Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.4.1.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.0011	0.211
27DAP/17DAP	1.06414	0.92
39DAP/27DAP	1.72394	0.378
41DAP/39DAP	0.54909	0.042
42DAP/41DAP	0.9516	1
43DAP/42DAP	1.30554	0.906
47DAP/43DAP	0.22217	0.04
52DAP/47DAP	0.53202	0.058
57DAP/52DAP	1.02617	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66181	0.024
17DAP/reference	0.64351	0.007
27DAP/reference	0.91823	0.232
39DAP/reference	0.75159	0.015
41DAP/reference	0.59828	0.008
42DAP/reference	1.08974	0.311
43DAP/reference	0.8985	0.113
47DAP/reference	1.12141	0.524
52DAP/reference	1.82111	0.009
57DAP/reference	1.51656	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	4.89481	0.036
27DAP/17DAP	0.73497	0.58
39DAP/27DAP	0.87996	0.456
41DAP/39DAP	1.49217	1
42DAP/41DAP	0.86526	0.451
43DAP/42DAP	1.55372	0.056
47DAP/43DAP	0.49275	0.008
52DAP/47DAP	2.63789	0.036
57DAP/52DAP	1.37192	0.204
57DAP/7DAP	1.94502	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77657	0.071
17DAP/reference	0.95872	0.389
27DAP/reference	1.25598	0.01
39DAP/reference	0.83307	0.023
41DAP/reference	1.53719	0.039
42DAP/reference	1.30599	0.076
43DAP/reference	0.89737	0.079
47DAP/reference	0.89585	0.383
52DAP/reference	0.80291	0.049
57DAP/reference	1.07843	0.438

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65254	0.009
17DAP/reference	0.61721	0.006
27DAP/reference	0.9265	0.304
39DAP/reference	1.14582	0.824
41DAP/reference	1.19081	0.234
42DAP/reference	1.08356	0.621
43DAP/reference	0.69244	0.02
47DAP/reference	0.77998	0.012
52DAP/reference	0.94702	0.259
57DAP/reference	0.81271	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6898	0.037
17DAP/reference	1.08035	0.833
27DAP/reference	1.18771	0.227
39DAP/reference	0.93983	0.222
41DAP/reference	0.7544	0.035
42DAP/reference	1.37197	0.189
43DAP/reference	1.12153	0.88
47DAP/reference	0.98399	0.574
52DAP/reference	1.41765	0.257
57DAP/reference	2.04632	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09778	0.966
26DAP/20DAP	3.53213	0.05
34DAP/26DAP	1.45675	0.19
51DAP/34DAP	0.915	0.555
52DAP/51DAP	1.37109	0.253
53DAP/52DAP	0.47554	0.049
55DAP/53DAP	0.78421	0.085
57DAP/55DAP	0.6923	0.202
62DAP/57DAP	1.20872	0.515
68DAP/62DAP	2.64036	0.013
68DAP/14DAP	3.38385	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.37772	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	4.6477	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.21232	0.293
Mature Eggplant/Ripe Tomato	0.99386	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.36078	0.574
1-1-2/M82	1.19767	1
12-2/M82	0.7174	0.955
12-4/M82	0.64816	0.358
1-3/M82	N/A	N/A
2-1-1/M82	3.78635	N/A
2-1/M82	N/A	N/A
2-6/M82	1.48778	0.594
3-2/M82	2.88729	0.84
4-1-1/M82	0.49148	0.667
4-1/M82	N/A	N/A
4-3-2/M82	0.71644	N/A
4-3/M82	0.59282	0.72
5-3/M82	2.02215	0.572
6-2/M82	N/A	N/A
6-3/M82	0.53514	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.88918	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.57203	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	0.74563	0.581
IL1-4/WTpooled	1.88143	N/A
WT/WTpooled	0.98655	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	0.88017	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93361	1
DC3000/delta hrp 6h	1.48744	1
DC3000/delta hrp 12h	1.03953	1
DC3000/delta hrp 24h	0.95492	0.692

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08013	0.183
DC3000 delta B/DC3000 delta AB	1.09171	0.381

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	1.07646	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01872	1
Var 0h	0.88752	0.933
Var 12h I row2-row1	0.76282	0.353
Var 12h NI row2-row1	1.18639	0.649
Var 36h I row2-row1	1.22316	0.742
Var 36h NI row2-row1	1.18559	1
Var 60h I row2-row1	0.69611	0.374
Var 60h NI row2-row1	0.87077	0.932
Time course 0hI-0hNI	0.90798	0.418
Time course 12hI-12hNI	0.96012	0.776
Time course 36hI-36hNI	0.65744	0.024
Time course 60hI-60hNI	0.90505	0.319

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)	0.55329	0.297
transgenic ySAMdc/azygous control (breaker)	1.92789	1
transgenic ySAMdc/azygous control (red)	0.82526	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9499	0.101

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71987	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.90393	0.307
Manapal/WT (break)	0.83273	1
Manapal/WT (red)	3.04159	0.133