Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.4.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70847	0.103
27DAP/17DAP	0.91405	0.819
39DAP/27DAP	1.60188	0.095
41DAP/39DAP	0.72047	0.114
42DAP/41DAP	0.94135	1
43DAP/42DAP	0.99619	0.937
47DAP/43DAP	0.78654	0.377
52DAP/47DAP	1.13962	0.861
57DAP/52DAP	1.02849	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39587	0.025
17DAP/reference	1.19852	0.089
27DAP/reference	1.20002	0.045
39DAP/reference	1.22133	0.082
41DAP/reference	1.11698	0.365
42DAP/reference	1.50388	0.001
43DAP/reference	1.20178	0.008
47DAP/reference	1.13702	0.011
52DAP/reference	1.00859	1
57DAP/reference	1.10049	0.05

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18709	0.201
27DAP/17DAP	0.90886	0.363
39DAP/27DAP	0.85887	0.176
41DAP/39DAP	1.10599	1
42DAP/41DAP	0.9449	0.607
43DAP/42DAP	0.93006	0.351
47DAP/43DAP	1.06066	0.798
52DAP/47DAP	0.84729	0.109
57DAP/52DAP	0.93459	0.426
57DAP/7DAP	0.8074	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.90927	0.033
17DAP/reference	1.3301	0.011
27DAP/reference	1.50906	0.006
39DAP/reference	1.68529	0.005
41DAP/reference	1.65901	0.01
42DAP/reference	2.47279	0.006
43DAP/reference	3.04799	0.007
47DAP/reference	1.91282	0.015
52DAP/reference	2.6307	0.007
57DAP/reference	1.77952	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06325	0.926
17DAP/reference	1.31557	0.086
27DAP/reference	1.53001	0.014
39DAP/reference	1.5214	0.011
41DAP/reference	1.2961	0.112
42DAP/reference	1.46053	0.259
43DAP/reference	0.82678	0.095
47DAP/reference	1.42903	0.008
52DAP/reference	0.99436	0.713
57DAP/reference	1.00742	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.64294	0.022
17DAP/reference	1.10638	0.572
27DAP/reference	1.51919	0.019
39DAP/reference	1.73647	0.005
41DAP/reference	1.3156	0.014
42DAP/reference	2.07018	0.006
43DAP/reference	1.8203	0.007
47DAP/reference	0.85076	0.06
52DAP/reference	1.04504	0.724
57DAP/reference	1.03511	0.636

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14523	0.966
26DAP/20DAP	1.54439	0.223
34DAP/26DAP	0.98845	1
51DAP/34DAP	1.10514	0.281
52DAP/51DAP	0.7841	0.151
53DAP/52DAP	1.18025	0.343
55DAP/53DAP	0.71139	0.031
57DAP/55DAP	1.52786	0.072
62DAP/57DAP	0.7883	0.681
68DAP/62DAP	0.97079	0.81
68DAP/14DAP	1.76271	0.074

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.79168	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.9185	0.503
Mature Green Tomato/Ripe Tomato	1.37758	0.024
Immature Eggplant/Mature Eggplant	0.98772	1
Ripe Pepper/Ripe Tomato	1.32725	1
Mature Eggplant/Ripe Tomato	1.34399	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.77575	0.673
1-1-2/M82	1.34689	1
12-2/M82	0.97243	1
12-4/M82	1.14564	1
1-3/M82	2.67069	0.277
2-1-1/M82	0.89655	0.92
2-1/M82	0.89707
2-6/M82	0.99888	1
3-2/M82	N/A	N/A
4-1-1/M82	0.78034	1
4-1/M82	1.20354	1
4-3-2/M82	1.59486	0.508
4-3/M82	1.49395	0.268
5-3/M82	1.14634	1
6-2/M82	1.60177	0.188
6-3/M82	1.02934	1
7-1/M82	1.29927
7-2/M82	1.54276	0.385
9-3-2/M82	1.47832	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98425	1
IL2-6/WTpooled	1.01566	1
IL7-5/WTpooled	0.75162	1
IL7-3/WTpooled	1.03868	1
IL12-4/WTpooled	0.97601	1
IL1-4/WTpooled	1.12416	0.426
WT/WTpooled	1.05726	0.774

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	1.10063	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.19925	0.875
DC3000/delta hrp 6h	0.96674	0.95
DC3000/delta hrp 12h	1.07071	1
DC3000/delta hrp 24h	1.09037	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12544	0.052
DC3000 delta B/DC3000 delta AB	1.21486	0.167

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0571	1
Exp 36h	1.12416	1
Exp 60h	1.13062	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.75596	0.206
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	1.12638
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.01584	0.921
transgenic ySAMdc/azygous control (breaker)	0.83504	0.142
transgenic ySAMdc/azygous control (red)	0.92696	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.79611	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98214	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.72108	0.172
Manapal/WT (break)	0.76213	0.333
Manapal/WT (red)	0.8036	0.199