270 publications

References 54 publications

Characterization of genes and pathways that respond to heat stress in Holstein calves through transcriptome analysis

Characterization of genes and pathways that respond to heat stress in Holstein calves through transcriptome analysis

Genome‐wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron‐based splicing and its possible function through network analysis

Whippet: an efficient method for the detection and quantification of alternative splicing reveals extensive transcriptomic complexity

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