Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.15.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92279	0.596
27DAP/17DAP	1.19785	0.905
39DAP/27DAP	1.00225	0.84
41DAP/39DAP	1.69605	0.575
42DAP/41DAP	0.63127	0.397
43DAP/42DAP	1.19414	1
47DAP/43DAP	0.6771	0.173
52DAP/47DAP	2.45519	0.362
57DAP/52DAP	0.93012	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97793	0.55
17DAP/reference	1.17191	0.1
27DAP/reference	1.12713	0.771
39DAP/reference	1.14967	0.639
41DAP/reference	1.07613	0.624
42DAP/reference	0.87529	0.111
43DAP/reference	0.95295	0.5
47DAP/reference	1.08644	0.575
52DAP/reference	0.91643	0.3
57DAP/reference	0.9801	0.553

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.57256	0.062
27DAP/17DAP	1.20768	0.476
39DAP/27DAP	1.21709	0.19
41DAP/39DAP	1.64077	0.022
42DAP/41DAP	0.83193	0.312
43DAP/42DAP	2.26977	0.015
47DAP/43DAP	1.29155	0.038
52DAP/47DAP	0.81414	0.522
57DAP/52DAP	2.79694	0.036
57DAP/7DAP	1.85332	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01364	1
17DAP/reference	0.78636	0.014
27DAP/reference	0.81264	0.013
39DAP/reference	0.91434	0.198
41DAP/reference	0.79682	0.042
42DAP/reference	0.85683	0.07
43DAP/reference	0.7365	0.013
47DAP/reference	0.86809	0.168
52DAP/reference	0.75747	0.013
57DAP/reference	0.80891	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03277	0.842
17DAP/reference	0.87265	0.26
27DAP/reference	0.8967	0.212
39DAP/reference	1.0887	0.657
41DAP/reference	0.93812	0.422
42DAP/reference	0.65356	0.017
43DAP/reference	1.00482	0.681
47DAP/reference	0.84898	0.053
52DAP/reference	0.93642	0.433
57DAP/reference	0.92056	0.46

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95511	0.335
17DAP/reference	0.8828	0.348
27DAP/reference	0.86201	0.102
39DAP/reference	0.82167	0.019
41DAP/reference	0.91871	0.237
42DAP/reference	1.11184	1
43DAP/reference	0.7678	0.084
47DAP/reference	0.92665	0.383
52DAP/reference	0.75515	0.164
57DAP/reference	0.74185	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20048	1
26DAP/20DAP	0.91346	1
34DAP/26DAP	0.89887	0.728
51DAP/34DAP	1.02943	0.927
52DAP/51DAP	1.08798	0.439
53DAP/52DAP	0.95285	0.835
55DAP/53DAP	0.97932	0.82
57DAP/55DAP	0.80775	0.327
62DAP/57DAP	0.96213	0.994
68DAP/62DAP	0.89003	0.668
68DAP/14DAP	0.83638	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.02069	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.23988	0.02
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.62956

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	0.9602	1
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	N/A	N/A
4-3-2/M82	1.19624
4-3/M82	N/A	N/A
5-3/M82	0.88728	0.642
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.96901	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.13131	1
IL12-4/WTpooled	1.11604	0.516
IL1-4/WTpooled	1.00832
WT/WTpooled	0.89986	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	0.98915	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08601	0.921
DC3000/delta hrp 6h	0.97695
DC3000/delta hrp 12h	1.0978	1
DC3000/delta hrp 24h	1.09378	0.271

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	1.01211	0.729

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	0.82128	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96409	1
Var 0h	0.79144	1
Var 12h I row2-row1	0.88632	0.467
Var 12h NI row2-row1	0.87721	0.546
Var 36h I row2-row1	1.12351	0.908
Var 36h NI row2-row1	1.23149	1
Var 60h I row2-row1	0.99309	1
Var 60h NI row2-row1	0.94826	1
Time course 0hI-0hNI	0.97717	0.873
Time course 12hI-12hNI	0.91917	0.352
Time course 36hI-36hNI	0.81355	0.032
Time course 60hI-60hNI	0.77975	0.007

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)	1.16987	0.699
transgenic ySAMdc/azygous control (breaker)	1.46467	0.162
transgenic ySAMdc/azygous control (red)	0.99385	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94183	0.075

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98997	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96168	1
Manapal/WT (break)	1.11619	1
Manapal/WT (red)	0.78932	0.36