Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.10.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80589	0.082
27DAP/17DAP	0.97913	0.99
39DAP/27DAP	0.92888	0.62
41DAP/39DAP	1.40644	0.293
42DAP/41DAP	1.01941	1
43DAP/42DAP	0.95039	0.877
47DAP/43DAP	1.02586	0.895
52DAP/47DAP	1.19393	0.676
57DAP/52DAP	1.0347	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94981	0.326
17DAP/reference	1.01853	0.476
27DAP/reference	1.01536	0.863
39DAP/reference	0.94789	0.24
41DAP/reference	1.03489	0.552
42DAP/reference	0.89423	0.003
43DAP/reference	0.99948	0.882
47DAP/reference	0.9523	0.322
52DAP/reference	0.85511	0.128
57DAP/reference	0.75113	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88789	0.289
27DAP/17DAP	1.1971	0.279
39DAP/27DAP	1.09796	0.471
41DAP/39DAP	1.02172	1
42DAP/41DAP	1.034	0.727
43DAP/42DAP	1.08044	0.176
47DAP/43DAP	0.98444	0.933
52DAP/47DAP	0.99025	0.941
57DAP/52DAP	1.04532	0.732
57DAP/7DAP	1.22184	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21832	0.17
17DAP/reference	1.15641	0.221
27DAP/reference	1.01116	0.748
39DAP/reference	1.14002	0.511
41DAP/reference	1.23609	0.101
42DAP/reference	1.41925	0.059
43DAP/reference	1.18553	0.124
47DAP/reference	0.9504	0.293
52DAP/reference	1.17819	0.286
57DAP/reference	1.31257	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0841	0.224
17DAP/reference	1.01809	0.674
27DAP/reference	0.87801	0.15
39DAP/reference	0.84683	0.062
41DAP/reference	0.79646	0.017
42DAP/reference	0.837	0.061
43DAP/reference	0.99294	0.692
47DAP/reference	0.89352	0.026
52DAP/reference	1.05244	0.528
57DAP/reference	1.24997	0.314

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00697	1
17DAP/reference	1.18326	0.306
27DAP/reference	1.19349	0.149
39DAP/reference	1.09565	0.422
41DAP/reference	1.02985	1
42DAP/reference	0.75906	0.22
43DAP/reference	0.71046	0.088
47DAP/reference	0.89355	0.24
52DAP/reference	0.96517	0.623
57DAP/reference	0.45453	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07662	0.966
26DAP/20DAP	1.17003	0.713
34DAP/26DAP	0.88218	0.565
51DAP/34DAP	1.27153	0.232
52DAP/51DAP	0.8907	1
53DAP/52DAP	0.9973	1
55DAP/53DAP	1.05332	0.885
57DAP/55DAP	0.89042	0.427
62DAP/57DAP	1.22037	0.217
68DAP/62DAP	1.02726	1
68DAP/14DAP	1.00847	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02712	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.69133	0.223
Mature Green Tomato/Ripe Tomato	1.14035	0.331
Immature Eggplant/Mature Eggplant	0.7079	0.07
Ripe Pepper/Ripe Tomato	1.83444	0.256
Mature Eggplant/Ripe Tomato	0.89792	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9967	1
1-1-2/M82	0.98064	1
12-2/M82	0.94923	0.955
12-4/M82	1.0933	1
1-3/M82	0.94528	1
2-1-1/M82	0.86196	0.465
2-1/M82	N/A	N/A
2-6/M82	1.07311	0.594
3-2/M82	1.23905
4-1-1/M82	0.89028	1
4-1/M82	0.97326
4-3-2/M82	0.87545	0.487
4-3/M82	0.9228	0.72
5-3/M82	0.97401	1
6-2/M82	N/A	N/A
6-3/M82	0.93695
7-1/M82	0.8661
7-2/M82	0.93819	0.881
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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.6441
IL12-4/WTpooled	0.91845	1
IL1-4/WTpooled	1.11458
WT/WTpooled	0.83113	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	0.90155	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96782	1
DC3000/delta hrp 6h	1.14536	0.978
DC3000/delta hrp 12h	1.52574	1
DC3000/delta hrp 24h	1.11138	0.254

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04469	0.355
DC3000 delta B/DC3000 delta AB	1.06043	0.491

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03803	0.196
Exp 36h	1.06728	1
Exp 60h	1.05802	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01262	1
Var 0h	0.91932	0.933
Var 12h I row2-row1	1.26175	0.473
Var 12h NI row2-row1	0.98917	1
Var 36h I row2-row1	1.16644	0.742
Var 36h NI row2-row1	0.88892	0.549
Var 60h I row2-row1	1.08262	0.562
Var 60h NI row2-row1	1.0288	1
Time course 0hI-0hNI	0.96901	0.795
Time course 12hI-12hNI	1.05461	0.467
Time course 36hI-36hNI	1.12664	0.316
Time course 60hI-60hNI	1.12511	0.06

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)	1.13304	0.267
transgenic ySAMdc/azygous control (breaker)	0.90137	0.173
transgenic ySAMdc/azygous control (red)	1.12342	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00474	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.60165	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91586	1
Manapal/WT (break)	1.04633	1
Manapal/WT (red)	0.87082	0.216