ORTom: a multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato.
Co-expressed genes are often expected to be functionally related and many bioinformatics approaches based on co-expression have been developed to infer their biological role. However, such annotations may be unreliable, whereas the evolutionary conservation of gene co-expression among species may form a basis for more confident predictions. The huge amount of expression data (microarrays, SAGE, ESTs) has already allowed functional studies based on conserved co-expression in animals. Up to now, the implementation of analogous tools for plants has been strongly limited probably by the paucity and heterogeneity of data. Here we present ORTom, a tomato-centred EST data-mining approach based on conserved co-expression in the Solanaceae family. ORTom can be used to predict functional relationships among genes and to prioritize candidate genes for targeted studies. The method consists in ranking ESTs co-expressed with a gene of interest according to the level of expression pattern conservation in phylogenetically-related plants (potato, tobacco and pepper) to obtain lists of putative functionally-related genes. The lists are then analyzed for Gene Ontology keyword enrichment. The web server ORTom has been implemented to make the results publicly-available and searchable. Few biological examples on how the tool can be used are presented.
Miozzi
Laura
L
Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135 Turin, Italy. l.miozzi@ivv.cnr.it
Provero
Paolo
P
Accotto
Gian Paolo
GP
D017360:Arabidopsis / Q000235:genetics; D057225:Data Mining / Q000379:methods*; D005638:Fruit / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant / Q000235:genetics*; D054884:Host-Pathogen Interactions / Q000235:genetics; D020407:Internet; D018551:Solanum lycopersicum / Q000235:genetics*; D009928:Organ Specificity / Q000235:genetics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012985:Software Design; D013045:Species Specificity
J Biol Chem. 2004 May 21;279(21):22548-57
15024005
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W673-6
15980560
Plant Physiol. 2007 Mar;143(3):1327-46
17208958
Plant Mol Biol. 2004 May;55(2):183-92
15604674
Plant Cell. 2005 Nov;17(11):2954-65
16243903
Gene. 2005 Jan 17;345(1):119-26
15716085
Plant Physiol. 1996 Apr;110(4):1337-47
8934628
Plant Mol Biol. 2005 Jul;58(5):739-50
16158246
J Exp Bot. 2002 Oct;53(377):2039-55
12324528
Plant Physiol. 1998 Dec;118(4):1213-22
9847095
Trends Genet. 2003 May;19(5):238-42
12711213
Planta. 1986 Sep;168(3):390-4
24232150
Bioinformatics. 2002 Apr;18(4):555-65
12016053
Mol Syst Biol. 2008;4:180
18414481
BMC Bioinformatics. 2008 Apr 23;9:208
18433471
Bioinformatics. 2005 Nov 1;21 Suppl 3:iii3-11
16306389
Plant Mol Biol. 1993 Oct;23(1):193-207
8219049
Plant Cell. 1989 Oct;1(10):1025-34
2562553
J Virol. 2006 Sep;80(17):8329-44
16912284
Plant Physiol. 2001 Oct;127(2):398-415
11598216
Plant Cell. 2002;14 Suppl:S131-51
12045274
Genome Res. 2002 Jan;12(1):37-46
11779829
Trends Plant Sci. 2004 May;9(5):244-52
15130550
Biochim Biophys Acta. 1996 Dec 12;1314(3):187-90
8982274
PLoS One. 2008 Jun 18;3(6):e2439
18560577
PLoS Biol. 2004 Jan;2(1):E9
14737187
Plant Physiol. 2009 Sep;151(1):16-33
19605550
Genetics. 2006 Apr;172(4):2529-40
16489216
PLoS Biol. 2004 May;2(5):E132
15138501
Plant Cell Environ. 2009 Dec;32(12):1633-51
19712066
Plant Physiol. 2005 Jul;138(3):1372-82
15951486
J Cell Biol. 1999 Nov 29;147(5):945-58
10579716
Plant Physiol. 2005 Oct;139(2):750-69
16183847
Genome Biol. 2001;2(5):REVIEWS3007
11387043
BMC Bioinformatics. 2005 Sep 14;6:227
16162296
Annu Rev Phytopathol. 2006;44:393-416
16602950
Nat Genet. 2002 Jul;31(3):255-65
12089522
BMC Bioinformatics. 2004 Nov 19;5:179
15550177
Virology. 2002 Apr 10;295(2):307-19
12033790
Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8
9843981
J Virol. 2003 Nov;77(22):12357-62
14581573
PLoS Comput Biol. 2008 Mar 28;4(3):e1000043
18369433
Science. 1995 Dec 22;270(5244):1983-5
8533089
Plant Mol Biol. 2005 May;58(2):229-45
16027976
Plant Physiol. 1984 Jan;74(1):32-8
16663381
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W320-6
18480120
Plant J. 2006 Apr;46(2):336-48
16623895
Plant Mol Biol. 1999 Jul;40(4):545-54
10480379
Trends Microbiol. 1998 Jan;6(1):31-5
9481822
Trends Biochem Sci. 2004 May;29(5):243-9
15130560
New Phytol. 2008;180(3):587-593
18801004
Trends Biotechnol. 2002 Oct;20(10):407-10; discussion 410
12220896
Nucleic Acids Res. 2008 Jan;36(Database issue):D77-82
17932064
Yi Chuan Xue Bao. 2006 Aug;33(8):757-64
16939010
BMC Genomics. 2005 Sep 14;6:124
16162286
Bioinformatics. 2005 Jun 1;21(11):2730-8
15797912
Plant Cell. 2001 Aug;13(8):1819-33
11487695
BMC Genomics. 2004 Jan 13;5(1):4
14718066
Plant J. 2006 Mar;45(6):968-81
16507087
Plant Physiol Biochem. 2007 Sep;45(9):665-72
17764967
Plant Physiol. 1994 Aug;105(4):1457-8
7972510
Plant Physiol. 2006 Dec;142(4):1380-96
17071647
BMC Syst Biol. 2008 Sep 22;2:81
18808668