FunRich: An open access standalone functional enrichment and interaction network analysis tool

Pathan, Mohashin; Keerthikumar, Shivakumar; Ang, Ching‐Seng; Gangoda, Lahiru; Quek, Camelia; Williamson, Nicholas A.; Mouradov, Dmitri; Sieber, Oliver M.; Simpson, Richard J.; Salim, Agus; Bacic, Antony; Hill, Andrew F.; Stroud, David A.; Ryan, Michael; Agbinya, Johnson I.; Mariadason, John M.; Burgess, Antony W.; Mathivanan, Suresh

doi:10.1002/pmic.201400515

Cited by 1,111 publications

(885 citation statements)

References 7 publications

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“…(a) A Venn diagram showing the common and unique number of proteins of the UBtip cell line and the UBtip cell line-derived exosomes (both protein sets are the common proteins derived from two independent biological replicates). Venn diagrams were generated using FunRich [31]. (b) Analysis of cellular component GO terms.…”

Section: Resultsmentioning

confidence: 99%

Exosomes as secondary inductive signals involved in kidney organogenesis

Krause

Rak-Raszewska

Naillat

et al. 2018

J of Extracellular Vesicle

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The subfraction of extracellular vesicles, called exosomes, transfers biological molecular information not only between cells but also between tissues and organs as nanolevel signals. Owing to their unique properties such that they contain several RNA species and proteins implicated in kidney development, exosomes are putative candidates to serve as developmental programming units in embryonic induction and tissue interactions. We used the mammalian metanephric kidney and its nephron-forming mesenchyme containing the nephron progenitor/stem cells as a model to investigate if secreted exosomes could serve as a novel type of inductive signal in a process defined as embryonic induction that controls organogenesis. As judged by several characteristic criteria, exosomes were enriched and purified from a cell line derived from embryonic kidney ureteric bud (UB) and from primary embryonic kidney UB cells, respectively. The cargo of the UB-derived exosomes was analysed by qPCR and proteomics. Several miRNA species that play a role in Wnt pathways and enrichment of proteins involved in pathways regulating the organization of the extracellular matrix as well as tissue homeostasis were identified. When labelled with fluorescent dyes, the uptake of the exosomes by metanephric mesenchyme (MM) cells and the transfer of their cargo to the cells can be observed. Closer inspection revealed that besides entering the cytoplasm, the exosomes were competent to also reach the nucleus. Furthermore, fluorescently labelled exosomal RNA enters into the cytoplasm of the MM cells. Exposure of the embryonic kidney-derived exosomes to the whole MM in an ex vivo organ culture setting did not lead to an induction of nephrogenesis but had an impact on the overall organization of the tissue. We conclude that the exosomes provide a novel signalling system with an apparent role in secondary embryonic induction regulating organogenesis.

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Section: Resultsmentioning

confidence: 99%

Exosomes as secondary inductive signals involved in kidney organogenesis

Krause

Rak-Raszewska

Naillat

et al. 2018

J of Extracellular Vesicle

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“…Protein abundance was determined according to the intensity-based absolute quantification (iBAQ) metric [23]. Gene ontology was investigated with FunRich v3.1.3 using the Gene Ontology Database [24,25]. The peptides identified by mass spectrometry were visualised using Protter [26] with membrane orientations as specified in UniProt annotations [27].…”

Section: Methodsmentioning

confidence: 99%

Enrichment of extracellular vesicles from human synovial fluid using size exclusion chromatography

Foers

Chatfield

Dagley

et al. 2018

J of Extracellular Vesicle

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As a complex biological fluid, human synovial fluid (SF) presents challenges for extracellular vesicle (EV) enrichment using standard methods. In this study of human SF, a size exclusion chromatography (SEC)-based method of EV enrichment is shown to deplete contaminants that remain after standard ultracentrifugation-based enrichment methods. Specifically, considerable levels of serum albumin, the high-density lipoprotein marker, apolipoprotein A-I, fibronectin and other extracellular proteins and debris are present in EVs prepared by differential ultracentrifugation. While the addition of a sucrose density gradient purification step improved purification quality, some contamination remained. In contrast, using a SEC-based approach, SF EVs were efficiently separated from serum albumin, apolipoprotein A-I and additional contaminating proteins that co-purified with high-speed centrifugation. Finally, using high-resolution mass spectrometry analysis, we found that residual contaminants which remain after SEC, such as fibronectin and other extracellular proteins, can be successfully depleted by proteinase K. Taken together, our results highlight the limitations of ultracentrifugation-based methods of EV isolation from complex biological fluids and suggest that SEC can be used to obtain higher purity EV samples. In this way, SEC-based methods are likely to be useful for identifying EV-enriched components and improving understanding of EV function in disease.

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“…The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Vizcaino et al., 2016) partner repository with the dataset identifier PXD006463. GO analysis was performed with FunRich software (2.1.2) (Pathan et al., 2015). The Entrez Gene IDs retrieved from UniProtKB accession numbers were mapped to cellular components (CC), molecular functions (MF), and biological processes (BP) items using default statistical parameters (threshold: count 2, ease 0.1).…”

Section: Methodsmentioning

confidence: 99%

Involvement of serum‐derived exosomes of elderly patients with bone loss in failure of bone remodeling via alteration of exosomal bone‐related proteins

et al. 2018

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SummaryExosomes are secreted into the blood by various types of cells. These extracellular vesicles are involved in the contribution of exosomal proteins to osteoblastic or osteoclastic regulatory networks during the failure of bone remodeling, which results in age‐related bone loss. However, the molecular changes in serum‐derived exosomes (SDEs) from aged patients with low bone density and their functions in bone remodeling remain to be fully elucidated. We present a quantitative proteomics analysis of exosomes purified from the serum of the elderly patients with osteoporosis/osteopenia and normal volunteers; these data are available via Proteome Xchange with the identifier PXD006463. Overall, 1,371 proteins were identified with an overlap of 1,160 Gene IDs among the ExoCarta proteins. Bioinformatics analysis and in vitro studies suggested that protein changes in SDEs of osteoporosis patients are not only involved in suppressing the integrin‐mediated mechanosensation and activation of osteoblastic cells, but also trigger the differentiation and resorption of osteoclasts. In contrast, the main changes in SDEs of osteopenia patients facilitated both activation of osteoclasts and formation of new bone mass, which could result in a compensatory elevation in bone remodeling. While the SDEs from aged normal volunteers might play a protective role in bone health through facilitating adhesion of bone cells and suppressing aging‐associated oxidative stress. This information will be helpful in elucidating the pathophysiological functions of SDEs and aid in the development of senile osteoporosis diagnostics and therapeutics.

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FunRich: An open access standalone functional enrichment and interaction network analysis tool

Cited by 1,111 publications

References 7 publications

Exosomes as secondary inductive signals involved in kidney organogenesis

Exosomes as secondary inductive signals involved in kidney organogenesis

Enrichment of extracellular vesicles from human synovial fluid using size exclusion chromatography

Involvement of serum‐derived exosomes of elderly patients with bone loss in failure of bone remodeling via alteration of exosomal bone‐related proteins

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