scholarly journals An integrated view of baseline protein expression in human tissues

2021 ◽  
Author(s):  
Ananth Prakash ◽  
David García-Seisdedos ◽  
Shengbo Wang ◽  
Deepti Jaiswal Kundu ◽  
Andrew Collins ◽  
...  
Keyword(s):  
Protein Expression ◽  
Large Scale ◽  
Expression Data ◽  
Healthy Human ◽  
The Public ◽  
Pathway Enrichment ◽  
Expression Atlas ◽  
Consistent Manner ◽  
Organ Specific ◽  
Structural Region

AbstractThe availability of proteomics datasets in the public domain, and in the PRIDE database in particular, has increased dramatically in recent years. This unprecedented large-scale availability of data provides an opportunity for combined analyses of datasets to get organism-wide protein expression data in a consistent manner. We have reanalysed 25 public proteomics datasets from healthy human individuals, to assess baseline protein abundance in 32 organs. We defined tissue as a distinct functional or structural region within an organ. Overall, the aggregated dataset contains 68 healthy tissues, corresponding to 3,167 mass spectrometry runs covering 501 samples, coming from 492 individuals.We compared protein expression between the different organs, studied the distribution of proteins across organs, and identified proteins, as well as their isoforms, that are uniquely expressed in certain organs. We also performed gene ontology and pathway enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point, we have integrated the protein expression results into the resource Expression Atlas, where it can be accessed and visualised either individually or together with gene expression data coming from transcriptomics datasets.

scholarly journals Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

2021 ◽  
Author(s):  
Shengbo Wang ◽  
David García-Seisdedos ◽  
Ananth Prakash ◽  
Deepti Jaiswal Kundu ◽  
Andrew Collins ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Protein Expression ◽  
Rat Tissues ◽  
Protein Abundance ◽  
Proteomics Data ◽  
Pathway Enrichment ◽  
Expression Atlas ◽  
Organ Specific ◽  
High Level ◽  
Widespread Dissemination

The increasingly large amount of public proteomics data enables, among other applications, the combined analyses of datasets to create comparative protein expression maps covering different organisms and different biological conditions. Here we have reanalysed public proteomics datasets from mouse and rat tissues (14 and 9 datasets, respectively), to assess baseline protein abundance. Overall, the aggregated dataset contains 23 individual datasets, which have a total of 211 samples coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively. We compared protein expression between the different organs, including the distribution of proteins across them. We also performed gene ontology and pathway enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point we carried out a comparative analysis of protein expression between mouse, rat and human tissues. We observed a high level of correlation of protein expression among orthologs between all three species in brain, kidney, heart and liver samples. Finally, it should be noted that protein expression results have been integrated into the resource Expression Atlas for widespread dissemination.

scholarly journals The mouse Gene Expression Database (GXD): 2021 update

2020 ◽  
Vol 49 (D1) ◽  
pp. D924-D931 ◽  
Author(s):  
Richard M Baldarelli ◽  
Constance M Smith ◽  
Jacqueline H Finger ◽  
Terry F Hayamizu ◽  
Ingeborg J McCright ◽  
...  
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Mouse Genome Informatics ◽  
Expression Data ◽  
Rna Seq ◽  
Gene Expression Database ◽  
Heat Map ◽  
Developmental Gene Expression ◽  
Related Information ◽  
Expression Atlas

Abstract The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental gene expression information. For many years, GXD has collected and integrated data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot, and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Since our last report in 2019, we have continued to acquire these classical types of expression data; developed a searchable index of RNA-Seq and microarray experiments that allows users to quickly and reliably find specific mouse expression studies in ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) and GEO (https://www.ncbi.nlm.nih.gov/geo/); and expanded GXD to include RNA-Seq data. Uniformly processed RNA-Seq data are imported from the EBI Expression Atlas and then integrated with the other types of expression data in GXD, and with the genetic, functional, phenotypic and disease-related information in Mouse Genome Informatics (MGI). This integration has made the RNA-Seq data accessible via GXD’s enhanced searching and filtering capabilities. Further, we have embedded the Morpheus heat map utility into the GXD user interface to provide additional tools for display and analysis of RNA-Seq data, including heat map visualization, sorting, filtering, hierarchical clustering, nearest neighbors analysis and visual enrichment.

Is economic inequality a universal evil?

2019 ◽  
pp. 91-106 ◽  
Author(s):  
Rostislav I. Kapeliushnikov
Keyword(s):  
Quantitative Data ◽  
Large Scale ◽  
Economic Inequality ◽  
The State ◽  
Fair Play ◽  
Left Wing ◽  
Ordinary People ◽  
The Public ◽  
Discursive Power ◽  
A Current

Using published estimates of inequality for two countries (Russia and USA) the paper demonstrates that inequality measuring still remains in the state of “statistical cacophony”. Under this condition, it seems at least untimely to pass categorical normative judgments and offer radical political advice for governments. Moreover, the mere practice to draw normative conclusions from quantitative data is ethically invalid since ordinary people (non-intellectuals) tend to evaluate wealth and incomes as admissible or inadmissible not on the basis of their size but basing on whether they were obtained under observance or violations of the rules of “fair play”. The paper concludes that a current large-scale ideological campaign of “struggle against inequality” has been unleashed by left-wing intellectuals in order to strengthen even more their discursive power over the public.

KETERTINDASAN MELAYU DALAM CERPEN “SUKU POMPONG” KARYA FEDLI AZIS DAN CERPEN “RUMAH DI UJUNG KAMPUNG” KARYA HANG KAFRAWI

2017 ◽  
Vol 6 (1) ◽  
pp. 1
Author(s):  
Marlina Marlina
Keyword(s):  
Short Stories ◽  
Large Scale ◽  
Social Aspects ◽  
Land Conversion ◽  
The Public ◽  
Historical Reality ◽  
Sociological Approach ◽  
The Social ◽  
Imaginative Literature ◽  
The Village

Reading short stories “Suku Pompong” (Pompong Tribe) and “Rumah di Ujung Kampung” (House at the End of the Village) is like reading a historical reality that is happening on the ground of Riau Malay. The exploitation of forest resources on a large scale in recent decades in Riau Province has changed the land use of the area of intact forest into plantation area. The exploitation process causes friction in the community. The friction is eventually lead to conflict between communities and plantation companies. Their struggle to resolve conflicts and maintain their ancestral land, the strength of the company that has the license to the land and sadness when the public finally has always been on the losing side. This study objected to describe the objective reality of the Malay community in terms of land conversion, the communal land into plantations and reality of imaginative literature contained in the short stories “Suku Pompong” dan “Rumah di Ujung Kampung”. This study applied the sociology of literature approach, while the sociological approach to literature is a literary approach that specializes in reviewing literature by considering the social aspects. Based on these approaches, it can be concluded that short stories Suku Pompong and Rumah di Ujung Jalan are short stories that raised the reality of the Malay community.AbstrakMembaca cerpen “Suku Pompong” dan cerpen “Rumah di Ujung Kampung” seperti membaca sebuah realita sejarah yang terjadi di tanah Melayu Riau. Ekploitasi sumber daya hutan secara besar-besaran pada beberapa dekade terakhir di Provinsi Riau telah mengubah tata guna lahan dari kawasan hutan yang utuh menjadi kawasan perkebunan. Proses eksploitasi tersebut menimbulkan gesekan-gesekan dalam masyarakat. Gesekan-gesekan inilah yang akhirnya menimbulkan konflik antara masyarakat dengan pihak perusahaan perkebunan. Perjuangan masyarakat dalam menyelesaikan konflik dan mempertahankan tanah leluhur mereka, kekuatan pihak perusahaan yang memiliki surat izin atas tanah tersebut, dan kesedihan ketika masyarakat akhirnya selalu berada di pihak yang kalah. Penelitian ini bertujuan untuk mendeskripsikan realitas objektif masyarakat Melayu Riau dalam hal alih fungsi lahan, dari lahan tanah ulayat menjadi lahan perkebunan, dan realititas imajinatif sastra yang terdapat dalam cerpen “Suku Pompong” dan cerpen “Rumah di Ujung Kampung”. Penelitian ini menggunakan pendekatan sosiologi sastra, yaitu suatu pendekatan sastra yang mengkhususkan diri dalam menelaah karya sastra dengan mempertimbangkan segi-segi sosial kemasyarakatan. Dari pendekatan tersebut dapat diambil kesimpulan bahwa cerpen “Suku Pompong” dan cerpen “Rumah di Ujung Kampung” memang merupakan cerpen yang mengangkat realitas masyarakat Melayu Riau.

Approaches to Supporting Local and Community Development

2018 ◽  
Author(s):  
Liesel Mack Filgueiras ◽  
Andreia Rabetim ◽  
Isabel Aché Pillar
Keyword(s):  
Large Scale ◽  
Mining Company ◽  
The Sustainable Development ◽  
Social Partnership ◽  
The Public ◽  
Mining Investment ◽  
The Social ◽  
Corporate Social

Reflection about the role of community engagement and corporate social investment in Brazil, associated with the presence of a large economic enterprise, is the major stimulus of this chapter. It seeks to present how cross-sector governance can contribute to the social development of a city and how this process can be led by a partnership comprising a corporate foundation, government, and civil society. The concept of the public–private social partnership (PPSP) is explored: a strategy for building a series of inter-sectoral alliances aimed at promoting the sustainable development of territories where the company has large-scale enterprises, through joint efforts towards integrated long-term strategic planning, around a common agenda. To this end, the case of Canaã dos Carajás is introduced, a municipality in the State of Pará, in the Amazon region, where large-scale mining investment is being carried out by the mining company Vale SA.

scholarly journals Graph Convolutional Network for Drug Response Prediction Using Gene Expression Data

Mathematics ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 772
Author(s):  
Seonghun Kim ◽  
Seockhun Bae ◽  
Yinhua Piao ◽  
Kyuri Jo
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Large Scale ◽  
Drug Response ◽  
Response Prediction ◽  
Biological Data ◽  
Expression Data ◽  
Convolutional Network ◽  
Essential Information ◽  
Protein Protein Interaction

Genomic profiles of cancer patients such as gene expression have become a major source to predict responses to drugs in the era of personalized medicine. As large-scale drug screening data with cancer cell lines are available, a number of computational methods have been developed for drug response prediction. However, few methods incorporate both gene expression data and the biological network, which can harbor essential information about the underlying process of the drug response. We proposed an analysis framework called DrugGCN for prediction of Drug response using a Graph Convolutional Network (GCN). DrugGCN first generates a gene graph by combining a Protein-Protein Interaction (PPI) network and gene expression data with feature selection of drug-related genes, and the GCN model detects the local features such as subnetworks of genes that contribute to the drug response by localized filtering. We demonstrated the effectiveness of DrugGCN using biological data showing its high prediction accuracy among the competing methods.

Sex in the City that Peter Built: The Demimonde and Sociability in Mid-Eighteenth Century St. Petersburg

Slavic Review ◽  
2017 ◽  
Vol 76 (4) ◽  
pp. 907-930
Author(s):  
Igor Fedyukin
Keyword(s):  
Eighteenth Century ◽  
Public Sphere ◽  
Large Scale ◽  
Historical Context ◽  
Reading Public ◽  
Associational Life ◽  
The Public ◽  
The World ◽  
The Public Sphere ◽  
The City

This article uses the materials of the Drezdensha affair, a large-scale investigation of “indecency” in St. Petersburg in 1750, to explore unofficial sociability among the Imperial elite, and to map out the institutional, social, and economic dimensions of the post-Petrine “sexual underworld.” Sociability and, ultimately, the public sphere in eighteenth century Russia are usually associated with loftier practices, with joining the ranks of the reading public, reflecting on the public good, and generally, becoming more civil and polite. Yet, it is the privately-run, commercially-oriented, and sexually-charged “parties” at the focus of this article that arguably served as a “training ground” for developing the habits of sociability. The world of these “parties” provides a missing link between the debauchery and carousing of Peter I's era and the more polite formats of associational life in the late eighteenth century, as well as the historical context for reflections on morality, sexual licentiousness, foppery, and the excesses of “westernization.”

scholarly journals Limits of data anonymity: lack of public awareness risks trust in health system activities

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Felix Gille ◽  
Caroline Brall
Keyword(s):  
Large Scale ◽  
Public Awareness ◽  
Personal Data ◽  
Public Trust ◽  
Online News ◽  
Healthcare Management ◽  
Contact Tracing ◽  
Common Denominator ◽  
The Public ◽  
Privacy And Anonymity

AbstractPublic trust is paramount for the well functioning of data driven healthcare activities such as digital health interventions, contact tracing or the build-up of electronic health records. As the use of personal data is the common denominator for these healthcare activities, healthcare actors have an interest to ensure privacy and anonymity of the personal data they depend on. Maintaining privacy and anonymity of personal data contribute to the trustworthiness of these healthcare activities and are associated with the public willingness to trust these activities with their personal data. An analysis of online news readership comments about the failed care.data programme in England revealed that parts of the public have a false understanding of anonymity in the context of privacy protection of personal data as used for healthcare management and medical research. Some of those commenting demanded complete anonymity of their data to be willing to trust the process of data collection and analysis. As this demand is impossible to fulfil and trust is built on a false understanding of anonymity, the inability to meet this demand risks undermining public trust. Since public concerns about anonymity and privacy of personal data appear to be increasing, a large-scale information campaign about the limits and possibilities of anonymity with respect to the various uses of personal health data is urgently needed to help the public to make better informed choices about providing personal data.

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