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Abstract Background Visual exploration of gene product behavior across multiple omic datasets can pinpoint technical limitations in data and reveal biological trends. Still, such exploration is challenging as there is a need for visualizations that are tailored for the purpose. Results The OmicLoupe software was developed to facilitate visual data exploration and provides more than 15 interactive cross-dataset visualizations for omics data. It expands visualizations to multiple datasets for quality control, statistical comparisons and overlap and correlation analyses, while allowing for rapid inspection and downloading of selected features. The usage of OmicLoupe is demonstrated in three different studies, where it allowed for detection of both technical data limitations and biological trends across different omic layers. An example is an analysis of SARS-CoV-2 infection based on two previously published studies, where OmicLoupe facilitated the identification of gene products with consistent expression changes across datasets at both the transcript and protein levels. Conclusions OmicLoupe provides fast exploration of omics data with tailored visualizations for comparisons within and across data layers. The interactive visualizations are highly informative and are expected to be useful in various analyses of both newly generated and previously published data. OmicLoupe is available at quantitativeproteomics.org/omicloupe

Abstract Background The changing climate and the desire to use renewable oil sources necessitate the development of new oilseed crops. Field cress (Lepidium campestre) is a species in the Brassicaceae family that has been targeted for domestication not only as an oilseed crop that produces seeds with a desirable industrial oil quality but also as a cover/catch crop that provides valuable ecosystem services. Lepidium is closely related to Arabidopsis and display significant proportions of syntenic regions in their genomes. Arabidopsis genes are among the most characterized genes in the plant kingdom and, hence, comparative genomics of Lepidium-Arabidopsis would facilitate the identification of Lepidium candidate genes regulating various desirable traits. Results Homologues of 30 genes known to regulate vernalization, flowering time, pod shattering, oil content and quality in Arabidopsis were identified and partially characterized in Lepidium. Alignments of sequences representing field cress and two of its closely related perennial relatives: L. heterophyllum and L. hirtum revealed 243 polymorphic sites across the partial sequences of the 30 genes, of which 95 were within the predicted coding regions and 40 led to a change in amino acids of the target proteins. Within field cress, 34 polymorphic sites including nine non-synonymous substitutions were identified. The phylogenetic analysis of the data revealed that field cress is more closely related to L. heterophyllum than to L. hirtum. Conclusions There is significant variation within and among Lepidium species within partial sequences of the 30 genes known to regulate traits targeted in the present study. The variation within these genes are potentially useful to speed-up the process of domesticating field cress as future oil crop. The phylogenetic relationship between the Lepidium species revealed in this study does not only shed some light on Lepidium genome evolution but also provides important information to develop efficient schemes for interspecific hybridization between different Lepidium species as part of the domestication efforts.