WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit

Wang, Jing; Vasaikar, Suhas; Shi, Zhiao; Greer, Michael S.; Zhang, Bing

doi:10.1093/nar/gkx356

Cited by 1,018 publications

(899 citation statements)

References 19 publications

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“…We further evaluated these effects using DisGeNET28,29. At the gene level, overrepresentation enrichment analysis (ORA) with WebGestalt67 on the nearest genes to all BP loci was carried out. Moreover, we tested sentinel SNPs at all published and novel (N=901) loci for association with lifestyle related data including food, water and alcohol intake, anthropomorphic traits and urinary sodium, potassium and creatinine excretion using the recently developed Stanford Global Biobank Engine and the Gene ATLAS68.…”

Section: Methodsmentioning

confidence: 99%

Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits

Εvangelou¹,

Warren²,

et al. 2018

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High blood pressure is a highly heritable and modifiable risk factor for cardiovascular disease. We report the largest genetic association study of blood pressure traits (systolic, diastolic, pulse pressure) to date in over one million people of European ancestry. We identify 535 novel blood pressure loci that not only offer new biological insights into blood pressure regulation but also reveal shared genetic architecture between blood pressure and lifestyle exposures. Our findings identify new biological pathways for blood pressure regulation with potential for improved cardiovascular disease prevention in the future.

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Section: Methodsmentioning

confidence: 99%

Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits

Εvangelou¹,

Warren²,

et al. 2018

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“…The cutoffs for log2 fold change (log2FC) and PDR were |log2FC| > = 1 and FDR ≤ 0.001. Functional enrichment analysis was analyzed using WebGestalt (Wang et al, 2017). …”

Section: Methodsmentioning

confidence: 99%

Diverse Long RNAs Are Differentially Sorted into Extracellular Vesicles Secreted by Colorectal Cancer Cells

et al. 2018

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SUMMARY The regulation and functional roles of secreted coding and long noncoding RNAs (lncRNAs; >200 nt) are largely unknown. We previously showed that mutant KRAS colorectal cancer (CRC) cells release extracellular vesicles (EVs) containing distinct proteomes, microRNAs (miRNAs), and circular RNAs. Here, we comprehensively identify diverse classes of CRC extracellular long RNAs secreted in EVs and demonstrate differential export of specific RNAs. Distinct noncoding RNAs, including antisense transcripts and transcripts derived from pseudogenes, are enriched in EVs compared to cellular profiles. We detected strong enrichment of Rab13 in mutant KRAS EVs and demonstrate functional delivery of Rab13 mRNA to recipient cells. To assay functional transfer of lncRNAs, we implemented a CRISPR/ Cas9-based RNA-tracking system to monitor delivery to recipient cells. We show that gRNAs containing export signals from secreted RNAs can be transferred from donor to recipient cells. Our data support the existence of cellular mechanisms to selectively export diverse classes of RNA.

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“…19 2.4 | Gene ontology and pathway enrichment analysis of DEGs Gene ontology (GO) analysis, a common useful method for highthroughput genome or transcriptome data, was used to identify characteristic biological function of DEGs. 26 The Database for Annotation, Visualization, and Integrated Discovery (DAVID v6.8, https://david.ncifcrf.gov/tools. 24 Kyoto Encyclopedia of Genes and Genomes (KEGG, http:// www.genome.jp/kegg/pathway.html) is a knowledge base for systematic analysis of gene function, linking genomic information with highorder functional information.…”

Section: Degs Identificationmentioning

confidence: 99%

Comparison of rheumatoid arthritis (RA) and osteoarthritis (OA) based on microarray profiles of human joint fibroblast‐like synoviocytes

Cai

Jiang

et al. 2018

Cell Biochemistry & Function

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The purpose of the present study was to investigate the underlying molecular mechanism of osteoarthritis (OA) and rheumatoid arthritis (RA) based on microarray profiles. Three human joint fibroblast-like synoviocytes (FLSs) microarray profiles including 26 OA samples, 33 RA samples, and 20 healthy control (HC) samples were downloaded from the GEO database. Differentially expressed genes (DEGs) between OA and HC (DEGsOA) and RA and HC (DEGsRA) were identified. Co-expressed and specific genes were analysed between DEGsOA and DEGsRA. Gene ontology, KEGG pathway enrichment, PPI network, and GSEA were performed to predict the function of DEGs. Two hundred seventy-six and 410 differential genes in DEGsOA and DEGsRA were observed. One hundred fifty coexpressed genes and 126 OA-specific genes (SELE, SERPINE1, and NFKBIA were the key genes) between DEGsOA and DEGsRA were enriched in the tumour necrosis factor (TNF) signalling pathway. However, 260 RA-specific genes of which the key genes were CCR5, CCR7, CXCR4, CCL5, and CCR4 were enriched in chemokine signalling pathway. Therefore, FLSs might exert an inflammatory effect by regulating TNF signalling pathway, targeting SELE, SERPINE1, and NFKBIA during the process of OA. Although TNF signalling pathway was also involved in the synovitis of RA, chemokine signalling pathway played the key role in RA FLSs mediating cell migration, invasion, and release of chemotaxis. In addition, CCR5, CCR7, CXCR4, CCL5, and CCR4 might be hub genes in RA. The different biomarkers and pathways identified in OA and RA may provide references for further study.List of abbreviations: CCL5, C-C motif chemokine ligand 5; CCRs, C-C motif chemokine receptors; CD95, FAS cell surface death receptor; Co-expressed genes, the common genes both in DEGsOA and DEGsRA groups; CXCR4, C-X-C motif chemokine receptor 4; DAVID, Database for Annotation, Visualization, and Integrated Discovery; DEGs, differently expressed genes; DEGsOA, differently expressed genes between osteoarthritis and healthy fibroblast-like synoviocytes; DEGsRA, differently expressed genes between rheumatoid arthritis and healthy fibroblast-like synoviocytes; DLL1, delta-like protein 1

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WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit

Cited by 1,018 publications

References 19 publications

Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits

Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits

Diverse Long RNAs Are Differentially Sorted into Extracellular Vesicles Secreted by Colorectal Cancer Cells

Comparison of rheumatoid arthritis (RA) and osteoarthritis (OA) based on microarray profiles of human joint fibroblast‐like synoviocytes

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