Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.11.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96863	0.752
27DAP/17DAP	1.05982	0.902
39DAP/27DAP	0.77432	0.39
41DAP/39DAP	1.29874	0.293
42DAP/41DAP	0.95092	1
43DAP/42DAP	0.93026	0.795
47DAP/43DAP	1.04011	0.999
52DAP/47DAP	1.46796	0.37
57DAP/52DAP	0.95136	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91537	0.231
17DAP/reference	0.93337	0.111
27DAP/reference	0.94445	0.157
39DAP/reference	0.95506	0.155
41DAP/reference	0.88354	0.031
42DAP/reference	0.84133	0.003
43DAP/reference	0.96811	0.48
47DAP/reference	0.87958	0.023
52DAP/reference	0.89142	0.183
57DAP/reference	0.92596	0.096

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04453	0.65
27DAP/17DAP	1.02531	0.968
39DAP/27DAP	0.99359	1
41DAP/39DAP	1.00784	1
42DAP/41DAP	1.06525	0.526
43DAP/42DAP	0.99863	1
47DAP/43DAP	1.03314	0.848
52DAP/47DAP	0.97391	0.917
57DAP/52DAP	0.98284	0.742
57DAP/7DAP	1.11396	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96259	0.361
17DAP/reference	1.04692	0.134
27DAP/reference	1.06101	0.041
39DAP/reference	1.06282	0.066
41DAP/reference	1.02655	0.577
42DAP/reference	1.02841	0.405
43DAP/reference	1.03554	0.511
47DAP/reference	0.95978	0.383
52DAP/reference	1.02369	0.781
57DAP/reference	1.03573	0.5

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95722	0.518
17DAP/reference	0.80941	0.019
27DAP/reference	0.7719	0.056
39DAP/reference	0.7938	0.031
41DAP/reference	0.87289	0.083
42DAP/reference	0.90206	0.073
43DAP/reference	0.92315	0.336
47DAP/reference	0.94382	0.164
52DAP/reference	0.81077	0.017
57DAP/reference	0.80581	0.099

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99041	0.653
17DAP/reference	0.94055	0.328
27DAP/reference	1.00871	0.934
39DAP/reference	0.97594	0.464
41DAP/reference	0.97583	0.56
42DAP/reference	0.95342	0.445
43DAP/reference	0.9165	0.226
47DAP/reference	0.89651	0.174
52DAP/reference	0.99806	0.928
57DAP/reference	0.78187	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05204	0.966
26DAP/20DAP	0.94008	1
34DAP/26DAP	0.93347	0.539
51DAP/34DAP	1.05708	0.597
52DAP/51DAP	1.00854	0.915
53DAP/52DAP	0.93754
55DAP/53DAP	0.90593	0.725
57DAP/55DAP	0.96235	0.817
62DAP/57DAP	1.02147	0.902
68DAP/62DAP	0.9752	0.834
68DAP/14DAP	1.08113	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9804	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.65757	0.217
Mature Green Tomato/Ripe Tomato	0.70106	0.132
Immature Eggplant/Mature Eggplant	0.81239	0.407
Ripe Pepper/Ripe Tomato	1.07828	1
Mature Eggplant/Ripe Tomato	1.65331

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03736	1
1-1-2/M82	1.01384	1
12-2/M82	0.81613
12-4/M82	0.90718	1
1-3/M82	0.9448	1
2-1-1/M82	1.18325	0.354
2-1/M82	N/A	N/A
2-6/M82	1.16321	0.695
3-2/M82	1.08627
4-1-1/M82	0.97013	1
4-1/M82	1.02763	1
4-3-2/M82	0.75276	0.698
4-3/M82	N/A	N/A
5-3/M82	0.99885	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.9932	1
9-3-2/M82	0.97843

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	1.16851	1
IL12-4/WTpooled	1.01875	1
IL1-4/WTpooled	0.82237	0.699
WT/WTpooled	1.20841	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	1.01539	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05809	0.875
DC3000/delta hrp 6h	0.84074	0.95
DC3000/delta hrp 12h	0.99153	1
DC3000/delta hrp 24h	1.1256	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09576	0.145
DC3000 delta B/DC3000 delta AB	1.15023	0.23

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89321	1
Exp 36h	0.82602	0.589
Exp 60h	0.90277	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99695	1
Var 0h	0.92846	1
Var 12h I row2-row1	1.16588	0.209
Var 12h NI row2-row1	0.99425	1
Var 36h I row2-row1	0.98261	1
Var 36h NI row2-row1	0.97251	0.743
Var 60h I row2-row1	1.21771	0.562
Var 60h NI row2-row1	1.12136	0.904
Time course 0hI-0hNI	1.05658	0.852
Time course 12hI-12hNI	1.06561	0.65
Time course 36hI-36hNI	0.96003	0.337
Time course 60hI-60hNI	1.17953	0.042

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)	0.87943	0.314
transgenic ySAMdc/azygous control (breaker)	1.19773	0.248
transgenic ySAMdc/azygous control (red)	1.02473	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02314	0.204

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.29945	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)	1.40405	0.13
Manapal/WT (red)	1.96433	0.133