Research
MicroRNA profiling of the murine hematopoietic system
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* Corresponding author: Silvia Monticelli monticel@cbr.med.harvard.edu
- † Equal contributors
1 Department of Pathology, Harvard Medical School, and CBR Institute for Biomedical Research, Boston, MA 02115, USA
2 Department of Biology and Genetics of Medical Sciences, Universitá degli Studi di Milano, 20133 Milan, Italy
3 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
4 Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
5 Center for Functional Comparative Genomics, Department of Biology, New York University, New York, NY 10003, USA
6 Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
7 Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
Genome Biology 2005, 6:R71 doi:10.1186/gb-2005-6-8-r71
Published: 1 August 2005Additional files
Additional data file 1:
For normalization the VSN method was used [37]. A standard t-test on the generalized log transformed expression levels was used to rank the miRNAs and compute p values. The results were filtered to discard any miRNA whose signal was not three times above the background in at least one of the two groups and whose absolute fold change was less than 3.
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Additional data file 2:
To handle the low sample numbers, the Bayesian corrected t-test [38] was used to rank and compute p values. The different comparisons had greatly varying significances, so different cut offs were used on each list. For the BMMC versus Th1 and Th2 comparisons, a FDR cutoff of 10-2 was used, with a filter of three times background levels and a fold change of three. For the BMMC versus Pu.1-/- comparison a FDR of 10-6 and four times background filter was used.
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Additional data file 3:
The FDR cut off was 10-6 and the background filter was four times.
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Additional data file 4:
There is a clear correlation between Tm and strength of signal for all the probes used (left panel). The same is true if only the probes for miRNAs that were identified as 'high in hematopoietic cells' (see Figure 5a) are considered (right panel). Also, the latter probes have Tm that span almost the entire range of Tm seen for all the probes, and have an average Tm (56°C) only slightly higher than the average of all the probes (54°C). This means that overall, the use of these different oligos as probes in the arrays is in fact valid, even though we may have lost some of the low Tm miRNAs as false negative signals, and some of the high Tm probes may have given a few false positive signals.
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