Although HNF4A did not meet our strict threshold for significance in the primary analysis, it was ranked first in our secondary analysis using a test statistic that was more heavily weighted towards the mean shift between groups (see Methods).
For k = 2, IsoRank has greater coverage; however, this is likely due to IsoRankN having a strict threshold for edge inclusion.
In many cases, ESTs apparently encoding the same gene were assembled as separate clusters of highly similar sequence (albeit below the strict threshold for assembly).
Of these, 3057 exhibit unique genotype identities across the 53 strains, and the strict threshold for significance, following Bonferroni correction for multiple tests, was determined at 0.05/3,057, or 1.6 × 10−5.
The total length of all uniquely aligned sequence was recorded and the resulting alignments were classified into three levels: Level 1: global alignment, do not allow gaps, strict threshold for score Level 2: global alignment, allow gaps, permissive threshold for score Level 3: local alignment, permissive threshold.
For one object with a handle, palmar grasp was selected due to an error in object handle identification and for 4 objects pinch grasp was selected due to the strict threshold for small object classification, which was optimized based on a different object dataset (training).
ChIA-PET tool (Li et al., 2010) is the first one freely available to the public, which combines P-values from hyper-geometric test and an arbitrary and strict threshold for no less than 3 Paired- end tags (PETs) to identify chromatin interactions.
It is therefore likely that similar ASHM is present in both cell lines at this locus, but there is insufficient coverage of this region in the IMR90 cell line to obtain a P-value below the strict threshold for genome-wide significance we used in this study.
