- WBPaper00041609:hpl-1_hpl-2_downregulated
The gene expression fold change was calculated from the duplicate microarray data. The fold change cut-off was 1.5 from 2 biological replicates (FDR < 0.05). Fold change shown here are hpl-1; hpl-2; his-24 vs WT.
Genes with decreased expression level for L4 stage larvae in hpl-2; hpl-1 and his-24 hpl-1; hpl-2 compared to wild type (FDR < 0.05).
- WBPaper00041609:hpl-1_hpl-2_upregulated
The gene expression fold change was calculated from the duplicate microarray data. The fold change cut-off was 1.5 from 2 biological replicates (FDR < 0.05). Fold change shown here are hpl-1; hpl-2; his-24 vs WT.
Genes with increased expression level for L4 stage larvae in hpl-2; hpl-1 and his-24 hpl-1; hpl-2 compared to wild type (FDR < 0.05).
- WBPaper00054493:hpl-2(tm1489)_upregulated
DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2.
Transcripts that showed significantly increased expression in hpl-2(tm1489) comparing to in N2 animals.
- 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_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_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.
- WBPaper00065945:global-rpoa-2(-)_upregulated_transcript
DESeq2, fold change >= 2, FDR < 0.05.
Transcripts that showed significantly increased expression in global RPOA-2-depleted L1 animals (degron-GFP-rpoa-2;eft-3p-TIR1, +IAA), compared to controls (degron-GFP-rpoa-2,+IAA).