variance is shared between two genes. An r-value of 0.7 means
that coexpression explains 49% of the variance in common
between two genes. This is the reason why 0.7 to 0.75 is
often used as a cutoff for coexpression analysis.
14. ATTED II uses the MR (Mutual Rank) value to rank the
coexpressed genes, lower MR values means more correlation.
This method was determined by the authors to have higher
performance in the prediction of gene function than the Pearson correlation coefficient (PCC).
15. Available at http:/ /bar.utoronto.ca/~nprovart/ArabidopsisDAPv1.
meme.
16. Available at http:/ /bar.utoronto.ca/~nprovart/ABI3_coexpressed_
genes_500bp_upstream.fasta.
17. GOrilla is another useful tool for such analyses, and permits the
ability to upload a ranked list of genes for enrichment analysis.
It offers similar visualization of enriched categories. See http://
cbl-gorilla.cs.technion.ac.il/.
18. The GO database that AmiGO accesses is updated frequently,
and the numbers reported here will likely vary in your own
results. These values are for the 2019-02-02 release.
19. The Classification SuperViewer is also available for Medicago
truncatula: http://bar.utoronto.ca/ntools/cgi-bin/ntools_
classification_superviewer_medicago.cgi.
20. Note that it is not possible to select a background data set for
Classification SuperViewer. This is not so much of an issue for
gene lists that are derived from relatively comprehensive platforms but can be an issue for platforms that are less
comprehensive.
21. AraCyc is a part of the BioCyc metabolic databases. All the
metabolic databases present on BioCyc share the same software, so the tutorial described on this section can be applied to
the other databases.
22. We can include more expression columns: each one could
represent a different experiment or time point.
23. The MapMan version used in this chapter is 3.6.0RC1.
24. VirtualPlant currently integrates information from Arabidopsis
and rice sources.
25. In the case of subcellular location, information comes from
SUBA4 database. The shading denotes the protein localization, with red representing a more likely compartment.
26. Protein Data Bank: http://www.rcsb.org/pdb/home/
home.do. Phyre website: http://www.sbg.bio.ic.ac.uk/
phyre2/.
Arabidopsis Bioinformatics
85
that coexpression explains 49% of the variance in common
between two genes. This is the reason why 0.7 to 0.75 is
often used as a cutoff for coexpression analysis.
14. ATTED II uses the MR (Mutual Rank) value to rank the
coexpressed genes, lower MR values means more correlation.
This method was determined by the authors to have higher
performance in the prediction of gene function than the Pearson correlation coefficient (PCC).
15. Available at http:/ /bar.utoronto.ca/~nprovart/ArabidopsisDAPv1.
meme.
16. Available at http:/ /bar.utoronto.ca/~nprovart/ABI3_coexpressed_
genes_500bp_upstream.fasta.
17. GOrilla is another useful tool for such analyses, and permits the
ability to upload a ranked list of genes for enrichment analysis.
It offers similar visualization of enriched categories. See http://
cbl-gorilla.cs.technion.ac.il/.
18. The GO database that AmiGO accesses is updated frequently,
and the numbers reported here will likely vary in your own
results. These values are for the 2019-02-02 release.
19. The Classification SuperViewer is also available for Medicago
truncatula: http://bar.utoronto.ca/ntools/cgi-bin/ntools_
classification_superviewer_medicago.cgi.
20. Note that it is not possible to select a background data set for
Classification SuperViewer. This is not so much of an issue for
gene lists that are derived from relatively comprehensive platforms but can be an issue for platforms that are less
comprehensive.
21. AraCyc is a part of the BioCyc metabolic databases. All the
metabolic databases present on BioCyc share the same software, so the tutorial described on this section can be applied to
the other databases.
22. We can include more expression columns: each one could
represent a different experiment or time point.
23. The MapMan version used in this chapter is 3.6.0RC1.
24. VirtualPlant currently integrates information from Arabidopsis
and rice sources.
25. In the case of subcellular location, information comes from
SUBA4 database. The shading denotes the protein localization, with red representing a more likely compartment.
26. Protein Data Bank: http://www.rcsb.org/pdb/home/
home.do. Phyre website: http://www.sbg.bio.ic.ac.uk/
phyre2/.
Arabidopsis Bioinformatics
85