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Supplementary Figure 1 Analyses of RNAi phenotypes in Kamath et al.,
Gonczy et al. and Maeda et al. datasets. a. Comparison between RNAi
phenotypes and published loss-of-function phenotypes of known loci. Shown
are the numbers of loci with Nonv, Vpep or any phenotype (All) that were
screened in each study (‘Scrn’), the number that were detected in each screen
(‘Hit’), and the percentage detected. To determine the rate of false positives
(‘False +ve’) in each screen, we examined known loci with published non-lethal
loss-of-function phenotypes that had been analysed in each screen — any of
these having a Nonv phenotype by RNAi were classed as false positives (‘Hit’).
b. Comparison of RNAi phenotypes in Kamath et al., Gonczy et al. and Maeda
et al. datasets. The total number of genes screened in common in any pair of
screens is shown in plain type beside the central double-headed arrows; also
shown is the total number of genes that gave a Nonv phenotype when pooling
both screens. In the overlapping circles, we show the percentages of these
Nonv genes that were found in common between any pair of screens or
uniquely in one or other screen; numbers of genes in each category are shown
on parentheses. The high percentage of Nonv phenotypes found in the Maeda
et al dataset but absent from Kamath et al or Gonczy et al can be partially
explained by a higher rate of false positive Nonv RNAi phenotypes in the Maeda
et al screen.
Supplementary Figure 2. Relative representation of genes with different
molecular functions on each chromosome. Genes were placed into one of the
following putative molecular functional classes as described in Methods: protein
synthesis (P Synth), RNA synthesis (RNA Synth), DNA synthesis and repair/cell
cycle (DNA/CC), cellular architecture (Cell Arch), RNA binding (RNA Bind),
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chromatin regulation (Chromatin), protein degradation (Degrad), energy and
intermediary metabolism (Metab), transcription factors (Txn Factor), nucleicacid binding (NA Bind), signal transduction (Signaling), small molecule transport
(SM Txpt), specific proteases (Protease), retroviral- and transposon-derived
sequences (Viral), collagens (Collagen), and genes with neuronal functions
(Neuro); genes which could not be assigned to a functional class were placed
into the Unknown class (Unknown). Shown are the relative frequencies of
occurrence of genes in each functional class for each chromosome. Bars in
yellow denote a statistically significant overenrichment (p<0.01); red bars
represent an underenrichment (p<0.01).
Supplementary Figure 3. Regions of chromosomal enrichment (blue) and
underenrichment (green) of microarray mounts 0-29 from Kim et al
(2001) Science 293, 2087-92. Yellow and teal boxes represent the arm
and cluster regions, respectively of the six C. elegans chromosomes.
Black lines inside these show regions enriched for duplications. Shown
above each chromosome in one line for each mount are chromosomal
regions significantly (p<0.01) enriched (blue) or underenriched (green) in
a 250 gene window. Roman numerals label the chromosomes. Above
and to the left of each chromosome, numbers refer to the mount plotted.
Note that mount 2 is composed almost entirely of the genes identified in
Blumenthal et al.40 to be transpliced to SL2, and thus it marks
downstream genes in operons (T. Blumenthal and S. Kim, personal
communication). The regions enriched for mount 2 overlap nearly
identically with the regions enriched for Nonv genes (red bars in Figure
4b).