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The stringently identified TF-binding interactions reported appear robust, and provide a starting point to extend focused TF studies into primary hematopoietic progenitors, where ChIP-seq remains technically challenging due to cell-number constraints.
The 22 stringently identified genes were evaluated with the online software Database for Annotation, Visualization and Integrated Discovery of the National Institutes of Allergy and Infectious Diseases; this software identifies groups of genes that are overrepresented using an unbiased algorithm based upon the Gene Ontology classification (Huang da et al. 2009).
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To stringently identify human-mouse orthologs, we selected genes whose official gene symbols were identical between humans and mice.
The "lookahead test" and the "third alignment going inwards" options were also selected for the genome processing in order to more stringently identify IR sequences.
It is also possible that the mouse models have been searched more stringently to identify relevant phenotypes proposed by candidate genes.
In order to identify stringently controlled genes as precise as possible, a filtering of the genes appearing differentially regulated in the microarray experiments was performed and three classes were established.
A stringently selected control group was identified to only include men with negative haematuria tests and with no past history of bladder or prostate cancer.
Using all stringently filtered peptides, 6928 unique proteins were identified from 82 LC-MS/MS runs at a false discovery rate (FDR) of 1%.
To do this, we took the expression pattern of one of the most significantly upregulated genes in rejection patients, DYSF (P value = 2.79E-06) and identified additional genes that covaried stringently with its expression pattern over the entire time course from the 48 patients.
ILC2 were identified as CD45+ Lin− GATA3+ Scand and were more stringently gated on expression of KLRG1.
In a number of cases, the validation experiment even identified experimenters who did not flag bad spots stringently enough.
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