Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.16.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20936	0.656
27DAP/17DAP	1.0675	1
39DAP/27DAP	1.7771	0.123
41DAP/39DAP	1.19345	0.516
42DAP/41DAP	1.00768	1
43DAP/42DAP	0.91534	0.834
47DAP/43DAP	1.21726	0.689
52DAP/47DAP	1.13385	0.913
57DAP/52DAP	1.17582	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72535	0.027
17DAP/reference	0.87951	0.129
27DAP/reference	0.95091	0.406
39DAP/reference	1.29116	0.423
41DAP/reference	0.9074	0.201
42DAP/reference	1.0464	0.656
43DAP/reference	1.46974	0.01
47DAP/reference	1.34601	0.002
52DAP/reference	1.07135	0.576
57DAP/reference	1.38875	0.018

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24174	0.064
27DAP/17DAP	0.96223	0.887
39DAP/27DAP	1.11765	0.611
41DAP/39DAP	0.80873	0.083
42DAP/41DAP	1.21513	0.072
43DAP/42DAP	1.57	0.023
47DAP/43DAP	1.20648	0.119
52DAP/47DAP	0.93888	0.79
57DAP/52DAP	1.08797	0.869
57DAP/7DAP	1.36533	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9126	0.296
17DAP/reference	1.00731	1
27DAP/reference	1.43611	0.131
39DAP/reference	0.98741	0.64
41DAP/reference	1.22286	0.159
42DAP/reference	1.27226	0.046
43DAP/reference	1.30668	0.009
47DAP/reference	1.66125	0.021
52DAP/reference	1.27702	0.029
57DAP/reference	0.91889	0.176

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81609	0.14
17DAP/reference	0.73227	0.004
27DAP/reference	0.82248	0.06
39DAP/reference	0.78458	0.023
41DAP/reference	0.77314	0.067
42DAP/reference	0.92101	0.261
43DAP/reference	1.07193	0.611
47DAP/reference	1.01555	1
52DAP/reference	0.78832	0.012
57DAP/reference	0.77586	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98869	0.653
17DAP/reference	0.9564	0.528
27DAP/reference	0.90779	0.184
39DAP/reference	1.08352	0.307
41DAP/reference	1.30754	0.062
42DAP/reference	1.2179	0.246
43DAP/reference	1.11847	0.935
47DAP/reference	1.16163	0.07
52DAP/reference	1.01124	1
57DAP/reference	0.94735	0.394

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12429	0.966
26DAP/20DAP	1.73212	0.197
34DAP/26DAP	1.15974	0.819
51DAP/34DAP	3.19361	0.031
52DAP/51DAP	0.70799	1
53DAP/52DAP	0.94371	0.712
55DAP/53DAP	0.72434	0.028
57DAP/55DAP	1.21194	0.584
62DAP/57DAP	0.90559	0.681
68DAP/62DAP	1.10077	0.962
68DAP/14DAP	1.89417	0.419

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.60484	0.043

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.50873	0.058
Mature Green Tomato/Ripe Tomato	0.22224	0.017
Immature Eggplant/Mature Eggplant	1.40209	0.222
Ripe Pepper/Ripe Tomato	0.35983	0.224
Mature Eggplant/Ripe Tomato	0.11112	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.63519	0.591
1-1-2/M82	1.3047
12-2/M82	0.94537	1
12-4/M82	1.11393
1-3/M82	2.31162	0.248
2-1-1/M82	0.98374
2-1/M82	0.91174	0.74
2-6/M82	1.05664
3-2/M82	0.95813	1
4-1-1/M82	1.02501	1
4-1/M82	0.80907	1
4-3-2/M82	0.92643	1
4-3/M82	1.22883	1
5-3/M82	1.05224	1
6-2/M82	1.66765	1
6-3/M82	0.56922
7-1/M82	0.88277	0.509
7-2/M82	1.32863	0.385
9-3-2/M82	1.06279	1

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	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.74463

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89801	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.02128	1
DC3000/delta hrp 24h	1.20391	0.296

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12696	0.254
Exp 36h	1.20358	0.693
Exp 60h	1.2784	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03358	1
Var 0h	0.52674	0.252
Var 12h I row2-row1	0.64007	0.338
Var 12h NI row2-row1	0.8918	0.317
Var 36h I row2-row1	0.90506	1
Var 36h NI row2-row1	1.15158	1
Var 60h I row2-row1	1.12974
Var 60h NI row2-row1	0.96582	1
Time course 0hI-0hNI	1.07712	0.764
Time course 12hI-12hNI	1.01637	0.867
Time course 36hI-36hNI	0.89974	0.101
Time course 60hI-60hNI	0.34322	0.026

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)	0.93664	0.3
transgenic ySAMdc/azygous control (breaker)	0.91249	0.49
transgenic ySAMdc/azygous control (red)	0.94607	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01262	0.656

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19206	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.14857	0.307
Manapal/WT (break)	0.76725	0.333
Manapal/WT (red)	0.84001	0.242