Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.15.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84256	0.373
27DAP/17DAP	1.16694	0.847
39DAP/27DAP	0.84418	0.522
41DAP/39DAP	1.42159	0.488
42DAP/41DAP	0.6332	0.774
43DAP/42DAP	0.82465	0.613
47DAP/43DAP	0.8751	0.595
52DAP/47DAP	1.62203	0.444
57DAP/52DAP	0.83742	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48356	0.023
17DAP/reference	1.19266	0.022
27DAP/reference	1.12613	0.194
39DAP/reference	1.19756	0.104
41DAP/reference	1.37317	0.015
42DAP/reference	1.39364	0.035
43DAP/reference	1.18765	0.269
47DAP/reference	1.19396	0.002
52DAP/reference	1.21467	0.025
57DAP/reference	0.93585	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92286	0.526
27DAP/17DAP	0.9848	0.919
39DAP/27DAP	1.1317	0.343
41DAP/39DAP	1.10231	0.861
42DAP/41DAP	1.11677	0.593
43DAP/42DAP	1.1749	0.273
47DAP/43DAP	1.05296	0.837
52DAP/47DAP	1.03765	0.907
57DAP/52DAP	1.00099	1
57DAP/7DAP	1.17642	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86945	0.157
17DAP/reference	0.82905	0.064
27DAP/reference	0.99776	0.748
39DAP/reference	0.92485	0.23
41DAP/reference	0.88654	0.194
42DAP/reference	0.90846	0.178
43DAP/reference	0.92835	0.192
47DAP/reference	0.96114	0.504
52DAP/reference	0.80924	0.013
57DAP/reference	0.83635	0.048

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35566	0.041
17DAP/reference	1.70875	0.007
27DAP/reference	1.3781	0.04
39DAP/reference	1.36821	0.043
41DAP/reference	1.43065	0.006
42DAP/reference	1.35105	0.031
43DAP/reference	1.67674	0.024
47DAP/reference	1.24441	0.008
52DAP/reference	1.57881	0.006
57DAP/reference	2.33909	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90629	0.104
17DAP/reference	1.14866	0.62
27DAP/reference	0.90944	0.14
39DAP/reference	0.99405	0.755
41DAP/reference	1.01388	1
42DAP/reference	1.01822	1
43DAP/reference	1.10444	0.625
47DAP/reference	1.18774	0.279
52DAP/reference	0.91838	0.368
57DAP/reference	0.93659	0.416

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22599	0.045
26DAP/20DAP	0.90675	0.317
34DAP/26DAP	1.12045	0.819
51DAP/34DAP	1.07712	0.627
52DAP/51DAP	1.15722	0.404
53DAP/52DAP	1.11295	0.712
55DAP/53DAP	1.18779	0.185
57DAP/55DAP	1.05892	0.947
62DAP/57DAP	1.34271	0.8
68DAP/62DAP	0.58064	0.082
68DAP/14DAP	0.58394	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84257	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.72327	0.096
Immature Eggplant/Mature Eggplant	0.89749
Ripe Pepper/Ripe Tomato	0.54473	0.293
Mature Eggplant/Ripe Tomato	1.7389

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.78267
12-2/M82	N/A	N/A
12-4/M82	0.71388
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	0.93838	1
4-3-2/M82	0.63336
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	0.85829	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.55924	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.78617
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.87421	0.71
IL1-4/WTpooled	0.90409	0.699
WT/WTpooled	N/A	N/A

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	1.04344	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.113	1
DC3000/delta hrp 12h	1.44581	1
DC3000/delta hrp 24h	N/A	N/A

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.42677	0.042
DC3000 delta B/DC3000 delta AB	1.11813	0.332

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.35234	1
Exp 36h	1.25019	1
Exp 60h	1.67848	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98904	1
Var 0h	0.8985	1
Var 12h I row2-row1	1.01048	1
Var 12h NI row2-row1	0.96772	0.906
Var 36h I row2-row1	0.87117	1
Var 36h NI row2-row1	0.97165	0.791
Var 60h I row2-row1	1.38202	0.562
Var 60h NI row2-row1	1.14922	0.904
Time course 0hI-0hNI	1.08679	0.486
Time course 12hI-12hNI	1.04491	0.647
Time course 36hI-36hNI	1.02602	0.881
Time course 60hI-60hNI	0.98779	1

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)	1.08442	0.455
transgenic ySAMdc/azygous control (breaker)	0.92895	0.49
transgenic ySAMdc/azygous control (red)	1.08141	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91905	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.41899	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96346	1
Manapal/WT (break)	0.8446	1
Manapal/WT (red)	0.79988	0.229