PMC:2041973 / 71495-73045 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/2041973","sourcedb":"PMC","sourceid":"2041973","source_url":"http://www.ncbi.nlm.nih.gov/pmc/2041973","text":"Exon array analysis.\nThe Affymetrix Power Tools (APT) suite of programs was obtained from http://www.affymetrix.com/support/developer/powertools/index.affx. Exon (probeset) and gene-level signal estimates were derived from the CEL files by RMA–sketch normalization as a method in the apt-probeset-summarize program. To determine if the signal intensity for a given probeset is above the expected level of background noise, we utilized the DABG (detection above background) quantification method available in the apt-probeset-summarize program as part of Affymetrix Power Tools (APT). Briefly, DABG compared the signal for each probe to a background distribution of signals from anti-genomic probes with the same GC content. The DABG algorithm generated a p-value representing the probability that the signal intensity of a given probe was part of the background distribution. We considered a probeset with a DABG p-value lower than 0.05 as detected above background. The statistic thCNS-SCns,ESC = (μhCNS-SCns − μESC) / sqrt (((nhCNS-SCns − 1)σ2 hCNS-SCns + (nESC − 1)σ2 ESC)(nhCNS-SCns + nESC)) / ((nhCNS-SCnsnESC) (nhCNS-SCns + nESC − 2))), where nhCNS-SCns and nESC were the number of replicates, μhCNS-SCns and μESC were the mean, and σ2 hCNS-SCns and σ2 ESC were the variances of the expression values for the two datasets used to represent the differential enrichment of a gene using gene-level estimates in hCNS-SCns relative to hESCs. Multiple hypothesis testing was corrected by controlling for the false discovery rate (Benjamini-Hochberg).","divisions":[{"label":"Title","span":{"begin":0,"end":20}}],"tracks":[{"project":"CellFinder","denotations":[{"id":"T181","span":{"begin":1436,"end":1441},"obj":"CellType"},{"id":"T182","span":{"begin":1414,"end":1421},"obj":"CellType"},{"id":"T183","span":{"begin":1414,"end":1423},"obj":"CellType"},{"id":"T184","span":{"begin":1029,"end":1036},"obj":"CellType"},{"id":"T185","span":{"begin":1077,"end":1084},"obj":"CellType"},{"id":"T186","span":{"begin":1201,"end":1208},"obj":"CellType"},{"id":"T187","span":{"begin":1242,"end":1249},"obj":"CellType"},{"id":"T188","span":{"begin":1151,"end":1157},"obj":"CellType"},{"id":"T189","span":{"begin":1118,"end":1125},"obj":"CellType"},{"id":"T190","span":{"begin":982,"end":989},"obj":"CellType"},{"id":"T191","span":{"begin":1101,"end":1108},"obj":"CellType"},{"id":"T192","span":{"begin":1029,"end":1036},"obj":"CellType"},{"id":"T193","span":{"begin":1000,"end":1007},"obj":"CellType"}],"attributes":[{"subj":"T181","pred":"source","obj":"CellFinder"},{"subj":"T182","pred":"source","obj":"CellFinder"},{"subj":"T183","pred":"source","obj":"CellFinder"},{"subj":"T184","pred":"source","obj":"CellFinder"},{"subj":"T185","pred":"source","obj":"CellFinder"},{"subj":"T186","pred":"source","obj":"CellFinder"},{"subj":"T187","pred":"source","obj":"CellFinder"},{"subj":"T188","pred":"source","obj":"CellFinder"},{"subj":"T189","pred":"source","obj":"CellFinder"},{"subj":"T190","pred":"source","obj":"CellFinder"},{"subj":"T191","pred":"source","obj":"CellFinder"},{"subj":"T192","pred":"source","obj":"CellFinder"},{"subj":"T193","pred":"source","obj":"CellFinder"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"CellFinder","color":"#ec93a9","default":true}]}]}}