Multi-Dimensional Data Viewer (MDV) user manual for data exploration: "Systematic analysis of YFP traps reveals common discordance between mRNA and protein across the nervous system"
Creators
- 1. University of Oxford
- 2. University of Oxford, Wellcome Leap - Delta Tissue Program
Description
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The explosion in the volume of biological imaging data challenges the available technologies for data interrogation and its intersection with related published bioinformatics data sets. Moreover, intersection of highly rich and complex datasets from different sources provided as flat csv files requires advanced informatics skills, which is time consuming and not accessible to all. Here, we provide a “user manual” to our new paradigm for systematically filtering and analysing a dataset with more than 1300 microscopy data figures using Multi-Dimensional Viewer (MDV) -link, a solution for interactive multimodal data visualisation and exploration. The primary data we use are derived from our published systematic analysis of 200 YFP traps reveals common discordance between mRNA and protein across the nervous system (eprint link). This manual provides the raw image data together with the expert annotations of the mRNA and protein distribution as well as associated bioinformatics data. We provide an explanation, with specific examples, of how to use MDV to make the multiple data types interoperable and explore them together. We also provide the open-source python code (github link) used to annotate the figures, which could be adapted to any other kind of data annotation task.
Files
Annotate.OMERO.Fig.zip
Additional details
Related works
- Has part
- Software: https://github.com/ilandavislab/Annotate.OMERO.Fig (URL)
Funding
- Machine learning-based automated hypothesis generation from microscopy images and their associated genome-wide metadata BB/S507623/1
- UK Research and Innovation
- Micron Oxford: super-resolution imaging of cellular dynamics. 107457
- Wellcome Trust
- Regulated mRNA stability and translation in neural stem cell development 209412
- Wellcome Trust
- The mechanism of mRNA transport and localised translation during axis specification and synaptic plasticity. 096144
- Wellcome Trust
- Advanced Microscopy for Chromosome and RNA Dynamics. 091911
- Wellcome Trust
- The Oxford Interdisciplinary Bioscience Doctoral Training Partnership BB/M011224/1
- UK Research and Innovation
References
- Titlow, Joshua S, Maria Kiourlappou, Ana Palanca, Jeffrey Y Lee, Dalia S Gala, Darragh Ennis, Joyce J S Yu, et al. 'Systematic Analysis of YFP Gene Traps Reveals Common Discordance between MRNA and Protein across the Nervous System'. Preprint – Accepted for publication at JCB, https://doi.org/10.1083/jcb.202205129.