Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.4.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.69471	0.09
27DAP/17DAP	1.1557	0.859
39DAP/27DAP	1.14299	0.762
41DAP/39DAP	1.19818	0.833
42DAP/41DAP	1.07703	1
43DAP/42DAP	1.28997	0.728
47DAP/43DAP	1.10601	0.825
52DAP/47DAP	0.86032	0.651
57DAP/52DAP	1.27424	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97864	0.578
17DAP/reference	1.27985	0.037
27DAP/reference	0.90244	0.215
39DAP/reference	0.99638	0.941
41DAP/reference	1.08104	0.552
42DAP/reference	0.76309	0.012
43DAP/reference	1.01309	1
47DAP/reference	0.83345	0.012
52DAP/reference	0.85846	0.143
57DAP/reference	0.84832	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29116	0.482
27DAP/17DAP	N/A	N/A
39DAP/27DAP	0.96422	0.887
41DAP/39DAP	1.52955	0.849
42DAP/41DAP	0.55658	0.201
43DAP/42DAP	2.29961
47DAP/43DAP	0.93974	0.896
52DAP/47DAP	1.5235	0.372
57DAP/52DAP	2.05423	0.087
57DAP/7DAP	1.37461	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84145	0.08
17DAP/reference	0.82724	0.012
27DAP/reference	0.74521	0.01
39DAP/reference	0.92415	0.095
41DAP/reference	0.85338	0.031
42DAP/reference	0.83251	0.025
43DAP/reference	0.80205	0.011
47DAP/reference	0.73578	0.168
52DAP/reference	0.81944	0.021
57DAP/reference	0.82882	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32977	0.279
17DAP/reference	1.02569	1
27DAP/reference	0.97783	0.598
39DAP/reference	1.1312	0.783
41DAP/reference	1.09073	0.301
42DAP/reference	0.98267	0.534
43DAP/reference	0.92776	0.414
47DAP/reference	0.85972	0.023
52DAP/reference	1.03883	0.156
57DAP/reference	1.09441	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86918	0.087
17DAP/reference	0.92084	0.214
27DAP/reference	0.82358	0.032
39DAP/reference	0.72985	0.012
41DAP/reference	0.90116	0.293
42DAP/reference	0.83898	0.134
43DAP/reference	0.76619	0.051
47DAP/reference	1.0037	0.574
52DAP/reference	0.71507	0.109
57DAP/reference	0.85254	0.083

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06805	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.34963	1
51DAP/34DAP	1.37643	0.854
52DAP/51DAP	0.50361	1
53DAP/52DAP	0.98025	0.902
55DAP/53DAP	1.21724	0.271
57DAP/55DAP	0.31063
62DAP/57DAP	N/A	N/A
68DAP/62DAP	2.76056	0.808
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.21896	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	3.06886

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	1.04656
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	1.02697
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.71835	0.374
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	N/A	N/A
IL7-5/WTpooled	1.46674
IL7-3/WTpooled	0.69832
IL12-4/WTpooled	1.24912
IL1-4/WTpooled	0.81363
WT/WTpooled	0.81276	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	0.83855	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.21087	0.774
DC3000/delta hrp 6h	0.76458	0.914
DC3000/delta hrp 12h	0.99452	1
DC3000/delta hrp 24h	0.66438	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.63323
DC3000 delta B/DC3000 delta AB	1.11835	0.687

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88389	1
Exp 36h	0.61991	0.434
Exp 60h	0.60933	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	2.50777	0.921
transgenic ySAMdc/azygous control (breaker)	2.27942	0.248
transgenic ySAMdc/azygous control (red)	1.33574	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93951	0.051

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.24228	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84534	0.172
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	N/A	N/A