Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.3.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90639	0.503
27DAP/17DAP	1.16678	0.854
39DAP/27DAP	0.79529	0.487
41DAP/39DAP	1.20775	0.619
42DAP/41DAP	1.18665	0.933
43DAP/42DAP	1.05425	1
47DAP/43DAP	1.16198	0.727
52DAP/47DAP	1.29038	0.43
57DAP/52DAP	0.98489	0.978

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90646	0.231
17DAP/reference	0.96557	0.701
27DAP/reference	0.87144	0.395
39DAP/reference	0.97743	0.663
41DAP/reference	1.0767	0.48
42DAP/reference	0.9558	0.182
43DAP/reference	N/A	N/A
47DAP/reference	0.95771	0.418
52DAP/reference	0.81101	0.041
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84867	0.066
27DAP/17DAP	1.00968	1
39DAP/27DAP	0.99742	1
41DAP/39DAP	1.01518	0.914
42DAP/41DAP	0.92388	0.391
43DAP/42DAP	1.03727	0.664
47DAP/43DAP	0.9817	0.911
52DAP/47DAP	1.01024	0.991
57DAP/52DAP	1.09887	0.601
57DAP/7DAP	1.0513	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.96636	0.11
17DAP/reference	1.9088	0.006
27DAP/reference	1.49689	0.011
39DAP/reference	2.29053	0.005
41DAP/reference	1.92087	0.014
42DAP/reference	2.69998	0.006
43DAP/reference	3.03401	0.007
47DAP/reference	1.78764	0.195
52DAP/reference	2.46368	0.007
57DAP/reference	2.05517	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98904	0.848
17DAP/reference	0.90736	0.159
27DAP/reference	0.87201	0.09
39DAP/reference	0.88969	0.065
41DAP/reference	0.83873	0.058
42DAP/reference	0.90666	0.121
43DAP/reference	0.9159	0.25
47DAP/reference	0.86344	0.016
52DAP/reference	1.00323	1
57DAP/reference	0.96714	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.51566	0.038
17DAP/reference	1.19099	0.474
27DAP/reference	1.72767	0.031
39DAP/reference	1.82969	0.028
41DAP/reference	1.64111	0.008
42DAP/reference	1.57249	0.067
43DAP/reference	1.00737	0.66
47DAP/reference	1.04598	0.562
52DAP/reference	1.97129	0.056
57DAP/reference	1.17572	0.954

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05133	0.966
26DAP/20DAP	1.21149	0.196
34DAP/26DAP	1.03635	1
51DAP/34DAP	0.98248	0.883
52DAP/51DAP	1.07844	0.651
53DAP/52DAP	0.98391	0.876
55DAP/53DAP	1.08259	0.527
57DAP/55DAP	1.12136	0.818
62DAP/57DAP	1.14658	0.767
68DAP/62DAP	1.00017	0.885
68DAP/14DAP	0.90385	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91298	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.54894	0.058
Mature Green Tomato/Ripe Tomato	0.55202	0.021
Immature Eggplant/Mature Eggplant	0.14315
Ripe Pepper/Ripe Tomato	0.47684	0.224
Mature Eggplant/Ripe Tomato	0.46714	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98856	1
1-1-2/M82	0.89301	0.804
12-2/M82	1.02962	1
12-4/M82	0.77265	0.619
1-3/M82	0.85497
2-1-1/M82	1.00077	1
2-1/M82	N/A	N/A
2-6/M82	1.06336
3-2/M82	0.79091
4-1-1/M82	1.09471	1
4-1/M82	0.9868
4-3-2/M82	N/A	N/A
4-3/M82	0.88469	1
5-3/M82	1.14677	1
6-2/M82	0.86601
6-3/M82	N/A	N/A
7-1/M82	1.08095
7-2/M82	1.02899	1
9-3-2/M82	0.96359

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03885	1
IL2-6/WTpooled	1.08897
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.14981	1
IL12-4/WTpooled	0.8478	0.71
IL1-4/WTpooled	1.18887	1
WT/WTpooled	0.79647	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	0.90191	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91732	1
DC3000/delta hrp 6h	1.00916	1
DC3000/delta hrp 12h	0.99227	1
DC3000/delta hrp 24h	1.1447	0.254

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66992	0.027
DC3000 delta B/DC3000 delta AB	0.6431	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.70818	1
Exp 36h	1.23576	1
Exp 60h	1.09409	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96271	1
Var 0h	0.86956	0.291
Var 12h I row2-row1	0.84998	0.357
Var 12h NI row2-row1	1.07783	1
Var 36h I row2-row1	1.11934	0.489
Var 36h NI row2-row1	1.01255	1
Var 60h I row2-row1	1.13447	0.562
Var 60h NI row2-row1	0.88343	0.756
Time course 0hI-0hNI	0.98348	0.967
Time course 12hI-12hNI	0.96459	0.769
Time course 36hI-36hNI	0.9933	0.718
Time course 60hI-60hNI	0.42268	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)	1.02709	0.699
transgenic ySAMdc/azygous control (breaker)	2.83733	0.162
transgenic ySAMdc/azygous control (red)	1.21311	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03712	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90957	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.41285	0.088
Manapal/WT (break)	1.34405	0.14
Manapal/WT (red)	2.36899	0.137