metacore network building tools  (GeneGo Inc)

Journal: BMC Medical Genomics

Article Title: Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL ® platform

doi: 10.1186/1755-8794-3-60

Figure Lengend Snippet: MetaCore network analyses . The top 47 genes that matched to the probes that were differentially expressed between HER2+ and HER2- samples (p-values < 0.01 and log2-fold change > |1.0|) in the 24K panel are enriched with genes (marked by red cycles) belonging to two distinct regulatory networks. a . The first network includes genes (marked by red cycles) functionally connected to MYC ( c-Myc ). b . The second network is enriched by genes (marked by red cycles) centered around TP53 ( p53 ) and ESR1 . c . The 8 genes differentially expressed in both the 24K and 1.5K panels (marked by red cycles) are all connected in a network that includes TP53 (p53) , ESR1 , and MYC ( c-Myc ) d . Symbol legend. Abbreviations for gene names presented in Figure 5 are defined in Additional File , Tables S1-S3.

Article Snippet: Network analyses were performed using MetaCore network building tools (GeneGo Inc., St. Joseph, MI).

Techniques:

Journal: Journal of proteomics

Article Title: Differential response to intracellular stress in the skin from osteogenesis imperfecta Brtl mice with lethal and non lethal phenotype: A proteomic approach ☆

doi: 10.1016/j.jprot.2012.01.038

Figure Lengend Snippet: MetaCore Pathway and validation of Oct3/4 and vimentin. (A) MetaCore pathway analysis was used to map identified proteins on existing mammalian pathways and networks, in accordance with known protein–protein interactions and other features established in the literature. Network proteins are visualized by proper symbols, which specify the functional nature of the protein (network caption). The edges define the relationships existing between individual proteins, and the arrowheads represent the direction of the interaction. The following line colors designate the nature of the interaction: red=negative effect, green=positive effect, gray=unspecified effect. Links highlighted in thick cyan line refer to known canonical pathways which are significantly related to the path built by the program.

Article Snippet: Proteins changing in expression that were identified by MS were further analyzed by pathway analysis using the MetaCore network building tool (GeneGo Inc., St. Joneph, MI).

Techniques: Biomarker Discovery, Protein-Protein interactions, Functional Assay