RNA-Annotated (413)

1
RNA-Annotated (413) GO uncharacterized (589) Wu
predictions (285) Simple co-regulation
(308) Simple association (414) Multiple
associations (75) SVM expression (128) SVM Gavin
(40) RNA complexes (273) Andersen Human Nuc.
(165) Nuclease motifs (91) Recommended
(105) Negative control (31) Essential
(525) Conserved (575) Localization (776) Assayed
(468)
Gene expression over 424 microarray experiments
Genes with Non-coding RNA-related GO
annotations (413)
Log(ratio)
Genes with biological process unknown GO
annotation (578)
Genes with other GO annotations (341) (protein
metabolism nucleobase, nucleoside, nucleotide
and nucleic acid metabolism cell
cycle..) Negative controls (26)
Localization Nuclear Cytoplasmic
Peng et al. Supplementary Fig. 1
2
Supplementary Fig. 1. Yeast genes associated
with non-coding RNA annotations in databases, or
predicted from analysis of genome-scale data sets
to be in the same classes. Left, genes are
represented as rows and the associations and
other gene properties are columns colors
indicate a gene having an indicated association
or property the number with the indicated
property is in parenthesis. RNA-Annotated, genes
in non-coding RNA annotation classes. GO
uncharacterized, listed as GO biological process
unknown in December 2002 (Issel-Tarver et al.,
2002). Wu predictions, predicted RNA processing
and modification genes based on transcriptional
co-regulations across 424 microarray experiments
(Wu et al., 2002 a subset have been annotated
since the predictions were made). Simple
co-regulation, genes manually identified as
co-regulated with RNA processing and modification
genes. Simple association, all genes associated
with known RNA processing proteins in any of five
data sets (Uetz et al., 2000 Ito et al., 2001
Gavin et al., 2002 Ho et al., 2002 Wu et al.,
2002). Multiple associations, those with simple
associations in more than one data set. SVM
expression and SVM complexes, predictions using
Support Vector Machines (Brown et al., 2000) with
microarray data (Wu et al., 2002) or protein
complexes (Gavin et al., 2002) as inputs. RNA
complexes, essential and/or uncharacterized
proteins associated with protein complexes
enriched (P lt 0.01) for RNA-related activities
(Gavin et al., 2002 Ho et al., 2002 Robinson et
al., 2002). Andersen human nucleolus, homologs
of proteins contained in the human nucleolus
(Andersen et al., 2001). Nuclease motifs,
proteins with nuclease-like motifs. Recommended,
genes and proteins recommended by personal
contacts. Negative controls, genes with known
functions unrelated to RNA. Essential, essential
for viability. Conserved, BLASTP hit among known
or predicted human proteins at E lt 10-20.
Localization, according to Kumar et al. (2001).
Assayed, assayed using the RNA processing
microarray described herein. Right, microarray
expression data used in Wu et al. (2002) the
gene order on the vertical axis is the same as
that shown at left and the 424 microarray
experiments (horizontal axis) have been clustered.