Journal:

Article Title: Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci

doi: 10.1038/ng.401

Figure Lengend Snippet: Interferon response genes are coordinately upregulated relative to the rs17445836[G] allele of IRF8. Using the Ingenuity Pathways Analysis software suite, we illustrate the network of genes in the “interferon signaling pathway” whose expression is found to be correlated with the rs17445836[G] allele in untreated MS subjects. The diagram highlights those genes in this pathway whose expression are upregulated (red) in the presence of the rs17445836[G] allele. The magnitude of each gene’s association is reflected by the intensity of the color, with brighter red indicating a stronger correlation between rs17445836[G] and RNA expression. A white color denotes a gene found in the associated pathway but which failed to meet a nominal P < 0.05 threshold for association of its RNA expression with rs17445836[G]. The shapes of each gene symbol denote the class of that gene as defined by the Ingenuity Pathways application: horizontal oval, transcription regulator; vertical oval, transmembrane receptor; rectangle, G protein–coupled receptor; horizontal diamond, peptidase; vertical diamond, enzyme; triangle, kinase; square, cytokine; circle, other.

Article Snippet: Here, using the same set of quantitative trait analysis results, we find significant co-regulation, relative to the rs17445836[G] allele, of genes within Ingenuity Systems’ predefined “canonical interferon signaling pathway” among both untreated subjects ( P = 0.001) and IFNβ-treated subjects ( P = 0.01) ( ).

Techniques: Software, Expressing, RNA Expression

Journal: Toxicological Sciences

Article Title: Cadmium-Induced Differential Toxicogenomic Response in Resistant and Sensitive Mouse Strains Undergoing Neurulation

doi: 10.1093/toxsci/kfn221

Figure Lengend Snippet: Cd-induced alterations within the ingenuity canonical p53-signaling pathway in C57BL/6J and SWV embryos. Cd-induced alterations in C57 and SWV embryos were mapped to the p53 Signaling canonical ingenuity pathway (w/modifications). Genes are color coded based on Cd-effect specificity. Shapes of genes indicate known functions.

Article Snippet: We examined potential common and differential interactions between p53 and genes involved in cell cycle/apoptotic regulation using the canonical Ingenuity p53 Signaling pathway (Ingenuity Systems), color coded based on strain specificity of Cd response ( B Cd , p < 0.01, Models 1–3).

Techniques:

Journal: PLoS ONE

Article Title: Transcriptional Profiling of Chondrodysplasia Growth Plate Cartilage Reveals Adaptive ER-Stress Networks That Allow Survival but Disrupt Hypertrophy

doi: 10.1371/journal.pone.0024600

Figure Lengend Snippet: (A) qPCR performed in triplicate on the aRNA samples described in , using selected markers of the unfolded protein response (UPR) and endoplasmic reticulum associated degradation pathway, including ( i ) BiP , ( ii ) Calr , ( iii ) Derl2 , ( iv ) Derl3 , ( v ) Edem1 , ( vi ) ERdj4 , ( vii ) Erp72 , (viii ) Fgf21 , and ( ix ) Luman . Expression profiles are expressed as fold difference for homozygous Schmid (Schmid) or Tg cog (Cog) compared with wildtype (Wt), with profiles determined by the microarray analyses described in shaded dark grey, and profiles determined by qPCR shaded light grey. Error bars indicate standard deviation around the mean. (B) In situ analyses performed on 7 day old Wt and Schmid tibial growth plate cryosections using digoxigenin-labelled riboprobes specific for ( i , ii ) Col10a1 as well as novel markers of the UPR including ( iii , iv ) Armet , ( v , vi ) Creld2 , ( vii , viii ) Fgf21 , ( ix , x ) Luman , ( xi , xii ) Steap1 , ( xiii , xiv ) Syvn1 , and ( xv , xvi ) Wfs1 . Dashed lines demarcate approximate growth plate zone boundaries: R – Resting Zone, P – Proliferative Zone, H – Hypertrophic Zone. Boxes inset show magnified representative areas of the hypertrophic zones, to highlight the extent of riboprobe hybridization in these zones. Scale bars = 500 µm.

Article Snippet: Microarray analyses were also depicted by uploading the differential expression data into the Endoplasmic Reticulum Stress Canonical Pathway from the Ingenuity Pathways Analysis (Ingenuity Systems®, www.ingenuity.com ) library of canonical pathways, further revealing similarity between the UPRs of the Schmid ( ) and Cog mice ( ).

Techniques: Expressing, Microarray, Standard Deviation, In Situ, Hybridization

Journal: PLoS ONE

Article Title: Transcriptional Profiling of Chondrodysplasia Growth Plate Cartilage Reveals Adaptive ER-Stress Networks That Allow Survival but Disrupt Hypertrophy

doi: 10.1371/journal.pone.0024600

Figure Lengend Snippet: Transmission electron micrographs of representative chondrocytes from the (A–D) proliferative, (E–H) upper hypertrophic, (I–L) mid-hypertrophic, and (M–P) lower hypertrophic zones of 7 day old wildtype (Wt) and homozygous Schmid (Schmid) tibial growth plates. Italicized letters indicate intracellular features as follows: ER – endoplasmic reticulum, Gl – glycogen, Go – Golgi complex, N – nucleus, P – proteoglycan, V – vesicles. Scale bars = 1 µm.

Article Snippet: Microarray analyses were also depicted by uploading the differential expression data into the Endoplasmic Reticulum Stress Canonical Pathway from the Ingenuity Pathways Analysis (Ingenuity Systems®, www.ingenuity.com ) library of canonical pathways, further revealing similarity between the UPRs of the Schmid ( ) and Cog mice ( ).

Techniques: Transmission Assay