scholarly journals Giotto: a toolbox for integrative analysis and visualization of spatial expression data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ruben Dries ◽  
Qian Zhu ◽  
Rui Dong ◽  
Chee-Huat Linus Eng ◽  
Huipeng Li ◽  
...  

AbstractSpatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive and open-source toolbox for spatial data analysis and visualization. The analysis module provides end-to-end analysis by implementing a wide range of algorithms for characterizing tissue composition, spatial expression patterns, and cellular interactions. Furthermore, single-cell RNAseq data can be integrated for spatial cell-type enrichment analysis. The visualization module allows users to interactively visualize analysis outputs and imaging features. To demonstrate its general applicability, we apply Giotto to a wide range of datasets encompassing diverse technologies and platforms.

2019 ◽  
Author(s):  
Ruben Dries ◽  
Qian Zhu ◽  
Rui Dong ◽  
Chee-Huat Linus Eng ◽  
Huipeng Li ◽  
...  

AbstractThe rapid development of novel spatial transcriptomic and proteomic technologies has provided new opportunities to investigate the interactions between cells and their native microenvironment. However, effective use of such technologies requires the development of innovative computational tools that are easily accessible and intuitive to use. Here we present Giotto, a comprehensive, flexible, robust, and open-source toolbox for spatial transcriptomic and proteomic data analysis and visualization. The data analysis module provides end-to-end analysis by implementing a wide range of algorithms for characterizing cell-type distribution, spatially coherent gene expression patterns, and interactions between each cell and its surrounding neighbors. Furthermore, Giotto can also be used in conjunction with external single-cell RNAseq data to infer the spatial enrichment of cell types from data that do not have single-cell resolution. The data visualization module allows users to interactively visualize the gene expression data, analysis outputs, and additional imaging features, thereby providing a user-friendly workspace to explore multiple modalities of information for biological investigation. These two modules can be used iteratively for refined analysis and hypothesis development. We applied Giotto to a wide range of public datasets encompassing diverse technologies and platforms, thereby demonstrating its general applicability for spatial transcriptomic and proteomic data analysis and visualization.


Author(s):  
Patrick J. Ogao ◽  
Connie A. Blok

Measurements from dynamic environmental phenomena have resulted in the acquisition and generation of an enormous amount of data. This upsurge in data availability can be attributed to the interdisciplinary nature of environmental problem solving and the wide range of acquisition technology involved. In essence, users are dealing with data that is complex in nature, multidimensional and probably of a temporal nature. Also, the frequency by which this data is acquired far exceeds the rate at which it is being explored, a factor that has accelerated the search for innovative approaches and tools in spatial data analysis. These attempts have seen both analytical and visual techniques being used as aids in presentation and scientific data exploration. Examples are seen in techniques as in: data mining, data exploration and visualization.


Author(s):  
Stephen Matthews ◽  
Rachel Bacon ◽  
R. L’Heureux Lewis-McCoy ◽  
Ellis Logan

Recent years have seen a rapid growth in interest in the addition of a spatial perspective, especially in the social and health sciences, and in part this growth has been driven by the ready availability of georeferenced or geospatial data, and the tools to analyze them: geographic information science (GIS), spatial analysis, and spatial statistics. Indeed, research on race/ethnic segregation and other forms of social stratification as well as research on human health and behavior problems, such as obesity, mental health, risk-taking behaviors, and crime, depend on the collection and analysis of individual- and contextual-level (geographic area) data across a wide range of spatial and temporal scales. Given all of these considerations, researchers are continuously developing new ways to harness and analyze geo-referenced data. Indeed, a prerequisite for spatial analysis is the availability of information on locations (i.e., places) and the attributes of those locations (e.g., poverty rates, educational attainment, religious participation, or disease prevalence). This Oxford Bibliographies article has two main parts. First, following a general overview of spatial concepts and spatial thinking in sociology, we introduce the field of spatial analysis focusing on easily available textbooks (introductory, handbooks, and advanced), journals, data, and online instructional resources. The second half of this article provides an explicit focus on spatial approaches within specific areas of sociological inquiry, including crime, demography, education, health, inequality, and religion. This section is not meant to be exhaustive but rather to indicate how some concepts, measures, data, and methods have been used by sociologists, criminologists, and demographers during their research. Throughout all sections we have attempted to introduce classic articles as well as contemporary studies. Spatial analysis is a general term to describe an array of statistical techniques that utilize locational information to better understand the pattern of observed attribute values and the processes that generated the observed pattern. The best-known early example of spatial analysis is John Snow’s 1854 cholera map of London, but the origins of spatial analysis can be traced back to France during the 1820s and 1830s and the period of morale statistique, specifically the work of Guerry, d’Angeville, Duplin, and Quetelet. The foundation for current spatial statistical analysis practice is built on methodological development in both statistics and ecology during the 1950s and quantitative geography during the 1960s and 1970s and it is a field that has been greatly enhanced by improvements in computer and information technologies relevant to the collection, and visualization and analysis of geographic or geospatial data. In the early 21st century, four main methodological approaches to spatial analysis can be identified in the literature: exploratory spatial data analysis (ESDA), spatial statistics, spatial econometrics, and geostatistics. The diversity of spatial-analytical methods available to researchers is wide and growing, which is also a function of the different types of analytical units and data types used in formal spatial analysis—specifically, point data (e.g., crime events, disease cases), line data (e.g., networks, routes), spatial continuous or field data (e.g., accessibility surfaces), and area or lattice data (e.g., unemployment and mortality rates). Applications of geospatial data and/or spatial analysis are increasingly found in sociological research, especially in studies of spatial inequality, residential segregation, demography, education, religion, neighborhoods and health, and criminology.


2021 ◽  
Vol 12 ◽  
Author(s):  
Ling Wang ◽  
Hang Yin ◽  
Zhiguo Zhu ◽  
Shuai Yang ◽  
Jia Fan

The wide range of insect niches has led to a rapid expansion of chemosensory gene families as well as their relatively independent evolution and a high variation. Previous studies have revealed some functions for odorant-binding proteins (OBPs) in processes beyond olfaction, such as gustation and reproduction. In this study, a comparative transcriptomic analysis strategy was applied for the soybean aphid, Aphis glycines, focusing on various functional tissues and organs of winged aphids, including the antenna, head, leg, wing, thorax, cauda, and cornicle. Detailed spatial OBP expression patterns in winged and wingless parthenogenetic aphids were detected by RT-qPCR. Twelve OBPs were identified, and three new OBPs in A. glycines are first reported. All OBPs showed comparatively higher expression in sensory organs and tissues, such as the antenna, head, or leg. Additionally, we found some novel expression patterns for aphid OBPs (Beckendorf et al., 2008). Five OBPs exhibited high-expression levels in the cauda and four in the cornicle (Biasio et al., 2015). Three genes (OBP2/3/15) were highly expressed in the wing (Calvello et al., 2003). Two (OBP3/15) were significantly more highly expressed in the wingless thorax than in the winged thorax with the wings removed, and these transcripts were significantly enriched in the removed wings. More details regarding OBP spatial expression were revealed under our strategy. These findings supported the existence of carrier transport functions other than for foreign chemicals and therefore broader ligand ranges of aphid OBPs. It is important for understanding how insect OBPs function in chemical perception as well as their other potential physiological functions.


2013 ◽  
Vol 35 (12) ◽  
pp. 1377-1383
Author(s):  
Jing-Na WANG ◽  
Peng-Fei JIANG ◽  
Zhan-Zhan KANG ◽  
Deng-Yun LI ◽  
Lin-Lin HUA ◽  
...  

2019 ◽  
Vol 942 (12) ◽  
pp. 41-49
Author(s):  
A.M. Portnov

Using unified principles of formation and maintenance of register/cadaster with information about spatial data of landscape objects as the informational and technological basis for updating the public topographic maps and modernization of state cartographic system is proposed. The problems of informational relevancy of unified electronical cartographic basis and capacity of its renovation in case of public cadaster map data. The need to modernize the system of classification and coding of cartographic information, the use of unified standards for the coordinate description of register objects for their topological consistency, verification and updating is emphasized. Implementing such solutions is determined by economical expediency as well as necessity of providing a variety of real thematic data for wide range of consumers in the field of urban planning, territories development and completing the tasks of Governmental program “Digital economy of the Russian Federation”.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gulden Olgun ◽  
Afshan Nabi ◽  
Oznur Tastan

Abstract Background While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.


BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Wang ◽  
Lei Wang ◽  
Ling Wang ◽  
Meilian Tan ◽  
Collins O. Ogutu ◽  
...  

Abstract Background Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very little is known about how linseed coordinates the expression of drought resistance gene in response to different level of drought stress (DS) on the genome-wide level. Results To explore the linseed transcriptional response of DS and repeated drought (RD) stress, we determined the drought tolerance of different linseed varieties. Then we performed full-length transcriptome sequencing of drought-resistant variety (Z141) and drought-sensitive variety (NY-17) under DS and RD stress at the seedling stage using single-molecule real-time sequencing and RNA-sequencing. Gene Ontology (GO) and reduce and visualize GO (REVIGO) enrichment analysis showed that upregulated genes of Z141 were enriched in more functional pathways related to plant drought tolerance than those of NY-17 were under DS. In addition, 4436 linseed transcription factors were identified, and 1190 were responsive to stress treatments. Moreover, protein-protein interaction (PPI) network analysis showed that the proline biosynthesis pathway interacts with stress response genes through RAD50 (DNA repair protein 50) interacting protein 1 (RIN-1). Finally, proline biosynthesis and DNA repair structural gene expression patterns were verified by RT- PCR. Conclusions The drought tolerance of Z141 may be related to its upregulation of drought tolerance genes under DS. Proline may play an important role in linseed drought tolerance by maintaining cell osmotic and protecting DNA from ROS damage. In summary, this study provides a new perspective to understand the drought adaptability of linseed.


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