Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.16.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17198	0.545
27DAP/17DAP	1.22028	0.793
39DAP/27DAP	0.88138	0.594
41DAP/39DAP	1.60618	0.328
42DAP/41DAP	1.04983	1
43DAP/42DAP	0.88776	0.713
47DAP/43DAP	0.87035	0.568
52DAP/47DAP	1.0131	0.959
57DAP/52DAP	1.04436	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04469	0.48
17DAP/reference	1.01739	0.74
27DAP/reference	0.96263	0.295
39DAP/reference	0.93558	0.174
41DAP/reference	1.06292	0.421
42DAP/reference	1.06483	0.076
43DAP/reference	0.9561	0.259
47DAP/reference	0.98724	0.503
52DAP/reference	1.04493	0.302
57DAP/reference	0.93017	0.015

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99501	0.847
27DAP/17DAP	1.00797	1
39DAP/27DAP	1.03402	0.663
41DAP/39DAP	0.95879	0.849
42DAP/41DAP	1.05519	0.582
43DAP/42DAP	0.9678	0.729
47DAP/43DAP	1.01858	0.926
52DAP/47DAP	1.08312	0.681
57DAP/52DAP	1.07344	0.596
57DAP/7DAP	1.01344	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89892	0.104
17DAP/reference	0.96269	0.192
27DAP/reference	0.99648	0.748
39DAP/reference	1.01316	0.411
41DAP/reference	1.01451	0.812
42DAP/reference	1.04071	0.174
43DAP/reference	1.00621	0.923
47DAP/reference	0.92153	0.128
52DAP/reference	0.94754	0.066
57DAP/reference	0.99241	0.569

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01856	0.612
17DAP/reference	1.05574	0.426
27DAP/reference	0.95535	0.407
39DAP/reference	0.95471	0.173
41DAP/reference	0.87296	0.058
42DAP/reference	1.06273	0.969
43DAP/reference	0.94801	0.394
47DAP/reference	0.97324	0.379
52DAP/reference	1.01105	0.882
57DAP/reference	1.12069	0.036

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90552	0.112
17DAP/reference	0.9314	0.205
27DAP/reference	0.9986	0.843
39DAP/reference	1.01927	0.633
41DAP/reference	0.99567	0.826
42DAP/reference	0.92553	0.287
43DAP/reference	0.981	0.365
47DAP/reference	0.92281	0.089
52DAP/reference	0.96262	0.538
57DAP/reference	0.88214	0.089

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96128	1
26DAP/20DAP	0.97726	1
34DAP/26DAP	1.01603	1
51DAP/34DAP	0.98772	0.901
52DAP/51DAP	0.91329	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	1.06737	1
57DAP/55DAP	0.95138	0.754
62DAP/57DAP	0.94221	0.871
68DAP/62DAP	1.29262	0.831
68DAP/14DAP	0.87113	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95676	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94482
Mature Green Tomato/Ripe Tomato	0.79314	0.072
Immature Eggplant/Mature Eggplant	1.1365
Ripe Pepper/Ripe Tomato	1.13653	1
Mature Eggplant/Ripe Tomato	1.32943

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.77725
12-2/M82	N/A	N/A
12-4/M82	0.70404
1-3/M82	N/A	N/A
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.74073	0.998
4-3-2/M82	0.78822
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.73175	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.84191	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.28424	0.362
IL12-4/WTpooled	1.37743	0.511
IL1-4/WTpooled	1.16297
WT/WTpooled	0.87741	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	0.88129

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88504	1
DC3000/delta hrp 6h	0.97524	0.95
DC3000/delta hrp 12h	1.01625	1
DC3000/delta hrp 24h	0.96617	0.831

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08651	0.094
DC3000 delta B/DC3000 delta AB	1.04752	0.528

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17274	1
Exp 36h	0.84993	0.589
Exp 60h	0.95753	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00381	1
Var 0h	0.77777	1
Var 12h I row2-row1	1.07157	0.443
Var 12h NI row2-row1	1.02638	1
Var 36h I row2-row1	0.9984	1
Var 36h NI row2-row1	1.2444	1
Var 60h I row2-row1	1.20061	1
Var 60h NI row2-row1	0.92795	0.818
Time course 0hI-0hNI	1.06347	0.852
Time course 12hI-12hNI	1.03029	0.836
Time course 36hI-36hNI	0.99985	0.811
Time course 60hI-60hNI	1.17524	0.096

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)	1.05855	0.3
transgenic ySAMdc/azygous control (breaker)	1.06517	0.248
transgenic ySAMdc/azygous control (red)	0.98834	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93892	0.063

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95916	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.74405	0.172
Manapal/WT (break)	0.92299	1
Manapal/WT (red)	N/A	N/A