Applications of the Gaggle Genome Browser

The Gaggle Genome Browser has been applied to integrate diverse types of data in context of coordinates on the genome: microarrays, tiling arrays, RNA-seq, ChIP-chip, and quantitative proteomics. Datasets exist for several organisms:

Transcriptome structure of Halobacterium salinarum

Halobacterium salinarum transcript structure (blue) superimposed with segmentation (red) with transcription factor binding measurements (green) in low and high resolution. Heatmap shows expression measured by spotted microarry. There are several more datasets for Halobacterium salinarum.

Halobacterium salinarum tiling array measurements at 14 time points during growth. This work was published in Prevalence of transcription promoters within archaeal operons and coding sequences (Koide 2009)

Regulatory network rewiring

Adaptation by rewiring of regulatory networks was explored in Niche adaptation by expansion and reprogramming of general transcription factors, (Turkarslan 2011)

Methanococcus transcriptome structure

The paper Parallel evolution of transcriptome architecture during genome reorganization (Yoon 2011) characterizes and compares transcriptome architectures of four phylogenetically diverse extremophiles that span the range archaeal lineages.


Extremophilic archaea

There are GGB datasets for three extremophilic archaea Halobacterium salinarum, Pyrococcus furiosus and Sulfolobus solfataricus. More tools for these organisms are on the halo Gaggle page and the MAGGIE Gaggle page. These were analyzed along with Methanococcus maripaludis in Yoon 2011.

Mapping transcription factors with ChIP-seq

The Facciotti lab's paper A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq (Wilbanks 2012) demonstrates a ChIP-seq workflow for finding transcription factor binding sites in Halobacterium salinarum NRC-1.


Protein-DNA binding with ChIP-chip

Halobacterium salinarum transcription factor binding sites by ChIP-chip, plotted alongside transcriptome structure by tiling array and gene expression microarray data.

Peptide fractionation in Sulfolobus

This study of the localization of proteins in Sulfolobus solfataricus integrated transcription and proteomics data.

Transcriptome structure of Desulfovibrio

Plotted RNA-seq data published in Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. (Price 2011)

ncRNA and RNA degredation

A study in Halobacterium salinarum of the role of noncoding RNAs and RNA degradation in gene regulation.

Tiling array data from an oxygen shift experiment; the displayed region shows evidence of a noncoding RNA

Motif Cluster

The goal of these experimental visualization cMonkey motif clusters is to link experimentally derived protein-DNA binding sites with computationally derived promoter motifs, eventually linking them to specific transcription factors.

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