Figure 1.
IS analysis for miRNA expression data.
a. impact significance (IS) of nucleotides ,
,
,
,
, and
for TCGA miRNA expression across breast cancer specimens after excluding miRNA pairs with high alignment score (
) of the 3' portion. b. IS of the 3' portion for TCGA expression after excluding miRNA pairs with identical nucleotides
or
. Threshold of similar 3' portion is set to be
respectively. c. quantile curves of 3'-alignment scores for 7 groups from the TCGA expression data: the 6 classes and the remaining pairs. Groups with quantile curves above tend to be more similar in the 3' portion than groups with quantile curves below. KS test shows that CL
, and
tend to have more similar 3' portion (p values:
,
and
) d. e. f. same analysis as a. b. c. for miRNA time-course expression in ESCs.
Figure 2.
IS values of the searched contiguous segments of the 3' portion for each of the 6 classes from the TCGA expression data.
represents 3 contiguous nucleotides,
4 contiguous nucleotides, and so forth. The x-axis represents the starting position of the segments.
Figure 3.
a. IS of nucleotides ,
,
,
,
, and
for miRNA cell cycle regulation in breast cancer cells after excluding miRNA pairs with high alignment score (
) of the 3' portion. b. IS of the 3' portion for miRNA cell cycle regulation in breast cancer cells after excluding miRNA pairs with identical nucleotides
or
. Threshold of similar 3' portion is set to be
respectively. c. quantile curves of 3'-alignment scores for 7 groups from the breast cancer RPPA data: CL
,
,
,
,
,
and the remaining pairs. Groups with quantile curves above tend to be more similar in the 3' portion than groups with quantile curves below. KS test shows that CL
,
,
and
tend to have more similar 3' portion (p values:
,
,
,
) d. IS values of the searched contiguous segments of the 3' portion for all 6 classes from the breast cancer RPPA data.
represents 3 contiguous nucleotides,
4 contiguous nucleotides, and so forth. The x-axis represents the starting position of the segments.
Figure 4.
IS values of the searched contiguous segments of the 3' portion for each of the 6 classes from the expression data of ESCs.
represents 3 contiguous nucleotides,
4 contiguous nucleotides, and so forth. The x-axis represents the starting position of the segments.
Figure 5.
IS values of the searched contiguous segments of the 3' portion for each of the 6 classes from the RPPA data.
represents 3 contiguous nucleotides,
4 contiguous nucleotides, and so forth. The x-axis represents the starting position of the segments.
Figure 6.
Correlation between miRNA expression and function.
a. quantile curves of two groups for TCGA expression data. group 1: miRNA pairs of similar seed (seed alignment score) and similar expression (expression distance
), group 2: miRNA pairs of similar seed (seed alignment score
) and dissimilar expression distance (expression distance
). KS test shows that group 1 tend to have more similar cell cycle regulation than group 2 (p value:
). b. quantile curves of two groups for expression data of ESCs. group 1: miRNA pairs of similar seed (seed alignment score
) and similar expression (expression distance
), group 2: miRNA pairs of similar seed (seed alignment score
) and dissimilar expression distance (expression distance
). KS test shows that group 1 tend to have more similar cell cycle regulation than group 2 (p value:
). c. expression levels across breast cancer specimens and mature sequences of two miRNA pairs. d. time-course expression levels of ESCs and mature sequences of two miRNA pairs.