Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.6.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85732	0.413
27DAP/17DAP	1.05134	0.905
39DAP/27DAP	1.00781	0.876
41DAP/39DAP	0.90341	0.632
42DAP/41DAP	0.96948	1
43DAP/42DAP	0.98291	0.925
47DAP/43DAP	0.87772	0.603
52DAP/47DAP	0.94705	0.828
57DAP/52DAP	0.87449	0.727

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27777	0.188
17DAP/reference	1.45955	0.02
27DAP/reference	1.36192	0.101
39DAP/reference	1.23042	0.524
41DAP/reference	1.86536	0.014
42DAP/reference	1.45275	0.002
43DAP/reference	1.08888	0.471
47DAP/reference	1.30469	0.085
52DAP/reference	1.17303	0.302
57DAP/reference	0.89249	0.21

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92148	0.526
27DAP/17DAP	1.24511	0.403
39DAP/27DAP	0.60051	0.032
41DAP/39DAP	0.8951	0.849
42DAP/41DAP	1.28832	0.694
43DAP/42DAP	1.07476	1
47DAP/43DAP	0.92642	0.815
52DAP/47DAP	1.4775	0.264
57DAP/52DAP	1.25635
57DAP/7DAP	0.85836	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86925	0.27
17DAP/reference	0.93763	0.253
27DAP/reference	0.85616	0.066
39DAP/reference	0.83795	0.083
41DAP/reference	0.87137	0.153
42DAP/reference	0.69989	0.024
43DAP/reference	0.82036	0.054
47DAP/reference	1.33001	0.386
52DAP/reference	0.84408	0.097
57DAP/reference	0.84387	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12721	0.294
17DAP/reference	1.47517	0.018
27DAP/reference	1.34865	0.045
39DAP/reference	0.97972	0.621
41DAP/reference	1.12661	0.459
42DAP/reference	1.28507	0.115
43DAP/reference	1.44889	0.133
47DAP/reference	1.34584	0.065
52DAP/reference	1.32784	0.007
57DAP/reference	1.89704	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92026	0.335
17DAP/reference	1.05722	0.9
27DAP/reference	0.97389	0.539
39DAP/reference	0.94229	0.299
41DAP/reference	0.92171	0.293
42DAP/reference	1.04287	0.994
43DAP/reference	0.89707	0.246
47DAP/reference	1.13425	0.792
52DAP/reference	1.30148	0.369
57DAP/reference	0.67263	0.041

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21045	0.817
26DAP/20DAP	0.84899	1
34DAP/26DAP	1.02461
51DAP/34DAP	0.95193	0.807
52DAP/51DAP	1.21667	0.534
53DAP/52DAP	0.95436	0.811
55DAP/53DAP	1.02303	1
57DAP/55DAP	1.39141	0.037
62DAP/57DAP	1.31844	0.678
68DAP/62DAP	0.77806
68DAP/14DAP	0.45271

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.6303

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.82529	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	0.66612
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.37927
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.88187
4-3/M82	N/A	N/A
5-3/M82	1.00239	1
6-2/M82	N/A	N/A
6-3/M82	1.29391
7-1/M82	0.9936
7-2/M82	N/A	N/A
9-3-2/M82	0.84977

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90715	0.247
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.2874
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.17582	0.673
IL1-4/WTpooled	1.01506	1
WT/WTpooled	1.13706	0.911

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	0.79733	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93205	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	4.9651	0.017

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.78004	0.279

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	0.97573	1
Var 0h	1.1201	0.98
Var 12h I row2-row1	0.95214	0.856
Var 12h NI row2-row1	0.82265	0.627
Var 36h I row2-row1	0.80694	0.438
Var 36h NI row2-row1	1.05205	1
Var 60h I row2-row1	0.91121
Var 60h NI row2-row1	1.30338	0.904
Time course 0hI-0hNI	0.97889	0.906
Time course 12hI-12hNI	0.83811	0.05
Time course 36hI-36hNI	0.69111	0.023
Time course 60hI-60hNI	0.09065	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97704	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.20005	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	N/A	N/A