Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06915	0.798
27DAP/17DAP	0.91938	0.836
39DAP/27DAP	1.49466	0.504
41DAP/39DAP	0.62115	0.062
42DAP/41DAP	1.31966	0.806
43DAP/42DAP	1.03402	1
47DAP/43DAP	0.80252	0.407
52DAP/47DAP	1.13409	0.91
57DAP/52DAP	1.20221	0.826

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02667	0.846
17DAP/reference	1.0121	0.843
27DAP/reference	1.03967	0.509
39DAP/reference	0.98436	0.779
41DAP/reference	0.94145	0.434
42DAP/reference	0.96386	0.124
43DAP/reference	0.94585	0.36
47DAP/reference	0.96073	0.174
52DAP/reference	0.89163	0.215
57DAP/reference	0.96294	0.34

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.46691	0.081
27DAP/17DAP	1.11285	0.747
39DAP/27DAP	0.80334	0.161
41DAP/39DAP	1.18567	0.849
42DAP/41DAP	1.05324	1
43DAP/42DAP	0.74707	0.026
47DAP/43DAP	1.03113	0.926
52DAP/47DAP	0.92149	0.807
57DAP/52DAP	1.07712	0.708
57DAP/7DAP	0.54903	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.271	0.051
17DAP/reference	1.35027	0.006
27DAP/reference	1.17232	0.01
39DAP/reference	1.2433	0.077
41DAP/reference	1.16697	0.232
42DAP/reference	1.07692	0.686
43DAP/reference	1.14506	0.188
47DAP/reference	1.04073	0.732
52DAP/reference	1.15294	0.183
57DAP/reference	1.23691	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92227	0.257
17DAP/reference	0.99783	0.711
27DAP/reference	0.94208	0.327
39DAP/reference	0.9155	0.178
41DAP/reference	1.00261	0.702
42DAP/reference	0.9588	0.212
43DAP/reference	0.78608	0.021
47DAP/reference	0.92523	0.037
52DAP/reference	0.87379	0.023
57DAP/reference	0.70813	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3105	0.015
17DAP/reference	1.19672	0.137
27DAP/reference	1.2289	0.021
39DAP/reference	1.10908	0.084
41DAP/reference	1.25903	0.039
42DAP/reference	1.06439	0.612
43DAP/reference	1.10671	0.465
47DAP/reference	1.02539	1
52DAP/reference	1.15318	0.42
57DAP/reference	1.13099	0.2

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06438	0.966
26DAP/20DAP	1.52918	0.099
34DAP/26DAP	0.91685	0.619
51DAP/34DAP	0.9178	0.571
52DAP/51DAP	0.81696	0.151
53DAP/52DAP	1.17102	0.697
55DAP/53DAP	0.7083	0.082
57DAP/55DAP	1.26993	0.694
62DAP/57DAP	0.89039
68DAP/62DAP	0.82864	0.429
68DAP/14DAP	1.18829	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.13587	0.391

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.79141	0.058
Mature Green Tomato/Ripe Tomato	1.85262	0.149
Immature Eggplant/Mature Eggplant	0.9473	0.651
Ripe Pepper/Ripe Tomato	1.25441	0.258
Mature Eggplant/Ripe Tomato	1.96809	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12201	1
1-1-2/M82	1.13086	0.125
12-2/M82	0.67819
12-4/M82	1.08431	1
1-3/M82	N/A	N/A
2-1-1/M82	0.83227	0.683
2-1/M82	0.95758
2-6/M82	0.9902	1
3-2/M82	N/A	N/A
4-1-1/M82	0.98163	1
4-1/M82	N/A	N/A
4-3-2/M82	0.91783
4-3/M82	1.22399	1
5-3/M82	1.30089	0.496
6-2/M82	1.31442
6-3/M82	0.82571
7-1/M82	1.03514	1
7-2/M82	1.12393	0.385
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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.68188
IL1-4/WTpooled	0.77458
WT/WTpooled	0.80626

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	1.09997	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99916
DC3000/delta hrp 6h	1.16991	0.672
DC3000/delta hrp 12h	0.33582
DC3000/delta hrp 24h	0.81595	0.08

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94235	0.568
DC3000 delta B/DC3000 delta AB	1.01384	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9771	1
Var 0h	0.83393	0.936
Var 12h I row2-row1	0.97205	0.948
Var 12h NI row2-row1	1.01136	1
Var 36h I row2-row1	1.37288	0.742
Var 36h NI row2-row1	0.92072	0.743
Var 60h I row2-row1	1.00598	1
Var 60h NI row2-row1	0.93393	0.977
Time course 0hI-0hNI	0.93518	0.56
Time course 12hI-12hNI	0.99166	0.994
Time course 36hI-36hNI	1.11898	0.316
Time course 60hI-60hNI	0.85481	0.081

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)	1.16087	0.612
transgenic ySAMdc/azygous control (breaker)	2.36609	0.166
transgenic ySAMdc/azygous control (red)	1.16513	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97377	0.552

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.32962	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.70245	0.083
Manapal/WT (break)	5.81123	0.13
Manapal/WT (red)	4.83381	0.126