StemCellNet: an interactive platform for network-oriented investigations in stem cell biology

Pinto, José; Kalathur, Ravi Kiran Reddy; Machado, Rui S. R.; Xavier, Joana M.; Bragança, José; Futschik, Matthias E.

doi:10.1093/nar/gku455

Cited by 19 publications

(5 citation statements)

References 35 publications

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“…Finally, we plan to link StemMapper to other computational resources developed in our group for SC biology analysis, i.e. StemCellNet ( 32 ) and StemChecker ( 33 ) enabling the user to conduct a multitude of complementary in silico analyses within the domain of SC biology.…”

Section: Discussionmentioning

confidence: 99%

StemMapper: a curated gene expression database for stem cell lineage analysis

Pinto

Machado

Magno

et al. 2017

Nucleic Acids Research

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Transcriptomic data have become a fundamental resource for stem cell (SC) biologists as well as for a wider research audience studying SC-related processes such as aging, embryonic development and prevalent diseases including cancer, diabetes and neurodegenerative diseases. Access and analysis of the growing amount of freely available transcriptomics datasets for SCs, however, are not trivial tasks. Here, we present StemMapper, a manually curated gene expression database and comprehensive resource for SC research, built on integrated data for different lineages of human and mouse SCs. It is based on careful selection, standardized processing and stringent quality control of relevant transcriptomics datasets to minimize artefacts, and includes currently over 960 transcriptomes covering a broad range of SC types. Each of the integrated datasets was individually inspected and manually curated. StemMapper's user-friendly interface enables fast querying, comparison, and interactive visualization of quality-controlled SC gene expression data in a comprehensive manner. A proof-of-principle analysis discovering novel putative astrocyte/neural SC lineage markers exemplifies the utility of the integrated data resource. We believe that StemMapper can open the way for new insights and advances in SC research by greatly simplifying the access and analysis of SC transcriptomic data. StemMapper is freely accessible at http://stemmapper.sysbiolab.eu.

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Section: Discussionmentioning

confidence: 99%

StemMapper: a curated gene expression database for stem cell lineage analysis

Pinto

Machado

Magno

et al. 2017

Nucleic Acids Research

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“…StemChecker substantially expands the available repertoire of stem cell-related online analysis tools, offering the research community the ability to quickly check and explore the stemness genetic signatures contained in their gene sets, which greatly complements existing tools for integrative stem cell biology such as ESCAPE ( 27 ) or StemCellNet ( 28 ).…”

Section: Discussionmentioning

confidence: 99%

StemChecker: a web-based tool to discover and explore stemness signatures in gene sets

et al. 2015

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Stem cells present unique regenerative abilities, offering great potential for treatment of prevalent pathologies such as diabetes, neurodegenerative and heart diseases. Various research groups dedicated significant effort to identify sets of genes—so-called stemness signatures—considered essential to define stem cells. However, their usage has been hindered by the lack of comprehensive resources and easy-to-use tools. For this we developed StemChecker, a novel stemness analysis tool, based on the curation of nearly fifty published stemness signatures defined by gene expression, RNAi screens, Transcription Factor (TF) binding sites, literature reviews and computational approaches. StemChecker allows researchers to explore the presence of stemness signatures in user-defined gene sets, without carrying-out lengthy literature curation or data processing. To assist in exploring underlying regulatory mechanisms, we collected over 80 target gene sets of TFs associated with pluri- or multipotency. StemChecker presents an intuitive graphical display, as well as detailed statistical results in table format, which helps revealing transcriptionally regulatory programs, indicating the putative involvement of stemness-associated processes in diseases like cancer. Overall, StemChecker substantially expands the available repertoire of online tools, designed to assist the stem cell biology, developmental biology, regenerative medicine and human disease research community. StemChecker is freely accessible at http://stemchecker.sysbiolab.eu.

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“…The molecular interaction network for each set of proteins differentially abundant in our analyses was obtained by generating a comprehensive list of physical interactions gathered from five online databases: StemCellNet [ 29 ], UniHI [ 30 ], STRING [ 31 ], GeneMANIA [ 32 ] and QIAGEN’s Ingenuity Pathway Analysis [ 33 ]. The data retrieved from these sources were formatted, filtered and merged using customized Bash and R scripts.…”

Section: Methodsmentioning

confidence: 99%

Membrane-enriched proteome changes and prion protein expression during neural differentiation and in neuroblastoma cells

et al. 2017

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BackgroundThe function of the prion protein, involved in the so-called prion diseases, remains a subject of intense debate and the possibility that it works as a pleiotropic protein through the interaction with multiple membrane proteins is somehow supported by recent reports. Therefore, the use of proteomic and bioinformatics combined to uncover cellular processes occurring together with changes in the expression of the prion protein may provide further insight into the putative pleiotropic role of the prion protein.ResultsThis study assessed the membrane-enriched proteome changes accompanying alterations in the expression of the prion protein. A 2D-DIGE approach was applied to two cell lines after prefractionation towards the membrane protein subset: an embryonic stem cell line and the PK1 subline of neuroblastoma cells which efficiently propagates prion infection. Several proteins were differentially abundant with the increased expression of the prion protein during neural differentiation of embryonic stem cells and with the knockdown of the prion protein in PK1 cells. The identity of around 20% of the differentially abundant proteins was obtained by tandem MS. The catalytic subunit A of succinate dehydrogenase, a key enzyme for the aerobic energy metabolism and redox homeostasis, showed a similar abundance trend as the prion protein in both proteomic experiments. A gene ontology analysis revealed “myelin sheath”, “organelle membrane” and “focal adhesion” associated proteins as the main cellular components, and “protein folding” and “ATPase activity” as the biological processes enriched in the first set of differentially abundant proteins. The known interactome of these differentially abundant proteins was customized to reveal four interactors with the prion protein, including two heat shock proteins and a protein disulfide isomerase.ConclusionsOverall, our study shows that expression of the prion protein occurs concomitantly with changes in chaperone activity and cell-redox homeostasis, emphasizing the functional link between these cellular processes and the prion protein.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3694-6) contains supplementary material, which is available to authorized users.

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StemCellNet: an interactive platform for network-oriented investigations in stem cell biology

Cited by 19 publications

References 35 publications

StemMapper: a curated gene expression database for stem cell lineage analysis

StemMapper: a curated gene expression database for stem cell lineage analysis

StemChecker: a web-based tool to discover and explore stemness signatures in gene sets

Membrane-enriched proteome changes and prion protein expression during neural differentiation and in neuroblastoma cells

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