goCluster integrates statistical analysis and functional interpretation of microarray expression data

Motivation: Several tools that facilitate the interpretation of transcriptional profiles using gene annotation data are available but most of them combine a particular statistical analysis strategy with functional information. goCluster extends this concept by providing a modular framework that facilitates integration of statistical and functional microarray data analysis with data interpretation. Results: goCluster enables scientists to employ annotation information, clustering algorithms and visualization tools in their array data analysis and interpretation strategy. The package provides four clustering algorithms and GeneOntology terms as prototype annotation data. The functional analysis is based on the hypergeometric distribution whereby the Bonferroni correction or the false discovery rate can be used to correct for multiple testing. The approach implemented in goCluster was successfully applied to interpret the results of complex mammalian and yeast expression data obtained with high density oligonucleotide microarrays (GeneChips). Availability: goCluster is available via the BioConductor portal at www.bioconductor.org. The software package, detailed documentation, user- and developer guides as well as other background information are also accessible via a web portal at http://www.bioz.unibas.ch/gocluster. Contact: [email protected]

Remixing war: An analysis of the reimagination of the Russian–Ukraine war on TikTok

Interpretative struggles of global crises are increasingly being reflected on social media networks. TikTok is a relatively new social media platform that has achieved substantial popularity among young people in many parts of the world and is now being used to disseminate and make sense of information about the Russian invasion of Ukraine. Through a user-centered sampling approach, we collected 62 TikTok videos and conducted an in-depth qualitative analysis of them and their uploading profiles to explore how the war was being represented on the platform. Our analysis revealed a strong prevalence of remixing practices among content creators; that is, they recontextualise images, sounds and embodied self-performance within the platform-specific affordances of trends. We found that distant suffering is mediated through the emotive online self-performance of content creators, cuing their audiences toward appropriate emotional responses. Trending sounds situate videos within a singular-motif and context-diverse environment, facilitating what we theorize as affective audio networks

The Ashbya Genome Database (AGD)—a tool for the yeast community and genome biologists

The Ashbya Genome Database (AGD) is a comprehensive online source of information covering genes from the filamentous fungus Ashbya gossypii. The database content is based upon comparative genome annotation between A.gossypii and the closely related budding yeast Saccharomyces cerevisiae taking both sequence similarity and synteny (conserved order and orientation) into account. Release 2 of AGD contains 4718 protein-encoding loci located across seven chromosomes. Information can be retrieved using systematic or standard locus names from A.gossypii as well as budding and fission yeast. Approximately 90% of the genes in the genome of A.gossypii are homologous and syntenic to loci of budding yeast. Therefore, AGD is a useful tool not only for the various yeast communities in general but also for biologists who are interested in evolutionary aspects of genome research and comparative genome annotation. The database provides scientists with a convenient graphical user interface that includes various locus search and genome browsing options, data download and export functionalities and numerous reciprocal links to external databases including SGD, MIPS, GeneDB, KEGG, GermOnline and Swiss-Prot/TrEMBL. AGD is accessible at http://agd.unibas.c

GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle

GermOnline 4.0 is a cross-species database portal focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. It is thus a source of information for life scientists as well as clinicians who are interested in gene expression and regulatory networks. The GermOnline gateway provides unlimited access to information produced with high-density oligonucleotide microarrays (3′-UTR GeneChips), genome-wide protein–DNA binding assays and protein–protein interaction studies in the context of Ensembl genome annotation. Samples used to produce high-throughput expression data and to carry out genome-wide in vivo DNA binding assays are annotated via the MIAME-compliant Multiomics Information Management and Annotation System (MIMAS 3.0). Furthermore, the Saccharomyces Genomics Viewer (SGV) was developed and integrated into the gateway. SGV is a visualization tool that outputs genome annotation and DNA-strand specific expression data produced with high-density oligonucleotide tiling microarrays (Sc_tlg GeneChips) which cover the complete budding yeast genome on both DNA strands. It facilitates the interpretation of expression levels and transcript structures determined for various cell types cultured under different growth and differentiation conditions

MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation

BACKGROUND: The high-density oligonucleotide microarray (GeneChip) is an important tool for molecular biological research aiming at large-scale detection of small nucleotide polymorphisms in DNA and genome-wide analysis of mRNA concentrations. Local array data management solutions are instrumental for efficient processing of the results and for subsequent uploading of data and annotations to a global certified data repository at the EBI (ArrayExpress) or the NCBI (GeneOmnibus). DESCRIPTION: To facilitate and accelerate annotation of high-throughput expression profiling experiments, the Microarray Information Management and Annotation System (MIMAS) was developed. The system is fully compliant with the Minimal Information About a Microarray Experiment (MIAME) convention. MIMAS provides life scientists with a highly flexible and focused GeneChip data storage and annotation platform essential for subsequent analysis and interpretation of experimental results with clustering and mining tools. The system software can be downloaded for academic use upon request. CONCLUSION: MIMAS implements a novel concept for nation-wide GeneChip data management whereby a network of facilities is centered on one data node directly connected to the European certified public microarray data repository located at the EBI. The solution proposed may serve as a prototype approach to array data management between research institutes organized in a consortium

Grain boundary network evolution in electron-beam powder bed fusion nickel-based superalloy Inconel 738

Additive manufacturing (AM) of alloys has attracted much attention in recent years for making geometrically complex engineering parts owing to its unique benefits, such as high flexibility and low waste. The in-service performance of AM parts is dependent on the microstructures and grain boundary networks formed during AM, which are often significantly different from their wrought counterparts. Characteristics such as grain size and morphology, texture, and the detailed grain boundary network are known to control various mechanical and corrosion properties. Advanced understanding on how AM parameters affect the formation of these microstructural characteristics is hence critical for optimising processing parameters to unlock superior properties. In this study, the difficult-to-weld nickel-based superalloy Inconel 738 was fabricated via electron-beam powder bed fusion (EPBF) following linear and random scanning strategies. Random scanning resulted in finer, less elongated, and crystallographically more random grains compared to the linear strategy. However, both scanning strategies achieve unique high grain structure stability up to 1250 ℃ due to the presence of carbides pinning the grain boundaries. Despite significant difference in texture and morphology, majority of grains terminated on {100} habit planes in both linear and random built samples. The results show potential for controlling grain boundary networks during EPBF by tuning scan strategies

The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction

We report a novel release of the GermOnline knowledgebase covering genes relevant for the cell cycle, gametogenesis and fertility. GermOnline was extended into a cross-species systems browser including information on DNA sequence annotation, gene expression and the function of gene products. The database covers eight model organisms and Homo sapiens, for which complete genome annotation data are available. The database is now built around a sophisticated genome browser (Ensembl), our own microarray information management and annotation system (MIMAS) used to extensively describe experimental data obtained with high-density oligonucleotide microarrays (GeneChips) and a comprehensive system for online editing of database entries (MediaWiki). The RNA data include results from classical microarrays as well as tiling arrays that yield information on RNA expression levels, transcript start sites and lengths as well as exon composition. Members of the research community are solicited to help GermOnline curators keep database entries on genes and gene products complete and accurate. The database is accessible at

Profiling spermatogenic failure in adult testes bearing Sox9-deficient Sertoli cells identifies genes involved in feminization, inflammation and stress

<p>Abstract</p> <p>Background</p> <p><it>Sox9 </it>(<it>Sry </it>box containing gene 9) is a DNA-binding transcription factor involved in chondrocyte development and sex determination. The protein's absence in testicular Sertoli nurse cells has been shown to disrupt testicular function in adults but little is known at the genome-wide level about molecular events concomitant with testicular break-down.</p> <p>Methods</p> <p>To determine the genome-wide effect on mRNA concentrations triggered by the absence of <it>Sox9 </it>in Sertoli cells we analysed adult testicular tissue from wild-type versus mutant mice with high-density oligonucleotide microarrays and integrated the output of this experiment with regulatory motif predictions and protein-protein network data.</p> <p>Results</p> <p>We report the genome-wide mRNA signature of adult testes lacking <it>Sox9 </it>in Sertoli cells before and after the onset of late spermatogenic failure as compared to fertile controls. The GeneChip data integrated with evolutionarily conserved <it>Sox9 </it>DNA binding motifs and regulatory network data identified genes involved in feminization, stress response and inflammation.</p> <p>Conclusions</p> <p>Our results extend previous observations that genes required for female gonadogenesis are up-regulated in the absence of <it>Sox9 </it>in fetal Sertoli cells to the adult stage. Importantly, we identify gene networks involved in immunological processes and stress response which is reminiscent of a phenomenon occurring in a sub-group of infertile men. This suggests mice lacking <it>Sox9 </it>in their Sertoli cells to be a potentially useful model for adult human testicular failure.</p

Fhl5/Act, a CREM-binding transcriptional activator required for normal sperm maturation and morphology, is not essential for testicular gene expression

<p>Abstract</p> <p>Background</p> <p>The LIM domain protein Fhl5 was previously found to interact with CREM, a DNA binding transcriptional regulator necessary for spermiogenesis in mammals. Co-transfection experiments using heterologous promoter constructs indicated a role for Fhl5 in transcriptional up-regulation of CREM-dependent testicular genes. Male mice lacking Fhl5 were reported to be fertile but displayed partially abnormal sperm maturation and morphology.</p> <p>Methods</p> <p>To identify Fhl5 testicular target genes we carried out two whole-genome expression profiling experiments using high-density oligonucleotide microarrays and total testis samples from Fhl5 wild-type versus homozygous mutant mice first in different and then in isogenic strain backgrounds.</p> <p>Results</p> <p>Weak signal differences were detected in non-isogenic samples but no statistically significant expression changes were observed when isogenic Fhl5 mutant and wild-type samples were compared.</p> <p>Conclusion</p> <p>The outcome of these experiments suggests that testicular expression profiling is extremely sensitive to the genetic background and that Fhl5 is not essential for testicular gene expression to a level detected by microarray-based measurements. This might be due to redundant function of the related and similarly expressed protein Fhl4.</p