After the young mouse networks (YNG) and middle-aged mouse networks (MID) networks were created and clustered, three integrated networks were generated: the union of clusters of density ≥65% from YNG and MID, the union of clusters of density ≥6 = 75% from YNG and MID, and the union of clusters of density ≥85% from YNG and MID.
To better visualize the extent of discordance or concordance in expression profiles within each tissue, bivariate plots and heat maps were generated using the union of all probesets differentially expressed in heart tissue or the union of all probesets differentially expressed in PBMC.
Lists with filtered genes were compared with each another using in-house Excel ad-ins for generating unions and intersections and pictures were generated with VENNY (Oliveros J.C. (2007) VENNY.
Microarrays were scanned using the GenePix 4000B scanner (Axon Instruments, Inc., Union City, CA) and GPR files were generated for data analysis according to protocols described in [39].
Protein-Protein Interaction (PPI) datasets were generated by taking the union of interactions from the MINT [ 27] and IntAct [ 26] resources, as they existed in Gene3D v5 [ 57].
Counts were generated using htseq-count v.0.5.3p9 with the default "union" overlapping mode.
Two channel ratios (Cy5/Cy3) for each spot were generated and quantified using GenePix Pro 5.1 (Axon Instruments, Inc., Union City, CA, USA).
A GenePix 4000B scanner (Axon Instruments, Union City, CA, USA) was used to scan individual chips and median spot intensities were generated using GenePix 4.0 (Axon Instruments).
The States/Union Territory-specific epidemic, for which first time States/Union Territory-specific prevalence curves was generated under the 2008−2009 HIV estimates.
Using "union" mode a fusion image was generated, including the visible spots for each 2-D gel.
