Similar protocols

Pipeline publication

[…] rned on by a particular stimulation pattern if it was not quantifiable (i.e. foreground fluorescence less than twice the background) in any of the unstimulated neuronal samples but quantifiable in all stimulated samples with that pattern. Turned off genes satisfied the opposite criterion i.e. expressed in all not stimulated samples but not expressed in any of the stimulated ones. Raw and normalized gene expression data were deposited into GEO and are publicly available under accession number GSE84872., Hierarchical clustering and frequency distribution of Agilent microarray expression data was performed using Cluster 3 (http://bonsai.hgc.jp/~mdehoon/software/cluster/) and JTree View (http://jtreeview.sourceforge.net/) on Log2 normalized data. Expression data was filtered according to direction (up- and down-regulated), pattern (18/1 and 90/5), and time (2 hr and 5 hr) where p < 0.05 and fold-change >|±1.4|. Gene ontology (GO), network, and pathway analyses was performed using pathway analysis software (Ingenuity Systems, Redwood City, CA). Four way Venn diagrams were constructed using the Java applet Venny, http://bioinfogp.cnb.csic.es/tools/venny/index.html., Prediction of TFBS was performed using either distant regulatory elements of co-regulated genes (DIRE) or gene set enrichment analysis (GSEA). Sensitivity of DIRE in predicting TFBS enrichment was validated by analysis of gene sets corresponding to (a) VP16 constitutively active CREB (526 transcripts), (b) NF-κB regulated transcripts (403 transcripts) (http://www.bu.edu/nf-kb/gene-resources/target-genes/), and (c) sensory neuron specific ERK1/2 conditional knockout (210). DIRE accurately predicted the presence of ATF/CREB, NF-κB, and downstream MAPK TFBS (). For DIRE analysis of DRG transcriptome data, a background set of genes was identified as not regulated (fold-change < |1.1|) by either stimulation pattern (18/1 and 90/5) and time (2 hr and 5 hr). Gene symbols for co-regulated ge […]

Pipeline specifications

Software tools JTreeView, VENNY, DiRE