The Cancer Genome Anatomy Project (CGAP) was designed and implemented to provide public datasets, material resources and informatics tools to serve as a platform to support the elucidation of the molecular signatures of cancer.
Stat5a and Stat5b mRNA expression levels were evaluated in the context of clinical outcome in RNA microarray datasets (Material II) compiled from public repositories, Gene Expression Omnibus [ 36] and ArrayExpress [ 37], as described previously [ 38].
Supplementary dataset, materials and methods, figures S1– S5, and tables are available at Genome Biology and Evolution online (http://www.gbe.oxfordjournals.org/).org/
The datasets and materials (anonymized) can be shared with other researchers on request.
All datasets and materials that were used in this research are available at https://pan.baidu.com/s/1qXLFvq8.
The datasets and materials that comprise the educational module described in the text are available in the AIM-UP "For Educators" repository, and can be found at the following link: http://aimup.unm.edu/for-educators/Climate%20change.html.html
Comparison of enrichment levels between microarray experiments was performed after quantile normalization and signal smoothing of individual ChIP-chip datasets (see Materials and Methods).
In order to assess the performance of the MDP-based fine mapping, we decided to restrict the analysis to eQTL with very strong association signals in both the BXD and MDP datasets (see Materials and Methods).
We employed the CARPET package [8] Com&Easy function and Galaxy [9] to further compare the overlap of peak calls between HLH-1 ChIP datasets (see Materials and Methods).
Furthermore, we confirmed expression for ∼8000 putative hairpins in T. gondii, using publicly-available next generation sequencing datasets (see Materials and methods).
