A microarray analysis was conducted (Bacac et al, 2006) (data accessible at NCBI GEO database, accession ) to evaluate the response of stromal cells to tumour invasion.
"Prezi allows you to prioritize the big picture and to go deeper if needed, with your research data accessible at all times from the cloud," Britos Cavagnaro says.
N-myc is inhibited by retinoblastoma (Rb1) and expression of Ndrg3 and Ndrg4 are reduced in the Rb knockout retina (data accessible at NCBI GEO database, accession number GSE1129; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi acc=GSE1129).nih.gov/geo/query/acc.cgi acc=GSE1129
The raw ChIP-seq (data accessible at NCBI GEO database [ 17– 19], accession GSE34019) was processed using the TFTargetCaller [settings: Ouyang, TFAS and closestGene methods] package in R [ 20] to produce an annotated list of ChIP-seq peaks.
Most users of the tool will have no idea of the data manipulation routines developed to ingest, index and ultimately make this data accessible at a speed that is consistent with the pace of the web.
At the time of this analysis, five datasets were publicly available; we reference these by primary author: Desmedt [ 7] (data accessible at NCBI GEO database [ 8], accession GSE7390), Miller [ 9] (accession GSE3494), Pawitan [ 10] (accession GSE1456), VAN DE Vijver [ 11] http://microarray-pubs.stanford.edu/wound_NKI/, and Bild [ 12] (accession GSE3143).
We processed the mRNA transcript time series data from [ 33] (data accessible at NCBI GEO database [ 17], accession GSE54650) using JTKcycle [ 34] to obtain phases of master list genes.
Smirnov et al. performed microarray experiments to measure human gene expression levels in CEPH [23] (data accessible at NCBI GEO database [24], accession GSE12626).
We processed their raw data (data accessible at NCBI GEO database [ 17], accession GSE59486) using HOMER (v4.7.2) [ 24] for peak-calling and assigning peaks to the nearest gene.
Data accessible at http://www.networkrepository.com.com
