We have used this array to generate an expression atlas for the pig, comparable to the human/mouse expression atlases, and, using advanced visualization and clustering analysis techniques, we have identified networks of co-expressed genes.
We have established an expression atlas for all known H. glycines parasitism genes.
Similar results were observed using the expression atlas generated by Libault et al. [ 54], with the exception of highest mean expression of genes belonging to each of the subfamilies was noticed in shoot apical meristem.
We mapped the top 10%% highly expressed genes to tissues/cells using the gene expression atlas data downloaded from Genomics Institute of the Novartis Research Foundation (GNF) [ 19].
Using expression atlas data, we could classify japonica-indica differentially expressed (jiDE) genes into two different types, global jiDE genes and changed-tissues jiDE genes.
Additionally, we found using Expression Atlas (Kapushesky et al., 2012) that nine of the positive candidates (including PPARγ and the top candidate ZEB1) are expressed significantly higher in adipose tissue compared to their mean expression across tissues.
Using the gene expression atlas published by three independent groups (Table 1) [ 15- 17], and the conserved miRNA target predictions from PicTar [ 9] and TargetScanS [ 2], we generated a global view of the transcript levels of miRNA targets in prostate cancer.
Cultured keratinocytes were stimulated with IL-21 and assessed for differential expression compared with nonstimulated controls using a human Atlas cDNA expression array (Clontech, Palo Alto, CA, USA).
Cell-type enrichment analysis using a mouse gene expression atlas showed that the gene network is enriched for osteoclast genes (enrichment p value = 4 × 10−7, Z test for relative overexpression of the network genes in a tissue/cell type, see Supplemental Experimental Procedures), suggesting a role for the network in macrophage multinucleation.
