Using GenePattern for Gene Expression Analysis

Abstract

The abundance of genomic data now available in biomedical research has stimulated the development of sophisticated statistical methods for interpreting the data, and of special visualization tools for displaying the results in a concise and meaningful manner. However, biologists often find these methods and tools difficult to understand and use correctly. GenePattern is a freely available software package that addresses this issue by providing more than 100 analysis and visualization tools for genomic research in a comprehensive user‐friendly environment for users at all levels of computational experience and sophistication. This unit demonstrates how to prepare and analyze microarray data in GenePattern. Curr. Protoc. Bioinform. 22:7.12.1–7.12.39. © 2008 by John Wiley & Sons, Inc.

TGF-β receptor maintains CD4 T helper cell identity during chronic viral infections

“…The reciprocal analysis in which we gated first on splenic virus-specific CD4 T cells that express EOMES showed that these cells expressed equivalent amounts of PD1 ( Figure 2E), but TGFβ-RII-deficient EOMES + cells were enriched for Ly6C + PSGL1 + cells ( Figure 2F). In addition, IFN-γ-producing Th1 CD4 T cells after GP [67][68][69][70][71][72][73][74][75][76][77] peptide stimulation (from Figure 1F) expressed more granzyme B in the spleen and lung (Figure 2G). Collectively, these results demonstrate that in the absence of TGF-β signaling, virus-specific CD4 T cells showed enhanced terminal differentiation and increased expression of cytotoxic molecules.…”

“…Cytokine measurements. Secretion of IFN-γ, TNF-α, and IL-2 from LCMV-specific T cells was performed ex vivo using GP [31][32][33][34][35][36][37][38][39][40][41] or GP [67][68][69][70][71][72][73][74][75][76][77] peptide stimulation of splenocytes incubated in the presence of 1 μg/ ml brefeldin A (BFA; Sigma-Aldrich) for 5 hours at 37˚C before staining.…”

“…The following antibodies were used: CD16/CD32 Fc block (2.4G2 BD); TGFβ-RII-PE (FAB532P, R&D Systems); EOMES PE-TR (Dan11mag, eBioscience); CD8a Alexa700 (53-6.7, eBioscience); CD4 BV650 (RM4-5, Biolegend) or Alexa700 (RM4-5, eBioscience); granzyme B PE (GB12, Invitrogen); granzyme A PE-Cy7 (GzA-3G8. :GP [67][68][69][70][71][72][73][74][75][76][77] were provided by the NIH tetramer core facility. Samples were acquired on a BD LSR II (BD Biosciences) and analyzed using FlowJo software (Treestar, Inc.).…”

SubZero: A fine-grained lineage system for scientific databases

“…-F ullOne and F ullM any are the two strategies to encode full lineage, and P ayOne and P ayM any encode payload lineage 4 . Figure 4 depicts how the backward-optimied implementation of these strategies encode two output cells with coordinates (0, 1) and (2, 3) that depend on input cells with coordinates (4, 5) and (6, 7).…”

“…Prior work in data lineage tracking systems has largely been limited to coarse-grained metadata tracking [3], [4], which stores relationships at the file or relational table level. Finegrained lineage tracks relationships at the array cell or tuple level.…”