Supplementary Data

Supplementary Figure Legends

Supplementary Fig. S1. Phylogenetic tree of the 257 RNA-binding proteins included in

RiceRBP. This tree was constructed using the FastTree phylogeny construction

program with default protein settings; branch lengths were ignored to permit ease of

interpretation. Label colors indicate the set of capture experiment in which each RNA-

binding protein was identified (see legend). Bootstrap symbols (grey ovals) indicate

branches with ≥ 80 percent support.

Supplementary Fig. S2. The protein search tool interface for querying the RiceRBP

database. (A) Users can search based on the Gene Name, AK accession, GI accession

or Keyword criteria. Individual RBPs can also be selected manually using the selection

box, or all RBPs can be selected ('View All' button). (B) Partial query results list after

searching for proteins containing RRM domains.

Supplementary Fig. S3. BLAST query for the RiceRBP database. (A) Display of the

BLAST tool interface. Users are able to customize various algorithm parameters as well

as submit sequences via text file. Here we BLAST the sorghum protein sequence

C5Y6Y8. (B) Example output for query sequence (C5Y6Y8, uncharacterized protein).

The RBP links in the BLAST results display either protein or transcript information

depending on the type of search database used (protein or nucleotide, respectively).

Supplementary Fig. S4. The transcript details page displays the RBP transcript

information. This page provides the chromosomal location of the transcript locus and

links to characterized gene models from RAP-DB or MSU rice genome project, when

available. The RBP transcript sequence is displayed with the coding region highlighted.

If a RAP-DB locus is defined for the RBP then an optional control at the bottom of the

transcript page allows users to query the Osiris promoter analysis website [1], which

contains information about transcription factor binding sites (TFBS) and promoter

elements for that gene.

Supplementary Fig. S5. Visualization of the RBP-A promoter using Osiris. (A)

Visualization of the proximal 2 Kb promoter sequence upstream of the transcription start

site for the RBP-A protein coding gene Os11g0637700. The colored vertical lines

indicate the positions of putative transcription factor binding sites in the promoter region.

(B) A summary table indicating the statistical enrichment of each transcription factor in

the visualized promoters. A more detailed description of the Osiris analysis platform

functionality is available [1].

Supplementary Fig. S6. The RBP expression visualization tool allow users to select

specific RBPs and visualize their expression profiles in 67 distinct microarray

experiments. (A) RBP selection lists allow users to define the set of RBP expression

profiles to visualize; here we have selected solely RBP-A. (B) Expression profile of

RBP-A. Only 42 of the 67 experiments are shown because expression data for RBP-A

were absent from the remaining experiments. The experiment labels are themselves

links to pages containing detailed information about the microarray experiment.

References

[1] R.T. Morris, T.R. O'Connor, J.J. Wyrick, Osiris: an integrated promoter database for

Oryza sativa L, Bioinformatics (Oxford, England), 24 (2008) 2915-2917.

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