PMC:512295 / 8003-10231
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/512295","sourcedb":"PMC","sourceid":"512295","source_url":"http://www.ncbi.nlm.nih.gov/pmc/512295","text":"Data Analysis\nThe Rat U34A GeneChip Microarray has probe sets for over 8,700 rat genes. Most probe sets have 20 different probes for the same gene on each array with 20 additional mismatch controls. The data were analyzed with Affymetrix Microarray Suite 5.0 and Affymetrix Data Mining Tool 3.0 software. Microarray Suite was used to scale the mRNA expression (signal value) of all genes to an average of 500 for each array. For each gene, the software reported a signal value and a Present/Marginal/Absent call. This latter algorithm was a statistical comparison of the variation among the several probe sets for each gene compared to the noise level and gave a call for each gene as Present, Marginal, or Absent. The program then compared the signal value of each gene in the fractured samples against the signal value of the same gene in the unfractured control sample. The difference between the two signal levels, relative to the variability between the multiple probes for each gene, yielded a probability of change due to chance alone. Genes with p less than 0.005 were judged significantly different from the same gene in the unfractured sample. This more conservative p value was employed to minimize false positive responses.\nThe Data Mining Tool was used for cluster analysis with the Self Organizing Map (SOM) algorithm. The data were clustered on the signal values between 20 and 20,000 with the maximum/minimum ratio of at least 3.0 and the maximum – minimum difference of at least 100. One hundred clusters were specified.\nNerve-related genes were identified by searches for nerve-related names in the gene descriptions of each gene on the microarray. This association was confirmed by a review of the information for that gene in the NetAffx web site and in the PubMed database . GenBank accession numbers and names are shown for each gene. Each graph shows the average ± SEM of the three microarrays that were done for each time point for each age. Significant changes in gene expression were demonstrated by t test and linear regression [20].\nThis report conforms to the MIAME standards of MGED . A copy of the full microarray data set has been deposited in the NCBI Gene Expression Omnibus as series GSE594.","divisions":[{"label":"Title","span":{"begin":0,"end":13}}],"tracks":[]}