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Pipeline publication

[…] n in transcript levels of every gene in a given mRNA sample, as detected on one array. The variations in transcript abundance for each gene are depicted by means of a color scale, in which shades of red represents increases and shades of green represent decrease in mRNA levels, relative to the unstressed culture, and the saturation of the color corresponds to the magnitude of the differences. Black coloration indicates no change in transcript level while grey represents missing data., The genome of Rhodopirellula baltica was automatically re-annotated based on updated homology searches (June 2005 - MicHanThi []). The updated annotation including all tool results is publicly available at []. JCoast [] was used as a tool for the visualization, interpretation, COG-assignment statistics and comparison of genomic data stored in GenDB V2.2 []. The Venn diagrams were generated by BioVenn []., Each microarray used in this study contained 7325 known or predicted R. baltica genes according to Glöckner et al. []. A detailed description of the array can be found at the NCBI's Gene Expression Omnibus (GEO) database under accession number GPL7654. The complete microarray datasets covering the expression of R. baltica cultures exposed to heat, cold and high salinity, are public available in the GEO repository under accession numbers GSE13769, G SE13856 and GSE14075 []., COG: Cluster of Orthologous Group of Genes; DUF: Domain of Unknown Function; ECF: Extra Cytoplasmic Function; ESR: Environmental Stress Response; FHA: Forkhead-associated; GEO: Gene Expression Omnibus; R.: R […]

Pipeline specifications

Software tools JCoast, GenDB, BioVenn
Databases GEO