VL1176

Caenorhabditis elegans

NC1528

Caenorhabditis elegans

NC1469

Caenorhabditis elegans

VL749

Caenorhabditis elegans

WBPaper00040560:hpl-2_embryo_downregulated

Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probe sets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction. Transcripts down regulated in hpl-2(tm1489) embryo comparing to N2 in tiling array analysis.

WBPaper00040560:hpl-2_embryo_upregulated

Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probe sets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction. Transcripts down regulated in hpl-2(tm1489) embryo comparing to N2 in tiling array analysis.

WBPaper00040560:hpl-2_L3_upregulated

Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probe sets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction. Transcripts down regulated in hpl-2(tm1489) L3 larva comparing to N2 in tiling array analysis.

WBPaper00040560:hpl-2_L3_downregulated

Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probe sets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction. Transcripts down regulated in hpl-2(tm1489) L3 larva comparing to N2 in tiling array analysis.

WBPaper00028344:adult_expr_change

Authors searched for targets with seed matches of perfect Watson-Crick base-pair complementarity to positions two-eight of the miRNAs (counting from the 5' end). In order to consider these seed matches as potential target sites, authors required a minimal cut-off for binding specificity of the remainder of the miRNA to the target. Recent evidence suggests that this is not required for function in humans, but 3' binding does occur in studies of C. elegans. Authors used the scoring algorithm from Robins et al. (2005). The binding cut-off is determined by creating a second-order Markov model of the background for the 3' UTRs. The cut off was p-value < = 0.05. micro RNAs that exhibit changes in expression during adulthood (p-value < = 0.05).