Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.1.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.66151	0.09
27DAP/17DAP	0.50878	0.032
39DAP/27DAP	0.66721	0.41
41DAP/39DAP	0.70562	0.216
42DAP/41DAP	1.29182	0.672
43DAP/42DAP	1.4894	0.317
47DAP/43DAP	0.76569	0.321
52DAP/47DAP	0.94711	0.761
57DAP/52DAP	0.79562	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.62787	0.006
17DAP/reference	1.29284	0.021
27DAP/reference	1.04911	0.82
39DAP/reference	1.04482	0.842
41DAP/reference	0.97684	0.667
42DAP/reference	1.58089	0.004
43DAP/reference	1.09242	0.233
47DAP/reference	0.97084	0.392
52DAP/reference	0.92585	0.25
57DAP/reference	0.91211	0.277

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.67457	0.046
27DAP/17DAP	1.00483	1
39DAP/27DAP	0.4503	0.028
41DAP/39DAP	0.96162	0.923
42DAP/41DAP	1.05242	0.947
43DAP/42DAP	1.89294	0.23
47DAP/43DAP	0.98116	0.919
52DAP/47DAP	0.88654	0.666
57DAP/52DAP	0.8427	0.223
57DAP/7DAP	0.41139	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06542	1
17DAP/reference	0.70747	0.049
27DAP/reference	0.84526	0.146
39DAP/reference	1.06342	0.96
41DAP/reference	1.01072	0.811
42DAP/reference	0.9772	0.531
43DAP/reference	0.85145	0.056
47DAP/reference	0.86632	0.293
52DAP/reference	1.07749	0.041
57DAP/reference	0.94921	0.314

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.13054	0.083
17DAP/reference	1.73239	0.066
27DAP/reference	1.19657	0.48
39DAP/reference	0.7851	0.072
41DAP/reference	1.1516	0.573
42DAP/reference	0.86285	0.108
43DAP/reference	0.87354	0.212
47DAP/reference	0.88327	0.022
52DAP/reference	0.65773	0.006
57DAP/reference	0.78842	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16127	1
17DAP/reference	1.66017	0.237
27DAP/reference	1.57999	0.51
39DAP/reference	0.99721	0.755
41DAP/reference	1.08681	0.916
42DAP/reference	0.9748	0.671
43DAP/reference	1.84745	0.026
47DAP/reference	3.04549	0.005
52DAP/reference	1.19191	0.779
57DAP/reference	2.07457	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.78455	0.44
26DAP/20DAP	0.83902	0.512
34DAP/26DAP	1.12354	1
51DAP/34DAP	1.07684	0.909
52DAP/51DAP	1.26943	0.446
53DAP/52DAP	0.94295	0.797
55DAP/53DAP	0.96642	0.775
57DAP/55DAP	1.28397	0.881
62DAP/57DAP	1.11834	0.902
68DAP/62DAP	1.18653	1
68DAP/14DAP	0.81241	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72146	0.034

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.82822	0.286
Mature Green Tomato/Ripe Tomato	2.73954	0.015
Immature Eggplant/Mature Eggplant	0.44062	0.063
Ripe Pepper/Ripe Tomato	3.9615	0.233
Mature Eggplant/Ripe Tomato	2.98687	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.46759	1
12-2/M82	0.6959	0.955
12-4/M82	0.40498	0.33
1-3/M82	N/A	N/A
2-1-1/M82	0.28026
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.69121
4-1-1/M82	0.24985
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.69855	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.45447
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.36644
IL7-5/WTpooled	0.67583
IL7-3/WTpooled	1.30659	1
IL12-4/WTpooled	0.74222	0.71
IL1-4/WTpooled	1.12149	1
WT/WTpooled	0.95653	1

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	1.12972	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95802	1
DC3000/delta hrp 6h	0.98066	0.95
DC3000/delta hrp 12h	1.24836	1
DC3000/delta hrp 24h	0.79956	0.231

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.43624	0.023
DC3000 delta B/DC3000 delta AB	0.41561	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98063	1
Exp 36h	0.70942	0.434
Exp 60h	0.6845	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9763	1
Var 0h	0.77964	0.457
Var 12h I row2-row1	0.7376	0.418
Var 12h NI row2-row1	1.04521	1
Var 36h I row2-row1	0.8853	1
Var 36h NI row2-row1	1.15381	1
Var 60h I row2-row1	1.03712	0.483
Var 60h NI row2-row1	0.85728	0.932
Time course 0hI-0hNI	0.93439	0.555
Time course 12hI-12hNI	0.98348	0.909
Time course 36hI-36hNI	0.86408	0.091
Time course 60hI-60hNI	0.16178	0.005

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)	0.93715	0.3
transgenic ySAMdc/azygous control (breaker)	1.03051	1
transgenic ySAMdc/azygous control (red)	1.29562	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.74856	0.133

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.29213	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.90393	0.084
Manapal/WT (break)	7.52114	0.13
Manapal/WT (red)	4.43962	0.133