shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction

Singh, Nishtha Manish; Sahu, Tanmaya Kumar; Rao, Atmakuri Ramakrishna; Mohapatra, Trilochan

doi:10.6026/97320630008629

Cited by 3 publications

(4 citation statements)

References 7 publications

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“…In addition, we inspected the co-expression patterns of components of light-dependent versus light-independent reactions of photosynthesis with the aim to evaluate their transcriptional regulation. Finally, we extended and enhanced CyanoEXpress ( http://cyanoexpress.sysbiolab.eu )-a web-based resource for Synechocystis transcriptomic data 8 -to facilitate independent analysis of the integrated expression data.…”

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confidence: 99%

The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803

Hernández‐Prieto

Semeniuk

Giner‐Lamia

et al. 2016

Sci Rep

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Cyanobacteria exhibit a great capacity to adapt to different environmental conditions through changes in gene expression. Although this plasticity has been extensively studied in the model cyanobacterium Synechocystis sp. PCC 6803, a detailed analysis of the coordinated transcriptional adaption across varying conditions is lacking. Here, we report a meta-analysis of 756 individual microarray measurements conducted in 37 independent studies-the most comprehensive study of the Synechocystis transcriptome to date. Using stringent statistical evaluation, we characterized the coordinated adaptation of Synechocystis’ gene expression on systems level. Evaluation of the data revealed that the photosynthetic apparatus is subjected to greater changes in expression than other cellular components. Nevertheless, network analyses indicated a significant degree of transcriptional coordination of photosynthesis and various metabolic processes, and revealed the tight co-regulation of components of photosystems I, II and phycobilisomes. Detailed inspection of the integrated data led to the discovery a variety of regulatory patterns and novel putative photosynthetic genes. Intriguingly, global clustering analyses suggested contrasting transcriptional response of metabolic and regulatory genes stress to conditions. The integrated Synechocystis transcriptome can be accessed and interactively analyzed via the CyanoEXpress website (http://cyanoexpress.sysbiolab.eu).

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confidence: 99%

The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803

Hernández‐Prieto

Semeniuk

Giner‐Lamia

et al. 2016

Sci Rep

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“…NC-1). Microarray data were deposited at GEO database (GSE39804) and can be interactively accessed via the CyanoEXpress database at http://cyanoexpress.sysbiolab.eu (Hernandez-Prieto and Futschik 2012). …”

Section: Methodsmentioning

confidence: 99%

Iron Deprivation inSynechocystis: Inference of Pathways, Non-coding RNAs, and Regulatory Elements from Comprehensive Expression Profiling

Hernández‐Prieto

Schön

Georg

et al. 2012

G3 Genes|Genomes|Genetics

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Iron is an essential cofactor in many metabolic reactions. Mechanisms controlling iron homeostasis need to respond rapidly to changes in extracellular conditions, but they must also keep the concentration of intracellular iron under strict control to avoid the generation of damaging reactive oxygen species. Due to its role as a redox carrier in photosynthesis, the iron quota in cyanobacteria is about 10 times higher than in model enterobacteria. The molecular details of how such a high quota is regulated are obscure. Here we present experiments that shed light on the iron regulatory system in cyanobacteria. We measured time-resolved changes in gene expression after iron depletion in the cyanobacterium Synechocystis sp. PCC 6803 using a comprehensive microarray platform, monitoring both protein-coding and non-coding transcripts. In total, less than a fifth of all protein-coding genes were differentially expressed during the first 72 hr. Many of these proteins are associated with iron transport, photosynthesis, or ATP synthesis. Comparing our data with three previous studies, we identified a core set of 28 genes involved in iron stress response. Among them were genes important for assimilation of inorganic carbon, suggesting a link between the carbon and iron regulatory networks. Nine of the 28 genes have unknown functions and constitute key targets for further functional analysis. Statistical and clustering analyses identified 10 small RNAs, 62 antisense RNAs, four 5′UTRs, and seven intragenic elements as potential novel components of the iron regulatory network in Synechocystis. Hence, our genome-wide expression profiling indicates an unprecedented complexity in the iron regulatory network of cyanobacteria.

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“…Our dataset currently contains more than 700 microarray measurements, and is regularly updated with newly available data. These expression profiles were clustered and made available to researchers through CyanoEXpress ( http://cyanoexpress.sysbiolab.eu/ ), a web-based user-friendly visualization tool, for exploration of expression profiles (Hernandez-Prieto and Futschik, 2012 ). Gene-directed search enables rapid detection of co-expression patterns, which can be highly indicative for the annotation of less-studied genes, and in the prediction of new gene functions.…”

Section: Transcriptomics: Gene Expression Profiling From Microarrays mentioning

confidence: 99%

“…CyanoEXpress is a web-served dedicated to transcriptomics data for cyanobacteria ( http://cyanoexpress.sysbiolab.eu/ ; Hernandez-Prieto and Futschik, 2012 ). Currently, it includes expression data only for Synechocystis PCC 6803, with 718 microarray measurements compiled from 33 independent studies with both environmental and genetic perturbations.…”

Section: Web-based Tools For System Biology Analysismentioning

confidence: 99%

Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

2014

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Cyanobacteria are essential primary producers in marine ecosystems, playing an important role in both carbon and nitrogen cycles. In the last decade, various genome sequencing and metagenomic projects have generated large amounts of genetic data for cyanobacteria. This wealth of data provides researchers with a new basis for the study of molecular adaptation, ecology and evolution of cyanobacteria, as well as for developing biotechnological applications. It also facilitates the use of multiplex techniques, i.e., expression profiling by high-throughput technologies such as microarrays, RNA-seq, and proteomics. However, exploration and analysis of these data is challenging, and often requires advanced computational methods. Also, they need to be integrated into our existing framework of knowledge to use them to draw reliable biological conclusions. Here, systems biology provides important tools. Especially, the construction and analysis of molecular networks has emerged as a powerful systems-level framework, with which to integrate such data, and to better understand biological relevant processes in these organisms. In this review, we provide an overview of the advances and experimental approaches undertaken using multiplex data from genomic, transcriptomic, proteomic, and metabolomic studies in cyanobacteria. Furthermore, we summarize currently available web-based tools dedicated to cyanobacteria, i.e., CyanoBase, CyanoEXpress, ProPortal, Cyanorak, CyanoBIKE, and CINPER. Finally, we present a case study for the freshwater model cyanobacteria, Synechocystis sp. PCC6803, to show the power of meta-analysis, and the potential to extrapolate acquired knowledge to the ecologically important marine cyanobacteria genus, Prochlorococcus.

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shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction

Cited by 3 publications

References 7 publications

The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803

The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803

Iron Deprivation inSynechocystis: Inference of Pathways, Non-coding RNAs, and Regulatory Elements from Comprehensive Expression Profiling

Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

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