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Methods tested on datasets generated in this manner may better generalize to true genetic association datasets.
The datasets generated in this study was treated by the Ward's method of linkage with squared Euclidean distance as a measure of similarity.
All protein identifications and MS/MS data have been submitted to the PRoteomics IDEntifications database (PRIDE [26]; accession #: 8691, 8692, 8693, 8694, 8695 and 8696, representing the 6 new datasets generated in this work).
Complex datasets generated in this way are referred to as MCL-GO datasets.
Microarray datasets generated in this study have been submitted in MIAME-compliant format to the EBI database [ 14].
Together, the datasets generated in this study advance gene-centric models of kidney development pathways towards more complete transcript-centric models, capturing the transcriptional landscape of gene expression.
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To analyze transcript abundance of Dicer-like, Argonaute and RDR genes at different stages of reproductive development in rice, microarray datasets generated in-house were utilized.
This result was found to be quite consistent across the many datasets generated in the field trial.
The phylogenetic networks for each of the datasets generated in the previous steps were constructed with the SplitsTree4 software [ 28].
Similarly, the large species-specific datasets generated in the present study can be further analyzed by other investigators to address species-specific questions.
The simulated datasets generated in the current study are available by request directly from the authors or through http://www4.stat.ncsu.edu/~motsinger.stat.ncsu.edu/~motsinger
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