An Organ-Wide Gene Expression Atlas of the Developing Human Heart

2018 ◽  
Author(s):  
Michaela Asp ◽  
Stefania Giacomello ◽  
Daniel Fürth ◽  
Johan Reimegård ◽  
Eva Wärdell ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Heart ◽  
Gene Expression Atlas ◽  
Expression Atlas

scholarly journals A gene expression atlas for different kinds of stress in the mouse brain

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Tiziano Flati ◽  
Silvia Gioiosa ◽  
Giovanni Chillemi ◽  
Andrea Mele ◽  
Alberto Oliverio ◽  
...  
Keyword(s):  
Gene Expression ◽  
Coping With Stress ◽  
Gene Expression Atlas ◽  
Sequence Read Archive ◽  
Brain Transcriptome ◽  
Expression Atlas ◽  
Differential Gene ◽  
Stress Related Genes ◽  
Public Repositories ◽  
The Brain

AbstractStressful experiences are part of everyday life and animals have evolved physiological and behavioral responses aimed at coping with stress and maintaining homeostasis. However, repeated or intense stress can induce maladaptive reactions leading to behavioral disorders. Adaptations in the brain, mediated by changes in gene expression, have a crucial role in the stress response. Recent years have seen a tremendous increase in studies on the transcriptional effects of stress. The input raw data are freely available from public repositories and represent a wealth of information for further global and integrative retrospective analyses. We downloaded from the Sequence Read Archive 751 samples (SRA-experiments), from 18 independent BioProjects studying the effects of different stressors on the brain transcriptome in mice. We performed a massive bioinformatics re-analysis applying a single, standardized pipeline for computing differential gene expression. This data mining allowed the identification of novel candidate stress-related genes and specific signatures associated with different stress conditions. The large amount of computational results produced was systematized in the interactive “Stress Mice Portal”.

scholarly journals A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Aliki Xanthopoulou ◽  
Javier Montero-Pau ◽  
Belén Picó ◽  
Panagiotis Boumpas ◽  
Eleni Tsaliki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cucurbita Pepo ◽  
Developmental Stages ◽  
Lateral Roots ◽  
Expression Patterns ◽  
Male Flower ◽  
Differentially Expressed ◽  
Gene Expression Atlas ◽  
Summer Squash ◽  
Expression Atlas

Abstract Background Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity. Conclusions These findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. This comprehensive gene expression atlas is expected not only to provide a global view of gene expression patterns in all major tissues in C. pepo but to also serve as a valuable resource for functional genomics and gene discovery in Cucurbitaceae.

scholarly journals PEATmoss ( Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

2020 ◽  
Vol 102 (1) ◽  
pp. 165-177 ◽  
Author(s):  
Noe Fernandez‐Pozo ◽  
Fabian B. Haas ◽  
Rabea Meyberg ◽  
Kristian K. Ullrich ◽  
Manuel Hiss ◽  
...  
Keyword(s):  
Gene Expression ◽  
Physcomitrella Patens ◽  
Model Plant ◽  
Gene Expression Atlas ◽  
Expression Atlas

Gene expression atlas of fruit ripening of octoploid strawberry (Fragaria×ananassa) and transcriptome assembly from RNA-seq data

2016 ◽  
Vol 33 ◽  
pp. S156
Author(s):  
José Federico Sánchez Sevilla ◽  
José G. Vallarino ◽  
Sonia Osorio ◽  
Aureliano Bombarely ◽  
Katharina Merchante ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruit Ripening ◽  
Transcriptome Assembly ◽  
Fragaria Ananassa ◽  
Rna Seq ◽  
Gene Expression Atlas ◽  
Expression Atlas

scholarly journals A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Dean A Baker ◽  
Tony Nolan ◽  
Bettina Fischer ◽  
Alex Pinder ◽  
Andrea Crisanti ◽  
...  
Keyword(s):  
Gene Expression ◽  
Anopheles Gambiae ◽  
Malaria Vector ◽  
Tissue Specificity ◽  
Gene Expression Atlas ◽  
Expression Atlas

scholarly journals Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo

Nature Plants ◽  
2017 ◽  
Vol 3 (11) ◽  
pp. 894-904 ◽  
Author(s):  
Joakim Palovaara ◽  
Shunsuke Saiga ◽  
Jos R. Wendrich ◽  
Nicole van ‘t Wout Hofland ◽  
J. Paul van Schayck ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Atlas ◽  
Expression Atlas

scholarly journals Transcriptome database resource and gene expression atlas for the rose

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 638 ◽  
Author(s):  
Annick Dubois ◽  
Sebastien Carrere ◽  
Olivier Raymond ◽  
Benjamin Pouvreau ◽  
Ludovic Cottret ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Atlas ◽  
Transcriptome Database ◽  
Expression Atlas ◽  
The Rose

scholarly journals A circadian gene expression atlas in mammals: Implications for biology and medicine

2014 ◽  
Vol 111 (45) ◽  
pp. 16219-16224 ◽  
Author(s):  
Ray Zhang ◽  
Nicholas F. Lahens ◽  
Heather I. Ballance ◽  
Michael E. Hughes ◽  
John B. Hogenesch
Keyword(s):  
Gene Expression ◽  
Circadian Gene ◽  
Gene Expression Atlas ◽  
Expression Atlas
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