Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.1.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43336	0.224
27DAP/17DAP	0.93488	0.877
39DAP/27DAP	1.82776	0.068
41DAP/39DAP	0.58262	0.045
42DAP/41DAP	1.17478	0.994
43DAP/42DAP	1.27566	0.929
47DAP/43DAP	1.12395	0.793
52DAP/47DAP	0.78001	0.466
57DAP/52DAP	1.0304	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96011	0.489
17DAP/reference	1.16563	0.874
27DAP/reference	1.63094	0.034
39DAP/reference	1.37624	0.119
41DAP/reference	1.10901	0.667
42DAP/reference	1.8052	0.001
43DAP/reference	1.45099	0.008
47DAP/reference	1.86839	0.001
52DAP/reference	1.28466	0.242
57DAP/reference	1.30813	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.69942	0.039
27DAP/17DAP	0.94855	0.854
39DAP/27DAP	1.1215	0.388
41DAP/39DAP	1.12748	0.986
42DAP/41DAP	0.86496	0.339
43DAP/42DAP	1.07733	0.382
47DAP/43DAP	1.14926	0.286
52DAP/47DAP	1.05501	0.804
57DAP/52DAP	0.71725	0.1
57DAP/7DAP	1.06421	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40513	0.07
17DAP/reference	1.31438	0.011
27DAP/reference	1.80464	0.007
39DAP/reference	2.94372	0.005
41DAP/reference	1.36999	0.039
42DAP/reference	2.62122	0.013
43DAP/reference	3.11177	0.006
47DAP/reference	2.5146	0.014
52DAP/reference	2.38678	0.007
57DAP/reference	1.69954	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71553	0.056
17DAP/reference	1.17964	0.437
27DAP/reference	1.51416	0.057
39DAP/reference	1.94332	0.037
41DAP/reference	1.46468	0.011
42DAP/reference	2.19683	0.008
43DAP/reference	1.22052	0.89
47DAP/reference	2.03986	0.008
52DAP/reference	1.2937	0.007
57DAP/reference	1.03644	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15223	0.218
17DAP/reference	1.13344	0.602
27DAP/reference	2.32564	0.014
39DAP/reference	2.20526	0.008
41DAP/reference	1.8638	0.006
42DAP/reference	2.40963	0.007
43DAP/reference	2.38754	0.01
47DAP/reference	1.57263	0.017
52DAP/reference	1.89067	0.073
57DAP/reference	3.42789	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97748	1
26DAP/20DAP	0.89944	1
34DAP/26DAP	0.70573	0.067
51DAP/34DAP	1.1156	0.785
52DAP/51DAP	0.75508	0.151
53DAP/52DAP	1.40063	0.077
55DAP/53DAP	0.78463	0.033
57DAP/55DAP	0.83182	0.318
62DAP/57DAP	0.81846	0.466
68DAP/62DAP	1.40041	0.04
68DAP/14DAP	0.97831	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.83182	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71827	0.197
Mature Green Tomato/Ripe Tomato	1.07232	0.881
Immature Eggplant/Mature Eggplant	0.85525	0.069
Ripe Pepper/Ripe Tomato	0.48018	0.293
Mature Eggplant/Ripe Tomato	0.65005	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91704	0.883
1-1-2/M82	1.3479	1
12-2/M82	0.95182	0.955
12-4/M82	0.99238	1
1-3/M82	1.55382	0.479
2-1-1/M82	0.86955	0.683
2-1/M82	0.89426	1
2-6/M82	0.95569	0.501
3-2/M82	1.1037	0.84
4-1-1/M82	1.02402	1
4-1/M82	2.27992	1
4-3-2/M82	0.98184	1
4-3/M82	0.95421	1
5-3/M82	0.96461	1
6-2/M82	0.98447	1
6-3/M82	1.0285	1
7-1/M82	1.08542	0.87
7-2/M82	1.03878	0.385
9-3-2/M82	1.31193	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.81047
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.64862
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.27488	0.426
WT/WTpooled	N/A	N/A

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.05604	1

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04785	0.894
DC3000/delta hrp 6h	0.84291	0.95
DC3000/delta hrp 12h	0.77817	1
DC3000/delta hrp 24h	1.04919	0.655

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94465	0.597
DC3000 delta B/DC3000 delta AB	1.14914	0.406

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.451	1
Exp 36h	1.19029	1
Exp 60h	1.13769	1

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.96627	1
Var 0h	1.1292	0.98
Var 12h I row2-row1	1.33909	0.406
Var 12h NI row2-row1	0.87463	0.713
Var 36h I row2-row1	1.06749	1
Var 36h NI row2-row1	1.41992	0.482
Var 60h I row2-row1	1.09066	1
Var 60h NI row2-row1	1.18577	0.904
Time course 0hI-0hNI	0.98384	0.961
Time course 12hI-12hNI	1.0694	0.572
Time course 36hI-36hNI	0.87881	0.034
Time course 60hI-60hNI	0.27857	0.006

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.05416	0.748
transgenic ySAMdc/azygous control (breaker)	0.96054	1
transgenic ySAMdc/azygous control (red)	1.25343	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.64275	0.045

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.33688	0.277

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91854	1
Manapal/WT (break)	1.20052	1
Manapal/WT (red)	1.01707	1