Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.19.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43942	0.63
27DAP/17DAP	2.36173	0.357
39DAP/27DAP	4.76668	0.254
41DAP/39DAP	2.39019	0.488
42DAP/41DAP	0.93458	1
43DAP/42DAP	1.29369	1
47DAP/43DAP	0.18224	0.036
52DAP/47DAP	0.7809	0.499
57DAP/52DAP	0.92025	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.696	0.027
17DAP/reference	0.88007	0.208
27DAP/reference	0.88127	0.304
39DAP/reference	0.78917	0.022
41DAP/reference	1.20374	1
42DAP/reference	2.10484	0.001
43DAP/reference	0.80966	0.113
47DAP/reference	0.81945	0.03
52DAP/reference	0.60718	0.017
57DAP/reference	0.85329	0.078

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77231	0.277
27DAP/17DAP	1.0365	0.969
39DAP/27DAP	4.16947	0.034
41DAP/39DAP	4.90904	0.005
42DAP/41DAP	0.53648	0.007
43DAP/42DAP	0.28741	0.019
47DAP/43DAP	1.20797	0.193
52DAP/47DAP	1.54876	0.749
57DAP/52DAP	0.66023	0.275
57DAP/7DAP	0.69302	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.61149	0.066
17DAP/reference	2.28136	0.361
27DAP/reference	2.66969	0.131
39DAP/reference	2.38459	0.157
41DAP/reference	0.88847	0.235
42DAP/reference	1.66672	0.889
43DAP/reference	1.33191	0.974
47DAP/reference	2.16619	0.118
52DAP/reference	2.40051	0.019
57DAP/reference	2.46164	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77567	0.079
17DAP/reference	0.92249	0.297
27DAP/reference	0.91103	0.22
39DAP/reference	2.80661	0.034
41DAP/reference	1.37939	0.011
42DAP/reference	2.13495	0.121
43DAP/reference	3.45173	0.047
47DAP/reference	5.15097	0.009
52DAP/reference	1.47366	0.012
57DAP/reference	5.39034	0.04

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.61565	0.074
17DAP/reference	1.24273	0.924
27DAP/reference	0.62537	0.023
39DAP/reference	1.41134	0.104
41DAP/reference	1.98313	0.039
42DAP/reference	0.7347	0.22
43DAP/reference	0.61369	0.019
47DAP/reference	0.68297	0.005
52DAP/reference	0.81073	0.262
57DAP/reference	0.82321	0.124

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.83935	1
26DAP/20DAP	0.92988	1
34DAP/26DAP	1.49499	0.542
51DAP/34DAP	1.10787	0.873
52DAP/51DAP	1.44969	0.167
53DAP/52DAP	1.06577	0.901
55DAP/53DAP	1.17834	0.893
57DAP/55DAP	0.9612	0.823
62DAP/57DAP	0.94868	0.871
68DAP/62DAP	1.13757	0.907
68DAP/14DAP	0.59186	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	6.43758	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	12.1526	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.23032	0.224
Mature Eggplant/Ripe Tomato	0.34362	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.48667	0.477
1-1-2/M82	1.37455	1
12-2/M82	1.85733	1
12-4/M82	1.58216	1
1-3/M82	2.29351
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.3895	0.505
3-2/M82	4.89493	0.426
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.43901
4-3/M82	N/A	N/A
5-3/M82	1.71505	0.447
6-2/M82	10.9117	0.219
6-3/M82	1.51797	1
7-1/M82	0.06437
7-2/M82	1.97256
9-3-2/M82	2.95465

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.17949	0.277
IL2-6/WTpooled	0.65894	0.473
IL7-5/WTpooled	1.14938	0.792
IL7-3/WTpooled	1.09552	1
IL12-4/WTpooled	1.16033	0.737
IL1-4/WTpooled	0.87468	0.402
WT/WTpooled	1.06327	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	1.94299	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07832	0.921
DC3000/delta hrp 6h	1.91252
DC3000/delta hrp 12h	1.13254	1
DC3000/delta hrp 24h	3.04263	0.029

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.93099	0.022
DC3000 delta B/DC3000 delta AB	4.61351	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.79948	1
Exp 36h	1.51521	1
Exp 60h	2.95295	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00424	1
Var 0h	0.90162	1
Var 12h I row2-row1	1.11392	0.654
Var 12h NI row2-row1	2.8685	0.191
Var 36h I row2-row1	1.4124	0.601
Var 36h NI row2-row1	0.48451	0.478
Var 60h I row2-row1	0.99445	1
Var 60h NI row2-row1	0.68756	0.69
Time course 0hI-0hNI	2.07769	0.63
Time course 12hI-12hNI	2.1415	0.621
Time course 36hI-36hNI	12.3839	0.004
Time course 60hI-60hNI	667.116	0.008

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)	0.31793	0.246
transgenic ySAMdc/azygous control (breaker)	0.45841	0.124
transgenic ySAMdc/azygous control (red)	0.97099	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92043	0.214

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.12724	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.81938	0.307
Manapal/WT (break)	0.3817	0.333
Manapal/WT (red)	0.18371	0.199