For each of the six sizes of regions, comparisons were made between the three types of "defined" regions (cis-eQTL clusters, control clusters, and regions centered on single cis-eQTLs) and the fourth type of region, consisting of random regions of matching size.
A cross-validation test confirmed that the held-out SGLs received significantly higher SE scores than the held-out DGLs (t = 8.777; p-value = 6.204e-16; Welch two-sample t-test; Figure 6A) and each was higher than random control modules of matching sizes (t = 4.802; paired7e-06; paired Student t-test; Figure S2c d).
Beginning from starting position, different defined window sizes lead to several sequence cutouts of matching sizes.
After submitting the list of identifiers, the application maps them onto an interaction network (Section 4), and computes topological properties for the entire network, the uploaded gene/protein set and random sets of matched sizes.
Representative examples that compare two cis-eQTL clusters and control clusters of matching sizes are shown in Figure 3. Altogether, polymorphic SINEs appeared to be a signature characteristic of cis-eQTL regions.
Assembly for contigs was performed with match size of 50, minimum match percentage of 97, minimum sequence length of 100.
This assembly was run with a minimum match size of 19 nucleotides, match percentage of 93%, mismatch penalty of 18, and gap penalty of 30.
For this assembly, we used a minimum match size of 19 nucleotides, match percentage of 88%, mismatch penalty of 18, and gap penalty of 30.
This assembly was completed using the default parameters for NGen 3.0's de novo transcriptome assembly of: 85% match, match size 21, genome length 225 MB.
Despite that familiarity, the two teams spent the first 10 minutes of this match sizing each other up cautiously.
By using the weight matrices, a specific score can be calculated for any segment of the matching size, based on its nucleotide sequence.
