Computational protocol: CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells

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Protocol publication

[…] A total 16 of human HG-U133A GeneChip arrays were used in this study (Affymetrix). 10 μg of fragmented cRNA per GeneChip hybridization were processed on the Affymetrix Fluidic station 450 and GeneChip scanner GCS2500 (Hewlett-Packard Company). Gene expression profile was analyzed with MAS5.0 (Microarray Suite version 5.0; Affymetrix) and used for data acquisition and normalization. Present genes were defined by selecting genes that were present in three out of four arrays. Signal intensities of all present genes for the activated and control groups were combined and analyzed by Student's t test. Significant genes were selected with P < 0.05. The "signal log ratio" (SLR) and "increase" or "decrease" call was generated by comparison analysis MAS5.0 and used for calculating fold changes between groups. We selected 9 out of 16 pair-wise comparisons for particular genes that showed increase or decrease at fold change >2.0. In the second step, signal intensities of present genes were analyzed with Significance Analysis of Microarrays (SAM) and applied for analyzing and determining the gene list based on the number of significant genes that were identified by Student's t test and fold change. The final significant genes were combined from the aforementioned two steps. Two-dimensional hierarchical clusters are generated using GeneSpring 6.0 software (Silicon Genetics). […]

Pipeline specifications

Software tools SAM, GeneSpring GX
Application Gene expression microarray analysis
Organisms Homo sapiens
Diseases Diabetes Mellitus, Leukemia, T-Cell